X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=pysam%2Fcsamtools.c;h=6e18ed67e74be88d34b093dda8deb09205244cda;hp=ca5fb4ea00c05ad980ef6a497207aa035c50d2ec;hb=e1756c41e7a1d7cc01fb95e42df9dd04da2d2991;hpb=ca46ef4ba4a883c57cea62d5bf1bc021f1185109 diff --git a/pysam/csamtools.c b/pysam/csamtools.c index ca5fb4e..6e18ed6 100644 --- a/pysam/csamtools.c +++ b/pysam/csamtools.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.14.1 on Fri Nov 25 19:51:23 2011 */ +/* Generated by Cython 0.13 on Tue Jun 7 17:24:36 2011 */ #define PY_SSIZE_T_CLEAN #include "Python.h" @@ -126,20 +126,15 @@ #define PyBytes_Repr PyString_Repr #define PyBytes_Concat PyString_Concat #define PyBytes_ConcatAndDel PyString_ConcatAndDel -#endif - -#if PY_VERSION_HEX < 0x02060000 #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type) #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type) #endif + #ifndef PySet_CheckExact - #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) +# define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif -#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) - #if PY_MAJOR_VERSION >= 3 - #define PyIntObject PyLongObject #define PyInt_Type PyLong_Type #define PyInt_Check(op) PyLong_Check(op) #define PyInt_CheckExact(op) PyLong_CheckExact(op) @@ -156,7 +151,7 @@ #endif #if PY_MAJOR_VERSION >= 3 - #define PyBoolObject PyLongObject + #define PyBoolObject PyLongObject #endif @@ -168,25 +163,6 @@ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) #endif -#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300) - #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b) - #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value) - #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b) -#else - #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \ - (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \ - (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \ - (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0))) - #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \ - (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ - (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \ - (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1))) - #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \ - (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ - (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \ - (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1))) -#endif - #if PY_MAJOR_VERSION >= 3 #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) #endif @@ -231,15 +207,12 @@ #include "stdint.h" #include "bam.h" #include "sam.h" +#include "glf.h" +#include "bam_maqcns.h" #include "faidx.h" #include "pysam_util.h" #include "pythread.h" -#ifdef PYREX_WITHOUT_ASSERTIONS -#define CYTHON_WITHOUT_ASSERTIONS -#endif - - /* inline attribute */ #ifndef CYTHON_INLINE #if defined(__GNUC__) @@ -249,7 +222,7 @@ #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L #define CYTHON_INLINE inline #else - #define CYTHON_INLINE + #define CYTHON_INLINE #endif #endif @@ -257,14 +230,14 @@ #ifndef CYTHON_UNUSED # if defined(__GNUC__) # if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) # else # define CYTHON_UNUSED # endif # elif defined(__ICC) || defined(__INTEL_COMPILER) -# define CYTHON_UNUSED __attribute__ ((__unused__)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) # else -# define CYTHON_UNUSED +# define CYTHON_UNUSED # endif #endif @@ -289,7 +262,7 @@ static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); #ifdef __GNUC__ /* Test for GCC > 2.95 */ -#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) +#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) #define likely(x) __builtin_expect(!!(x), 1) #define unlikely(x) __builtin_expect(!!(x), 0) #else /* __GNUC__ > 2 ... */ @@ -315,12 +288,11 @@ static const char *__pyx_f[] = { "csamtools.pyx", "csamtools.pxd", "bool.pxd", - "complex.pxd", }; /* Type declarations */ -/* "csamtools.pyx":388 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":388 * counter[0] += 1; * * ctypedef struct MateData: # <<<<<<<<<<<<<< @@ -334,7 +306,7 @@ typedef struct { uint32_t flag; } __pyx_t_9csamtools_MateData; -/* "csamtools.pyx":1537 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1478 * ##------------------------------------------------------------------- * ##------------------------------------------------------------------- * ctypedef struct __iterdata: # <<<<<<<<<<<<<< @@ -351,7 +323,7 @@ typedef struct { int seq_len; } __pyx_t_9csamtools___iterdata; -/* "csamtools.pyx":1717 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1655 * bam_plp_set_mask( self.pileup_iter, self.mask ) * * cdef setupIteratorData( self, # <<<<<<<<<<<<<< @@ -364,7 +336,99 @@ struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData { int reopen; }; -/* "csamtools.pyx":91 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3192 + * bam_maqindel_ret_destroy(self._r) + * + * cdef class IndelCallerBase: # <<<<<<<<<<<<<< + * '''Base class for SNP callers. + * + */ + +struct __pyx_obj_9csamtools_IndelCallerBase { + PyObject_HEAD + bam_maqindel_opt_t *options; + struct __pyx_obj_9csamtools_IteratorColumn *iter; + int cap_mapQ; + int max_depth; +}; + +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3330 + * return self._call() + * + * cdef class IteratorIndelCalls( IndelCallerBase ): # <<<<<<<<<<<<<< + * """*(IteratorColumn iterator)* + * + */ + +struct __pyx_obj_9csamtools_IteratorIndelCalls { + struct __pyx_obj_9csamtools_IndelCallerBase __pyx_base; +}; + +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":244 + * ## Public methods + * ###################################################################### + * cdef class Fastafile: # <<<<<<<<<<<<<< + * '''*(filename)* + * + */ + +struct __pyx_obj_9csamtools_Fastafile { + PyObject_HEAD + struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtab; + char *_filename; + faidx_t *fastafile; +}; + +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3103 + * return call + * + * cdef class IndelCall: # <<<<<<<<<<<<<< + * '''the results of an indel call.''' + * cdef int _tid + */ + +struct __pyx_obj_9csamtools_IndelCall { + PyObject_HEAD + int _tid; + int _pos; + int _coverage; + int _rms_mapping_quality; + bam_maqindel_ret_t *_r; +}; + +/* "pysam/csamtools.pxd":388 + * cdef bam1_t * _delegate + * + * cdef class Samfile: # <<<<<<<<<<<<<< + * cdef char * _filename + * # pointer to samfile + */ + +struct __pyx_obj_9csamtools_Samfile { + PyObject_HEAD + struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtab; + char *_filename; + samfile_t *samfile; + bam_index_t *index; + int isbam; + int isremote; + bam1_t *b; + char *mode; +}; + +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3287 + * return call + * + * cdef class IndelCaller( IndelCallerBase ): # <<<<<<<<<<<<<< + * '''*(IteratorColumn iterator_column )* + * + */ + +struct __pyx_obj_9csamtools_IndelCaller { + struct __pyx_obj_9csamtools_IndelCallerBase __pyx_base; +}; + +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":91 * return dest * * cdef class PileupRead # <<<<<<<<<<<<<< @@ -383,66 +447,103 @@ struct __pyx_obj_9csamtools_PileupRead { uint32_t _is_tail; }; -/* "csamtools.pxd":423 - * cdef char * _getrname( self, int tid ) +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2816 + * return retval, out_stderr, out_stdout * - * cdef class IteratorRow: # <<<<<<<<<<<<<< - * pass + * cdef class SNPCall: # <<<<<<<<<<<<<< + * '''the results of a SNP call.''' + * cdef int _tid + */ + +struct __pyx_obj_9csamtools_SNPCall { + PyObject_HEAD + int _tid; + int _pos; + char _reference_base; + char _genotype; + int _consensus_quality; + int _snp_quality; + int _rms_mapping_quality; + int _coverage; +}; + +/* "pysam/csamtools.pxd":383 + * + * # need to declare all C fields and methods here + * cdef class AlignedRead: # <<<<<<<<<<<<<< * + * # object that this AlignedRead represents */ -struct __pyx_obj_9csamtools_IteratorRow { +struct __pyx_obj_9csamtools_AlignedRead { PyObject_HEAD + bam1_t *_delegate; }; -/* "csamtools.pyx":1415 - * if self.owns_samfile: samclose( self.fp ) +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1542 + * return ret + * + * cdef class IteratorColumn: # <<<<<<<<<<<<<< + * '''abstract base class for iterators over columns. * - * cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<< - * """iterates over all mapped reads by chaining iterators over each reference - * """ */ -struct __pyx_obj_9csamtools_IteratorRowAllRefs { - struct __pyx_obj_9csamtools_IteratorRow __pyx_base; - struct __pyx_obj_9csamtools_Samfile *samfile; +struct __pyx_obj_9csamtools_IteratorColumn { + PyObject_HEAD + struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtab; + struct __pyx_obj_9csamtools_IteratorRowRegion *iter; int tid; - struct __pyx_obj_9csamtools_IteratorRowRegion *rowiter; + int pos; + int n_plp; + int mask; + const bam_pileup1_t * plp; + bam_plp_t pileup_iter; + __pyx_t_9csamtools___iterdata iterdata; + struct __pyx_obj_9csamtools_Samfile *samfile; + struct __pyx_obj_9csamtools_Fastafile *fastafile; + PyObject *stepper; }; -/* "csamtools.pxd":426 - * pass +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1712 + * self.iterdata.seq = NULL * - * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<< - * cdef bam1_t * b - * cdef samfile_t * fp + * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<< + * '''iterates over a region only. + * ''' */ -struct __pyx_obj_9csamtools_IteratorRowAll { - struct __pyx_obj_9csamtools_IteratorRow __pyx_base; - struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtab; - bam1_t *b; - samfile_t *fp; - int owns_samfile; +struct __pyx_obj_9csamtools_IteratorColumnRegion { + struct __pyx_obj_9csamtools_IteratorColumn __pyx_base; }; -/* "csamtools.pyx":82 - * return dest +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1187 + * ##------------------------------------------------------------------- + * ##------------------------------------------------------------------- + * cdef class IteratorRow: # <<<<<<<<<<<<<< + * '''abstract base class for iterators over mapped reads. * - * cdef class PileupProxy # <<<<<<<<<<<<<< - * cdef makePileupProxy( bam_pileup1_t * plp, int tid, int pos, int n ): - * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy) */ -struct __pyx_obj_9csamtools_PileupProxy { +struct __pyx_obj_9csamtools_IteratorRow { PyObject_HEAD - bam_pileup1_t *plp; +}; + +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1356 + * if self.owns_samfile: samclose( self.fp ) + * + * cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<< + * """iterates over all mapped reads by chaining iterators over each reference + * """ + */ + +struct __pyx_obj_9csamtools_IteratorRowAllRefs { + struct __pyx_obj_9csamtools_IteratorRow __pyx_base; + struct __pyx_obj_9csamtools_Samfile *samfile; int tid; - int pos; - int n_pu; + struct __pyx_obj_9csamtools_IteratorRowRegion *rowiter; }; -/* "csamtools.pyx":1265 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1206 * pass * * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<< @@ -461,22 +562,19 @@ struct __pyx_obj_9csamtools_IteratorRowRegion { int owns_samfile; }; -/* "csamtools.pyx":244 - * ## Public methods - * ###################################################################### - * cdef class Fastafile: # <<<<<<<<<<<<<< - * '''*(filename)* +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1741 + * self.n_plp ) * + * cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<< + * """iterates over all columns by chaining iterators over each reference + * """ */ -struct __pyx_obj_9csamtools_Fastafile { - PyObject_HEAD - struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtab; - char *_filename; - faidx_t *fastafile; +struct __pyx_obj_9csamtools_IteratorColumnAllRefs { + struct __pyx_obj_9csamtools_IteratorColumn __pyx_base; }; -/* "csamtools.pyx":1461 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1402 * raise StopIteration * * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<< @@ -494,86 +592,62 @@ struct __pyx_obj_9csamtools_IteratorRowSelection { int owns_samfile; }; -/* "csamtools.pyx":1601 - * return ret +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2873 * - * cdef class IteratorColumn: # <<<<<<<<<<<<<< - * '''abstract base class for iterators over columns. + * + * cdef class SNPCallerBase: # <<<<<<<<<<<<<< + * '''Base class for SNP callers. * */ -struct __pyx_obj_9csamtools_IteratorColumn { +struct __pyx_obj_9csamtools_SNPCallerBase { PyObject_HEAD - struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtab; - struct __pyx_obj_9csamtools_IteratorRowRegion *iter; - int tid; - int pos; - int n_plp; - int mask; - const bam_pileup1_t * plp; - bam_plp_t pileup_iter; - __pyx_t_9csamtools___iterdata iterdata; - struct __pyx_obj_9csamtools_Samfile *samfile; - struct __pyx_obj_9csamtools_Fastafile *fastafile; - PyObject *stepper; - int max_depth; + struct __pyx_vtabstruct_9csamtools_SNPCallerBase *__pyx_vtab; + bam_maqcns_t *c; + struct __pyx_obj_9csamtools_IteratorColumn *iter; }; -/* "csamtools.pyx":1806 - * self.n_plp ) +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3021 + * return call + * + * cdef class SNPCaller( SNPCallerBase ): # <<<<<<<<<<<<<< + * '''*(IteratorColumn iterator_column )* * - * cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<< - * """iterates over all columns by chaining iterators over each reference - * """ */ -struct __pyx_obj_9csamtools_IteratorColumnAllRefs { - struct __pyx_obj_9csamtools_IteratorColumn __pyx_base; +struct __pyx_obj_9csamtools_SNPCaller { + struct __pyx_obj_9csamtools_SNPCallerBase __pyx_base; }; -/* "csamtools.pxd":394 - * cdef bam1_t * _delegate +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2946 + * sys.stdout.flush() + * + * cdef class IteratorSNPCalls( SNPCallerBase ): # <<<<<<<<<<<<<< + * """*(IteratorColumn iterator)* * - * cdef class Samfile: # <<<<<<<<<<<<<< - * cdef char * _filename - * # pointer to samfile */ -struct __pyx_obj_9csamtools_Samfile { - PyObject_HEAD - struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtab; - char *_filename; - samfile_t *samfile; - bam_index_t *index; - int isbam; - int isstream; - int isremote; - bam1_t *b; - char *mode; - int64_t start_offset; +struct __pyx_obj_9csamtools_IteratorSNPCalls { + struct __pyx_obj_9csamtools_SNPCallerBase __pyx_base; }; -/* "csamtools.pyx":2902 - * return retval, out_stderr, out_stdout +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1292 + * if self.owns_samfile: samclose( self.fp ) + * + * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<< + * """*(Samfile samfile, int reopen = True)* * - * cdef class SNPCall: # <<<<<<<<<<<<<< - * '''the results of a SNP call.''' - * cdef int _tid */ -struct __pyx_obj_9csamtools_SNPCall { - PyObject_HEAD - int _tid; - int _pos; - char _reference_base; - char _genotype; - int _consensus_quality; - int _snp_quality; - int _rms_mapping_quality; - int _coverage; +struct __pyx_obj_9csamtools_IteratorRowAll { + struct __pyx_obj_9csamtools_IteratorRow __pyx_base; + struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtab; + bam1_t *b; + samfile_t *fp; + int owns_samfile; }; -/* "csamtools.pyx":3456 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3370 * * * cdef class IndexedReads: # <<<<<<<<<<<<<< @@ -589,33 +663,24 @@ struct __pyx_obj_9csamtools_IndexedReads { int owns_samfile; }; -/* "csamtools.pyx":1777 - * self.iterdata.seq = NULL +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":82 + * return dest * - * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<< - * '''iterates over a region only. - * ''' + * cdef class PileupProxy # <<<<<<<<<<<<<< + * cdef makePileupProxy( bam_pileup1_t * plp, int tid, int pos, int n ): + * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy) */ -struct __pyx_obj_9csamtools_IteratorColumnRegion { - struct __pyx_obj_9csamtools_IteratorColumn __pyx_base; -}; - -/* "csamtools.pxd":389 - * - * # need to declare all C fields and methods here - * cdef class AlignedRead: # <<<<<<<<<<<<<< - * - * # object that this AlignedRead represents - */ - -struct __pyx_obj_9csamtools_AlignedRead { +struct __pyx_obj_9csamtools_PileupProxy { PyObject_HEAD - bam1_t *_delegate; + bam_pileup1_t *plp; + int tid; + int pos; + int n_pu; }; -/* "csamtools.pyx":1601 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1542 * return ret * * cdef class IteratorColumn: # <<<<<<<<<<<<<< @@ -633,7 +698,7 @@ struct __pyx_vtabstruct_9csamtools_IteratorColumn { static struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtabptr_9csamtools_IteratorColumn; -/* "csamtools.pyx":1777 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1712 * self.iterdata.seq = NULL * * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<< @@ -647,7 +712,35 @@ struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion { static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *__pyx_vtabptr_9csamtools_IteratorColumnRegion; -/* "csamtools.pyx":1265 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2873 + * + * + * cdef class SNPCallerBase: # <<<<<<<<<<<<<< + * '''Base class for SNP callers. + * + */ + +struct __pyx_vtabstruct_9csamtools_SNPCallerBase { + PyObject *(*__dump)(struct __pyx_obj_9csamtools_SNPCallerBase *, glf1_t *, uint32_t, int); +}; +static struct __pyx_vtabstruct_9csamtools_SNPCallerBase *__pyx_vtabptr_9csamtools_SNPCallerBase; + + +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3021 + * return call + * + * cdef class SNPCaller( SNPCallerBase ): # <<<<<<<<<<<<<< + * '''*(IteratorColumn iterator_column )* + * + */ + +struct __pyx_vtabstruct_9csamtools_SNPCaller { + struct __pyx_vtabstruct_9csamtools_SNPCallerBase __pyx_base; +}; +static struct __pyx_vtabstruct_9csamtools_SNPCaller *__pyx_vtabptr_9csamtools_SNPCaller; + + +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1206 * pass * * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<< @@ -662,7 +755,7 @@ struct __pyx_vtabstruct_9csamtools_IteratorRowRegion { static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtabptr_9csamtools_IteratorRowRegion; -/* "csamtools.pyx":1461 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1402 * raise StopIteration * * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<< @@ -677,7 +770,7 @@ struct __pyx_vtabstruct_9csamtools_IteratorRowSelection { static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtabptr_9csamtools_IteratorRowSelection; -/* "csamtools.pyx":1806 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1741 * self.n_plp ) * * cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<< @@ -691,12 +784,12 @@ struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs { static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *__pyx_vtabptr_9csamtools_IteratorColumnAllRefs; -/* "csamtools.pyx":415 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":415 * * * cdef class Samfile: # <<<<<<<<<<<<<< - * '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None, - * add_sq_text = False )* + * '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None)* + * */ struct __pyx_vtabstruct_9csamtools_Samfile { @@ -709,7 +802,7 @@ struct __pyx_vtabstruct_9csamtools_Samfile { static struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtabptr_9csamtools_Samfile; -/* "csamtools.pyx":244 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":244 * ## Public methods * ###################################################################### * cdef class Fastafile: # <<<<<<<<<<<<<< @@ -723,7 +816,7 @@ struct __pyx_vtabstruct_9csamtools_Fastafile { static struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtabptr_9csamtools_Fastafile; -/* "csamtools.pyx":1351 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1292 * if self.owns_samfile: samclose( self.fp ) * * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<< @@ -737,6 +830,20 @@ struct __pyx_vtabstruct_9csamtools_IteratorRowAll { }; static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtools_IteratorRowAll; + +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2946 + * sys.stdout.flush() + * + * cdef class IteratorSNPCalls( SNPCallerBase ): # <<<<<<<<<<<<<< + * """*(IteratorColumn iterator)* + * + */ + +struct __pyx_vtabstruct_9csamtools_IteratorSNPCalls { + struct __pyx_vtabstruct_9csamtools_SNPCallerBase __pyx_base; +}; +static struct __pyx_vtabstruct_9csamtools_IteratorSNPCalls *__pyx_vtabptr_9csamtools_IteratorSNPCalls; + #ifndef CYTHON_REFNANNY #define CYTHON_REFNANNY 0 #endif @@ -810,7 +917,7 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/ #define __Pyx_TraceDeclarations \ static PyCodeObject *__pyx_frame_code = NULL; \ CYTHON_FRAME_MODIFIER PyFrameObject *__pyx_frame = NULL; \ - int __Pyx_use_tracing = 0; + int __Pyx_use_tracing = 0; #define __Pyx_TraceCall(funcname, srcfile, firstlineno) \ if (unlikely(PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc)) { \ @@ -840,9 +947,9 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/ #else #define __Pyx_TraceDeclarations - #define __Pyx_TraceCall(funcname, srcfile, firstlineno) - #define __Pyx_TraceException() - #define __Pyx_TraceReturn(result) + #define __Pyx_TraceCall(funcname, srcfile, firstlineno) + #define __Pyx_TraceException() + #define __Pyx_TraceReturn(result) #endif /* CYTHON_PROFILE */ @@ -863,19 +970,17 @@ static int __Pyx_EndUnpack(PyObject *, Py_ssize_t expected); /*proto*/ static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed); /*proto*/ -static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ -static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ - -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ - static void __Pyx_RaiseDoubleKeywordsError( const char* func_name, PyObject* kw_name); /*proto*/ -static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/ - static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/ +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/ + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ + static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact); /*proto*/ @@ -960,6 +1065,8 @@ static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) { return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b); } +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); + static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) { if (likely(PyList_CheckExact(L))) { if (PyList_Append(L, x) < 0) return NULL; @@ -978,6 +1085,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) { static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void); + #if PY_MAJOR_VERSION >= 3 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { PyObject *value; @@ -1058,27 +1166,12 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/ -static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/ - -static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, - PyObject *modname); /*proto*/ - -#define __pyx_binding_PyCFunctionType_USED 1 - -typedef struct { - PyCFunctionObject func; -} __pyx_binding_PyCFunctionType_object; - -static PyTypeObject __pyx_binding_PyCFunctionType_type; -static PyTypeObject *__pyx_binding_PyCFunctionType = NULL; - -static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module); /* proto */ -#define __pyx_binding_PyCFunctionType_New(ml, self) __pyx_binding_PyCFunctionType_NewEx(ml, self, NULL) - -static int __pyx_binding_PyCFunctionType_init(void); /* proto */ +static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, const char *modname); /*proto*/ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t); +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ + static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *); static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int32_t(int32_t); @@ -1091,6 +1184,14 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *); static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint8_t(uint8_t); +static int __Pyx_Print(PyObject*, PyObject *, int); /*proto*/ +#if PY_MAJOR_VERSION >= 3 +static PyObject* __pyx_print = 0; +static PyObject* __pyx_print_kwargs = 0; +#endif + +static int __Pyx_PrintOne(PyObject* stream, PyObject *o); /*proto*/ + static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint64_t(uint64_t); static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *); @@ -1177,11 +1278,8 @@ static PyTypeObject *__pyx_ptype_7cpython_4bool_bool = 0; /* Module declarations from cpython.float */ -/* Module declarations from __builtin__ */ - /* Module declarations from cpython.complex */ -static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0; /* Module declarations from cpython.string */ /* Module declarations from cpython.unicode */ @@ -1219,18 +1317,25 @@ static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0; static PyTypeObject *__pyx_ptype_9csamtools_file = 0; static PyTypeObject *__pyx_ptype_9csamtools_AlignedRead = 0; static PyTypeObject *__pyx_ptype_9csamtools_Samfile = 0; -static PyTypeObject *__pyx_ptype_9csamtools_IteratorRow = 0; -static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAll = 0; static PyTypeObject *__pyx_ptype_9csamtools_PileupProxy = 0; static PyTypeObject *__pyx_ptype_9csamtools_PileupRead = 0; static PyTypeObject *__pyx_ptype_9csamtools_Fastafile = 0; +static PyTypeObject *__pyx_ptype_9csamtools_IteratorRow = 0; static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowRegion = 0; +static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAll = 0; static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAllRefs = 0; static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowSelection = 0; static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumn = 0; static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnRegion = 0; static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnAllRefs = 0; static PyTypeObject *__pyx_ptype_9csamtools_SNPCall = 0; +static PyTypeObject *__pyx_ptype_9csamtools_SNPCallerBase = 0; +static PyTypeObject *__pyx_ptype_9csamtools_IteratorSNPCalls = 0; +static PyTypeObject *__pyx_ptype_9csamtools_SNPCaller = 0; +static PyTypeObject *__pyx_ptype_9csamtools_IndelCall = 0; +static PyTypeObject *__pyx_ptype_9csamtools_IndelCallerBase = 0; +static PyTypeObject *__pyx_ptype_9csamtools_IndelCaller = 0; +static PyTypeObject *__pyx_ptype_9csamtools_IteratorIndelCalls = 0; static PyTypeObject *__pyx_ptype_9csamtools_IndexedReads = 0; static char *__pyx_v_9csamtools_bam_nt16_rev_table; static int __pyx_v_9csamtools_max_pos; @@ -1249,7 +1354,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *); /*proto*/ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *, uint32_t, uint32_t); /*proto*/ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *, uint32_t, uint32_t); /*proto*/ #define __Pyx_MODULE_NAME "csamtools" -static int __pyx_module_is_main_csamtools = 0; +int __pyx_module_is_main_csamtools = 0; /* Implementation of csamtools */ static PyObject *__pyx_builtin_open; @@ -1259,65 +1364,106 @@ static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_IOError; static PyObject *__pyx_builtin_OverflowError; static PyObject *__pyx_builtin_NotImplementedError; -static PyObject *__pyx_builtin_OSError; -static PyObject *__pyx_builtin_AttributeError; static PyObject *__pyx_builtin_KeyError; static PyObject *__pyx_builtin_StopIteration; static PyObject *__pyx_builtin_cmp; static PyObject *__pyx_builtin_chr; static PyObject *__pyx_builtin_TypeError; +static PyObject *__pyx_builtin_range; static char __pyx_k_1[] = "\t"; static char __pyx_k_2[] = "\n"; static char __pyx_k_3[] = "calling len() on closed file"; -static char __pyx_k_5[] = "could not open file `%s`"; -static char __pyx_k_6[] = "I/O operation on closed file"; -static char __pyx_k_9[] = "no sequence/region supplied."; -static char __pyx_k_11[] = "invalid region: start (%i) > end (%i)"; -static char __pyx_k_12[] = ""; -static char __pyx_k_13[] = "start out of range (%i)"; -static char __pyx_k_14[] = "end out of range (%i)"; -static char __pyx_k_15[] = "%s:%i-%i"; -static char __pyx_k_17[] = "invalid file opening mode `%s`"; -static char __pyx_k_18[] = "-"; -static char __pyx_k_19[] = "http:"; -static char __pyx_k_20[] = "ftp:"; -static char __pyx_k_21[] = "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing"; -static char __pyx_k_22[] = "unequal names and lengths of reference sequences"; -static char __pyx_k_23[] = "@SQ\tSN:%s\tLN:%s\n"; -static char __pyx_k_24[] = "file `%s` not found"; -static char __pyx_k_25[] = "could not open file (mode='%s') - is it SAM/BAM format?"; -static char __pyx_k_26[] = "file does not have valid header (mode='%s') - is it SAM/BAM format?"; -static char __pyx_k_27[] = ".bai"; -static char __pyx_k_28[] = "error while opening index `%s` "; -static char __pyx_k_31[] = "tid %i out of range 0<=tid<%i"; -static char __pyx_k_33[] = "[:-]"; -static char __pyx_k_35[] = "invalid reference `%s`"; -static char __pyx_k_36[] = "invalid coordinates: start (%i) > end (%i)"; -static char __pyx_k_38[] = "seek only available in bam files"; -static char __pyx_k_40[] = "seek no available in streams"; -static char __pyx_k_46[] = "fetch called on bamfile without index"; -static char __pyx_k_48[] = "callback functionality requires a region/reference"; -static char __pyx_k_50[] = "no index available for fetch"; -static char __pyx_k_52[] = "fetching by region is not available for sam files"; -static char __pyx_k_54[] = "fetch called for samfile without header"; -static char __pyx_k_56[] = "callback not implemented yet"; -static char __pyx_k_58[] = "read %s: is unpaired"; -static char __pyx_k_59[] = "mate %s: is unmapped"; -static char __pyx_k_60[] = "mate not found"; -static char __pyx_k_65[] = "counting functionality requires a region/reference"; -static char __pyx_k_68[] = "count for a region is not available for sam files"; -static char __pyx_k_71[] = "no index available for pileup"; -static char __pyx_k_74[] = "pileup of samfiles not implemented yet"; -static char __pyx_k_81[] = "Samfile.mapped only available in bam files"; -static char __pyx_k_84[] = "Samfile.unmapped only available in bam files"; -static char __pyx_k_89[] = "@"; -static char __pyx_k_91[] = "header line without '@': '%s'"; -static char __pyx_k_93[] = "header line with invalid type '%s': '%s'"; -static char __pyx_k_94[] = ":"; -static char __pyx_k_96[] = "unknown field code '%s' in record '%s'"; -static char __pyx_k_97[] = "multiple '%s' lines are not permitted"; -static char __pyx_k_98[] = "@%s"; -static char __pyx_k_99[] = "%s:%s"; +static char __pyx_k_4[] = "could not open file `%s`"; +static char __pyx_k_5[] = "I/O operation on closed file"; +static char __pyx_k_6[] = "no sequence/region supplied."; +static char __pyx_k_7[] = "invalid region: start (%i) > end (%i)"; +static char __pyx_k_8[] = ""; +static char __pyx_k_9[] = "start out of range (%i)"; +static char __pyx_k_10[] = "end out of range (%i)"; +static char __pyx_k_11[] = "%s:%i-%i"; +static char __pyx_k_12[] = "invalid file opening mode `%s`"; +static char __pyx_k_13[] = "http:"; +static char __pyx_k_14[] = "ftp:"; +static char __pyx_k_15[] = "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing"; +static char __pyx_k_16[] = "unequal names and lengths of reference sequences"; +static char __pyx_k_17[] = "-"; +static char __pyx_k_18[] = "file `%s` not found"; +static char __pyx_k_19[] = "could not open file (mode='%s') - is it SAM/BAM format?"; +static char __pyx_k_20[] = "file does not have valid header (mode='%s') - is it SAM/BAM format?"; +static char __pyx_k_21[] = "file header is empty (mode='%s') - is it SAM/BAM format?"; +static char __pyx_k_22[] = ".bai"; +static char __pyx_k_23[] = "error while opening index `%s` "; +static char __pyx_k_24[] = "tid %i out of range 0<=tid<%i"; +static char __pyx_k_25[] = "[:-]"; +static char __pyx_k_26[] = "invalid reference `%s`"; +static char __pyx_k_27[] = "invalid coordinates: start (%i) > end (%i)"; +static char __pyx_k_28[] = "seek only available in bam files"; +static char __pyx_k_30[] = "fetch called on bamfile without index"; +static char __pyx_k_31[] = "callback functionality requires a region/reference"; +static char __pyx_k_32[] = "no index available for fetch"; +static char __pyx_k_33[] = "fetch called for samfile without header"; +static char __pyx_k_34[] = "fetch for a region is not available for sam files"; +static char __pyx_k_35[] = "callback not implemented yet"; +static char __pyx_k_36[] = "read %s: is unpaired"; +static char __pyx_k_37[] = "mate %s: is unmapped"; +static char __pyx_k_38[] = "mate not found"; +static char __pyx_k_40[] = "counting functionality requires a region/reference"; +static char __pyx_k_41[] = "count for a region is not available for sam files"; +static char __pyx_k_42[] = "no index available for pileup"; +static char __pyx_k_43[] = "pileup of samfiles not implemented yet"; +static char __pyx_k_44[] = "@"; +static char __pyx_k_45[] = "header line without '@': '%s'"; +static char __pyx_k_46[] = "header line with invalid type '%s': '%s'"; +static char __pyx_k_47[] = ":"; +static char __pyx_k_48[] = "unknown field code '%s' in record '%s'"; +static char __pyx_k_49[] = "multiple '%s' lines are not permitted"; +static char __pyx_k_50[] = "@%s"; +static char __pyx_k_51[] = "%s:%s"; +static char __pyx_k_52[] = "invalid type for record %s: %s, expected %s"; +static char __pyx_k_53[] = "incomplete sequence information in '%s'"; +static char __pyx_k_54[] = "no index available for iteration"; +static char __pyx_k_55[] = "can only use this iterator on bam files"; +static char __pyx_k_56[] = "reference sequence for '%s' (tid=%i) not found"; +static char __pyx_k_57[] = "unknown stepper option `%s` in IteratorColumn"; +static char __pyx_k_59[] = "error during iteration"; +static char __pyx_k_60[] = "Invalid clipping in CIGAR string"; +static char __pyx_k_61[] = "quality and sequence mismatch: %i != %i"; +static char __pyx_k_62[] = "%c"; +static char __pyx_k_63[] = "create_string_buffer"; +static char __pyx_k_64[] = "_delegate = bam_dup1(__pyx_v_src); - /* "csamtools.pyx":80 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":80 * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) * dest._delegate = bam_dup1(src) * return dest # <<<<<<<<<<<<<< @@ -2240,7 +2459,7 @@ static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *__pyx_v_src) { return __pyx_r; } -/* "csamtools.pyx":83 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":83 * * cdef class PileupProxy * cdef makePileupProxy( bam_pileup1_t * plp, int tid, int pos, int n ): # <<<<<<<<<<<<<< @@ -2256,7 +2475,7 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t *__pyx_v_plp, __Pyx_RefNannySetupContext("makePileupProxy"); __Pyx_TraceCall("makePileupProxy", __pyx_f[0], 83); - /* "csamtools.pyx":84 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":84 * cdef class PileupProxy * cdef makePileupProxy( bam_pileup1_t * plp, int tid, int pos, int n ): * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy) # <<<<<<<<<<<<<< @@ -2269,7 +2488,7 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t *__pyx_v_plp, __pyx_v_dest = ((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_t_1); __pyx_t_1 = 0; - /* "csamtools.pyx":85 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":85 * cdef makePileupProxy( bam_pileup1_t * plp, int tid, int pos, int n ): * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy) * dest.plp = plp # <<<<<<<<<<<<<< @@ -2278,7 +2497,7 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t *__pyx_v_plp, */ __pyx_v_dest->plp = __pyx_v_plp; - /* "csamtools.pyx":86 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":86 * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy) * dest.plp = plp * dest.tid = tid # <<<<<<<<<<<<<< @@ -2287,7 +2506,7 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t *__pyx_v_plp, */ __pyx_v_dest->tid = __pyx_v_tid; - /* "csamtools.pyx":87 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":87 * dest.plp = plp * dest.tid = tid * dest.pos = pos # <<<<<<<<<<<<<< @@ -2296,7 +2515,7 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t *__pyx_v_plp, */ __pyx_v_dest->pos = __pyx_v_pos; - /* "csamtools.pyx":88 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":88 * dest.tid = tid * dest.pos = pos * dest.n = n # <<<<<<<<<<<<<< @@ -2308,7 +2527,7 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t *__pyx_v_plp, if (PyObject_SetAttr(((PyObject *)__pyx_v_dest), __pyx_n_s__n, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "csamtools.pyx":89 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":89 * dest.pos = pos * dest.n = n * return dest # <<<<<<<<<<<<<< @@ -2334,7 +2553,7 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t *__pyx_v_plp, return __pyx_r; } -/* "csamtools.pyx":92 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":92 * * cdef class PileupRead * cdef makePileupRead( bam_pileup1_t * src ): # <<<<<<<<<<<<<< @@ -2350,7 +2569,7 @@ static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) __Pyx_RefNannySetupContext("makePileupRead"); __Pyx_TraceCall("makePileupRead", __pyx_f[0], 92); - /* "csamtools.pyx":94 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":94 * cdef makePileupRead( bam_pileup1_t * src ): * '''fill a PileupRead object from a bam_pileup1_t * object.''' * cdef PileupRead dest = PileupRead.__new__(PileupRead) # <<<<<<<<<<<<<< @@ -2363,7 +2582,7 @@ static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) __pyx_v_dest = ((struct __pyx_obj_9csamtools_PileupRead *)__pyx_t_1); __pyx_t_1 = 0; - /* "csamtools.pyx":95 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":95 * '''fill a PileupRead object from a bam_pileup1_t * object.''' * cdef PileupRead dest = PileupRead.__new__(PileupRead) * dest._alignment = makeAlignedRead( src.b ) # <<<<<<<<<<<<<< @@ -2379,7 +2598,7 @@ static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) __pyx_v_dest->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_t_1); __pyx_t_1 = 0; - /* "csamtools.pyx":96 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":96 * cdef PileupRead dest = PileupRead.__new__(PileupRead) * dest._alignment = makeAlignedRead( src.b ) * dest._qpos = src.qpos # <<<<<<<<<<<<<< @@ -2388,7 +2607,7 @@ static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) */ __pyx_v_dest->_qpos = __pyx_v_src->qpos; - /* "csamtools.pyx":97 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":97 * dest._alignment = makeAlignedRead( src.b ) * dest._qpos = src.qpos * dest._indel = src.indel # <<<<<<<<<<<<<< @@ -2397,7 +2616,7 @@ static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) */ __pyx_v_dest->_indel = __pyx_v_src->indel; - /* "csamtools.pyx":98 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":98 * dest._qpos = src.qpos * dest._indel = src.indel * dest._level = src.level # <<<<<<<<<<<<<< @@ -2406,7 +2625,7 @@ static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) */ __pyx_v_dest->_level = __pyx_v_src->level; - /* "csamtools.pyx":99 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":99 * dest._indel = src.indel * dest._level = src.level * dest._is_del = src.is_del # <<<<<<<<<<<<<< @@ -2415,7 +2634,7 @@ static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) */ __pyx_v_dest->_is_del = __pyx_v_src->is_del; - /* "csamtools.pyx":100 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":100 * dest._level = src.level * dest._is_del = src.is_del * dest._is_head = src.is_head # <<<<<<<<<<<<<< @@ -2424,7 +2643,7 @@ static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) */ __pyx_v_dest->_is_head = __pyx_v_src->is_head; - /* "csamtools.pyx":101 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":101 * dest._is_del = src.is_del * dest._is_head = src.is_head * dest._is_tail = src.is_tail # <<<<<<<<<<<<<< @@ -2433,7 +2652,7 @@ static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) */ __pyx_v_dest->_is_tail = __pyx_v_src->is_tail; 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/*proto*/ +static char __pyx_doc_9csamtools_11StderrStore_readAndRelease[] = "StderrStore.readAndRelease(self)"; +static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore_readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_readAndRelease)}; +static PyObject *__pyx_pf_9csamtools_11StderrStore_readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_v_lines; PyObject *__pyx_r = NULL; PyObject *__pyx_t_1 = NULL; @@ -3042,7 +3261,7 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__p __pyx_self = __pyx_self; __pyx_v_lines = Py_None; __Pyx_INCREF(Py_None); - /* "csamtools.pyx":185 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":185 * * def readAndRelease( self ): * return [] # <<<<<<<<<<<<<< @@ -3056,7 +3275,7 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__p __pyx_t_1 = 0; goto __pyx_L0; 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PyTuple_SET_ITEM(__pyx_t_3, 1, ((PyObject *)__pyx_n_s__r)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r)); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Call(__pyx_builtin_open, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__readlines); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -3146,7 +3365,7 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__p __pyx_v_lines = __pyx_t_2; __pyx_t_2 = 0; - /* "csamtools.pyx":190 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":190 * if os.path.exists(self.stderr_f): * lines = open( self.stderr_f, "r" ).readlines() * os.remove( self.stderr_f ) # <<<<<<<<<<<<<< @@ -3161,20 +3380,20 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__p __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__stderr_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_1)); + __Pyx_GOTREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Call(__pyx_t_3, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; goto __pyx_L5; } __pyx_L5:; - /* "csamtools.pyx":191 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":191 * lines = open( self.stderr_f, "r" ).readlines() * os.remove( self.stderr_f ) * return lines # <<<<<<<<<<<<<< @@ -3202,7 +3421,7 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__p return __pyx_r; } -/* "csamtools.pyx":193 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":193 * return lines * * def release(self): # <<<<<<<<<<<<<< @@ -3210,10 +3429,10 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__p * self.stderr_save.restore() */ -static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_9csamtools_11StderrStore_2release[] = "StderrStore.release(self)"; -static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_2release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore_2release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_2release)}; -static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11StderrStore_release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_9csamtools_11StderrStore_release[] = "StderrStore.release(self)"; +static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore_release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_release)}; +static PyObject *__pyx_pf_9csamtools_11StderrStore_release(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; @@ -3224,7 +3443,7 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self __Pyx_TraceCall("release", __pyx_f[0], 193); __pyx_self = __pyx_self; - /* "csamtools.pyx":194 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":194 * * def release(self): * return # <<<<<<<<<<<<<< @@ -3235,7 +3454,7 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "csamtools.pyx":195 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":195 * def release(self): * return * self.stderr_save.restore() # <<<<<<<<<<<<<< @@ -3252,7 +3471,7 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "csamtools.pyx":196 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":196 * return * self.stderr_save.restore() * if os.path.exists(self.stderr_f): # <<<<<<<<<<<<<< @@ -3270,19 +3489,19 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__stderr_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __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 = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_3)); + __Pyx_GOTREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Call(__pyx_t_1, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); 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if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 197; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Call(__pyx_t_3, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 197; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; goto __pyx_L5; } @@ -3325,7 +3544,7 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self return __pyx_r; } -/* "csamtools.pyx":199 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":199 * os.remove( self.stderr_f ) * * def __del__(self): # <<<<<<<<<<<<<< @@ -3333,10 +3552,10 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self * */ -static PyObject *__pyx_pf_9csamtools_11StderrStore_3__del__(PyObject *__pyx_self, PyObject *__pyx_v_self); 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+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; PyObject *__pyx_t_1 = NULL; __Pyx_TraceDeclarations @@ -3436,7 +3655,7 @@ static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_1readAndRelease(PyObje return __pyx_r; } -/* "csamtools.pyx":206 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":206 * def __init__(self): pass * def readAndRelease(self): return [] * def release(self): pass # <<<<<<<<<<<<<< @@ -3444,10 +3663,10 @@ static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_1readAndRelease(PyObje * if platform.system()=='Windows': */ -static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_9csamtools_18StderrStoreWindows_2release[] = "StderrStoreWindows.release(self)"; -static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_2release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pf_9csamtools_18StderrStoreWindows_2release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows_2release)}; -static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2release(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_9csamtools_18StderrStoreWindows_release[] = "StderrStoreWindows.release(self)"; +static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pf_9csamtools_18StderrStoreWindows_release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows_release)}; +static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_release(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("release"); @@ -3461,7 +3680,7 @@ static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2release(PyObject *__p return __pyx_r; } -/* "csamtools.pyx":260 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":260 * cdef faidx_t * fastafile * * def __cinit__(self, *args, **kwargs ): # <<<<<<<<<<<<<< @@ -3487,7 +3706,7 @@ static int __pyx_pf_9csamtools_9Fastafile___cinit__(PyObject *__pyx_v_self, PyOb __Pyx_INCREF(__pyx_args); __pyx_v_args = __pyx_args; - /* "csamtools.pyx":261 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":261 * * def __cinit__(self, *args, **kwargs ): * self.fastafile = NULL # <<<<<<<<<<<<<< @@ -3496,7 +3715,7 @@ static int __pyx_pf_9csamtools_9Fastafile___cinit__(PyObject *__pyx_v_self, PyOb */ ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile = NULL; - /* "csamtools.pyx":262 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":262 * def __cinit__(self, *args, **kwargs ): * self.fastafile = NULL * self._filename = NULL # <<<<<<<<<<<<<< @@ -3505,7 +3724,7 @@ static int __pyx_pf_9csamtools_9Fastafile___cinit__(PyObject *__pyx_v_self, PyOb */ ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename = NULL; - /* "csamtools.pyx":263 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":263 * self.fastafile = NULL * self._filename = NULL * self._open( *args, **kwargs ) # <<<<<<<<<<<<<< @@ -3538,7 +3757,7 @@ static int __pyx_pf_9csamtools_9Fastafile___cinit__(PyObject *__pyx_v_self, PyOb return __pyx_r; } -/* "csamtools.pyx":265 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":265 * self._open( *args, **kwargs ) * * def _isOpen( self ): # <<<<<<<<<<<<<< @@ -3546,16 +3765,16 @@ static int __pyx_pf_9csamtools_9Fastafile___cinit__(PyObject *__pyx_v_self, PyOb * return self.fastafile != NULL */ -static PyObject *__pyx_pf_9csamtools_9Fastafile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ -static char __pyx_doc_9csamtools_9Fastafile_1_isOpen[] = "Fastafile._isOpen(self)\nreturn true if samfile has been opened."; -static PyObject *__pyx_pf_9csamtools_9Fastafile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { +static PyObject *__pyx_pf_9csamtools_9Fastafile__isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static char __pyx_doc_9csamtools_9Fastafile__isOpen[] = "Fastafile._isOpen(self)\nreturn true if samfile has been opened."; +static PyObject *__pyx_pf_9csamtools_9Fastafile__isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { PyObject *__pyx_r = NULL; PyObject *__pyx_t_1 = NULL; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("_isOpen"); __Pyx_TraceCall("_isOpen", __pyx_f[0], 265); - /* "csamtools.pyx":267 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":267 * def _isOpen( self ): * '''return true if samfile has been opened.''' * return self.fastafile != NULL # <<<<<<<<<<<<<< @@ -3582,7 +3801,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_1_isOpen(PyObject *__pyx_v_self, return __pyx_r; } -/* "csamtools.pyx":269 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":269 * return self.fastafile != NULL * * def __len__(self): # <<<<<<<<<<<<<< @@ -3590,16 +3809,17 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_1_isOpen(PyObject *__pyx_v_self, * raise ValueError( "calling len() on closed file" ) */ -static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self); /*proto*/ -static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self) { +static Py_ssize_t __pyx_pf_9csamtools_9Fastafile___len__(PyObject *__pyx_v_self); /*proto*/ +static Py_ssize_t __pyx_pf_9csamtools_9Fastafile___len__(PyObject *__pyx_v_self) { Py_ssize_t __pyx_r; int __pyx_t_1; PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_3 = NULL; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__len__"); __Pyx_TraceCall("__len__", __pyx_f[0], 269); - /* "csamtools.pyx":270 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":270 * * def __len__(self): * if self.fastafile == NULL: # <<<<<<<<<<<<<< @@ -3609,23 +3829,29 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile == NULL); if (__pyx_t_1) { - /* "csamtools.pyx":271 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":271 * def __len__(self): * if self.fastafile == NULL: * raise ValueError( "calling len() on closed file" ) # <<<<<<<<<<<<<< * * return faidx_fetch_nseq(self.fastafile) */ - __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_4), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __Pyx_Raise(__pyx_t_2, 0, 0); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_3)); + PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_3)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_3)); + __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_Raise(__pyx_t_3, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L5; } __pyx_L5:; - /* "csamtools.pyx":273 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":273 * raise ValueError( "calling len() on closed file" ) * * return faidx_fetch_nseq(self.fastafile) # <<<<<<<<<<<<<< @@ -3639,6 +3865,7 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); __Pyx_AddTraceback("csamtools.Fastafile.__len__"); __pyx_r = -1; __pyx_L0:; @@ -3647,7 +3874,7 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self return __pyx_r; } -/* "csamtools.pyx":275 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":275 * return faidx_fetch_nseq(self.fastafile) * * def _open( self, # <<<<<<<<<<<<<< @@ -3655,9 +3882,9 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self * '''open an indexed fasta file. */ -static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_arg_filename); /*proto*/ -static char __pyx_doc_9csamtools_9Fastafile_3_open[] = "Fastafile._open(self, char *filename)\nopen an indexed fasta file.\n\n This method expects an indexed fasta file.\n "; -static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_arg_filename) { +static PyObject *__pyx_pf_9csamtools_9Fastafile__open(PyObject *__pyx_v_self, PyObject *__pyx_arg_filename); /*proto*/ +static char __pyx_doc_9csamtools_9Fastafile__open[] = "Fastafile._open(self, char *filename)\nopen an indexed fasta file.\n\n This method expects an indexed fasta file.\n "; +static PyObject *__pyx_pf_9csamtools_9Fastafile__open(PyObject *__pyx_v_self, PyObject *__pyx_arg_filename) { char *__pyx_v_filename; PyObject *__pyx_r = NULL; int __pyx_t_1; @@ -3676,7 +3903,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P return NULL; __pyx_L4_argument_unpacking_done:; - /* "csamtools.pyx":283 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":283 * * # close a previously opened file * if self.fastafile != NULL: self.close() # <<<<<<<<<<<<<< @@ -3695,7 +3922,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P } __pyx_L5:; - /* "csamtools.pyx":284 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":284 * # close a previously opened file * if self.fastafile != NULL: self.close() * if self._filename != NULL: free(self._filename) # <<<<<<<<<<<<<< @@ -3709,7 +3936,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P } __pyx_L6:; - /* "csamtools.pyx":285 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":285 * if self.fastafile != NULL: self.close() * if self._filename != NULL: free(self._filename) * self._filename = strdup(filename) # <<<<<<<<<<<<<< @@ -3718,7 +3945,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P */ ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename = strdup(__pyx_v_filename); - /* "csamtools.pyx":286 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":286 * if self._filename != NULL: free(self._filename) * self._filename = strdup(filename) * self.fastafile = fai_load( filename ) # <<<<<<<<<<<<<< @@ -3727,7 +3954,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P */ ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile = fai_load(__pyx_v_filename); - /* "csamtools.pyx":288 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":288 * self.fastafile = fai_load( filename ) * * if self.fastafile == NULL: # <<<<<<<<<<<<<< @@ -3737,7 +3964,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile == NULL); if (__pyx_t_1) { - /* "csamtools.pyx":289 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":289 * * if self.fastafile == NULL: * raise IOError("could not open file `%s`" % filename ) # <<<<<<<<<<<<<< @@ -3746,17 +3973,17 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P */ __pyx_t_3 = PyBytes_FromString(__pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_3)); - __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_5), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_4), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_3)); + __Pyx_GOTREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2)); __Pyx_GIVEREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Call(__pyx_builtin_IOError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_Raise(__pyx_t_2, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -3778,7 +4005,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P return __pyx_r; } -/* "csamtools.pyx":291 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":291 * raise IOError("could not open file `%s`" % filename ) * * def close( self ): # <<<<<<<<<<<<<< @@ -3786,16 +4013,16 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P * fai_destroy( self.fastafile ) */ -static PyObject *__pyx_pf_9csamtools_9Fastafile_4close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ -static char __pyx_doc_9csamtools_9Fastafile_4close[] = "Fastafile.close(self)"; -static PyObject *__pyx_pf_9csamtools_9Fastafile_4close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { +static PyObject *__pyx_pf_9csamtools_9Fastafile_close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static char __pyx_doc_9csamtools_9Fastafile_close[] = "Fastafile.close(self)"; +static PyObject *__pyx_pf_9csamtools_9Fastafile_close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { PyObject *__pyx_r = NULL; 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} -/* "csamtools.pyx":296 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":296 * self.fastafile = NULL * * def __dealloc__(self): # <<<<<<<<<<<<<< @@ -3841,8 +4068,8 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_4close(PyObject *__pyx_v_self, C * if self._filename != NULL: free(self._filename) */ -static void __pyx_pf_9csamtools_9Fastafile_5__dealloc__(PyObject *__pyx_v_self); /*proto*/ -static void __pyx_pf_9csamtools_9Fastafile_5__dealloc__(PyObject *__pyx_v_self) { +static void __pyx_pf_9csamtools_9Fastafile___dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pf_9csamtools_9Fastafile___dealloc__(PyObject *__pyx_v_self) { PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; int __pyx_t_3; @@ -3850,7 +4077,7 @@ static void __pyx_pf_9csamtools_9Fastafile_5__dealloc__(PyObject *__pyx_v_self) __Pyx_RefNannySetupContext("__dealloc__"); __Pyx_TraceCall("__dealloc__", __pyx_f[0], 296); - /* "csamtools.pyx":297 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":297 * * def __dealloc__(self): * self.close() # <<<<<<<<<<<<<< @@ -3864,7 +4091,7 @@ static void __pyx_pf_9csamtools_9Fastafile_5__dealloc__(PyObject *__pyx_v_self) __Pyx_DECREF(__pyx_t_1); 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+ __pyx_r = ((PyObject *)__pyx_t_1); + __pyx_t_1 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); @@ -3960,7 +4193,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__py return __pyx_r; } -/* "csamtools.pyx":306 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":306 * return self._filename * * def fetch( self, # <<<<<<<<<<<<<< @@ -3968,9 +4201,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__py * start = None, */ -static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_9csamtools_9Fastafile_6fetch[] = "Fastafile.fetch(self, reference=None, start=None, end=None, region=None)\n*(reference = None, start = None, end = None, region = None)*\n \n fetch :meth:`AlignedRead` objects in a :term:`region` using 0-based indexing. \n \n The region is specified by :term:`reference`, *start* and *end*. \n \n fetch returns an empty string if the region is out of range or addresses an unknown *reference*.\n\n If *reference* is given and *start* is None, the sequence from the \n first base is returned. Similarly, if *end* is None, the sequence \n until the last base is returned.\n \n Alternatively, a samtools :term:`region` string can be supplied.\n "; -static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_9csamtools_9Fastafile_fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_9csamtools_9Fastafile_fetch[] = "Fastafile.fetch(self, reference=None, start=None, end=None, region=None)\n*(reference = None, start = None, end = None, region = None)*\n \n fetch :meth:`AlignedRead` objects in a :term:`region` using 0-based indexing. \n \n The region is specified by :term:`reference`, *start* and *end*. \n \n fetch returns an empty string if the region is out of range or addresses an unknown *reference*.\n\n If *reference* is given and *start* is None, the sequence from the \n first base is returned. Similarly, if *end* is None, the sequence \n until the last base is returned.\n \n Alternatively, a samtools :term:`region` string can be supplied.\n "; +static PyObject *__pyx_pf_9csamtools_9Fastafile_fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_reference = 0; PyObject *__pyx_v_start = 0; PyObject *__pyx_v_end = 0; @@ -3992,7 +4225,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P Py_ssize_t kw_args = PyDict_Size(__pyx_kwds); PyObject* values[4] = {0,0,0,0}; - /* "csamtools.pyx":307 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":307 * * def fetch( self, * reference = None, # <<<<<<<<<<<<<< @@ -4001,7 +4234,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P */ values[0] = ((PyObject *)Py_None); - /* "csamtools.pyx":308 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":308 * def fetch( self, * reference = None, * start = None, # <<<<<<<<<<<<<< @@ -4010,7 +4243,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P */ values[1] = ((PyObject *)Py_None); - /* "csamtools.pyx":309 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":309 * reference = None, * start = None, * end = None, # <<<<<<<<<<<<<< @@ -4019,7 +4252,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P */ values[2] = ((PyObject *)Py_None); - /* "csamtools.pyx":310 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":310 * start = None, * end = None, * region = None): # <<<<<<<<<<<<<< @@ -4066,7 +4299,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P __pyx_v_region = values[3]; } else { - /* "csamtools.pyx":307 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":307 * * def fetch( self, * reference = None, # <<<<<<<<<<<<<< @@ -4075,7 +4308,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P */ __pyx_v_reference = ((PyObject *)Py_None); - /* "csamtools.pyx":308 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":308 * def fetch( self, * reference = None, * start = None, # <<<<<<<<<<<<<< @@ -4084,7 +4317,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P */ __pyx_v_start = ((PyObject *)Py_None); - /* "csamtools.pyx":309 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":309 * reference = None, * start = None, * end = None, # <<<<<<<<<<<<<< @@ -4093,7 +4326,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P */ __pyx_v_end = ((PyObject *)Py_None); - /* "csamtools.pyx":310 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":310 * start = None, * end = None, * region = None): # <<<<<<<<<<<<<< @@ -4123,7 +4356,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P __Pyx_INCREF(__pyx_v_region); __pyx_v_py_seq = Py_None; __Pyx_INCREF(Py_None); - /* "csamtools.pyx":327 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":327 * ''' * * if not self._isOpen(): # <<<<<<<<<<<<<< @@ -4140,23 +4373,29 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P __pyx_t_4 = (!__pyx_t_3); if (__pyx_t_4) { - /* "csamtools.pyx":328 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":328 * * if not self._isOpen(): * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * * cdef int length */ - __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_8), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __Pyx_Raise(__pyx_t_2, 0, 0); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_5)); + PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_5)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5)); + __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_Raise(__pyx_t_1, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L6; } __pyx_L6:; - /* "csamtools.pyx":333 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":333 * cdef char * seq * * if not region: # <<<<<<<<<<<<<< @@ -4167,7 +4406,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P __pyx_t_3 = (!__pyx_t_4); if (__pyx_t_3) { - /* "csamtools.pyx":334 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":334 * * if not region: * if reference is None: raise ValueError( 'no sequence/region supplied.' ) # <<<<<<<<<<<<<< @@ -4176,8 +4415,14 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P */ __pyx_t_3 = (__pyx_v_reference == Py_None); if (__pyx_t_3) { - __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_10), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_6)); + PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_6)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6)); + __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_Raise(__pyx_t_2, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -4185,7 +4430,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P } __pyx_L8:; - /* "csamtools.pyx":335 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":335 * if not region: * if reference is None: raise ValueError( 'no sequence/region supplied.' ) * if start is None: start = 0 # <<<<<<<<<<<<<< @@ -4201,7 +4446,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P } __pyx_L9:; - /* "csamtools.pyx":336 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":336 * if reference is None: raise ValueError( 'no sequence/region supplied.' ) * if start is None: start = 0 * if end is None: end = max_pos -1 # <<<<<<<<<<<<<< @@ -4219,7 +4464,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P } __pyx_L10:; - /* "csamtools.pyx":338 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":338 * if end is None: end = max_pos -1 * * if start > end: raise ValueError( 'invalid region: start (%i) > end (%i)' % (start, end) ) # <<<<<<<<<<<<<< @@ -4232,24 +4477,24 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_3) { __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_v_start); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_start); __Pyx_GIVEREF(__pyx_v_start); __Pyx_INCREF(__pyx_v_end); PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_end); __Pyx_GIVEREF(__pyx_v_end); - __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_11), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_7), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __Pyx_GOTREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1)); __Pyx_GIVEREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_Raise(__pyx_t_1, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -4257,7 +4502,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P } __pyx_L11:; - /* "csamtools.pyx":339 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":339 * * if start > end: raise ValueError( 'invalid region: start (%i) > end (%i)' % (start, end) ) * if start == end: return "" # <<<<<<<<<<<<<< @@ -4270,14 +4515,14 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_3) { __Pyx_XDECREF(__pyx_r); - __Pyx_INCREF(((PyObject *)__pyx_kp_s_12)); - __pyx_r = ((PyObject *)__pyx_kp_s_12); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_8)); + __pyx_r = ((PyObject *)__pyx_kp_s_8); goto __pyx_L0; goto __pyx_L12; } __pyx_L12:; - /* "csamtools.pyx":341 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":341 * if start == end: return "" * # valid ranges are from 0 to 2^29-1 * if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start ) # <<<<<<<<<<<<<< @@ -4298,16 +4543,16 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_4 = (!__pyx_t_3); if (__pyx_t_4) { - __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_13), __pyx_v_start); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_v_start); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __Pyx_GOTREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1)); __Pyx_GIVEREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_Raise(__pyx_t_1, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -4315,7 +4560,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P } __pyx_L13:; - /* "csamtools.pyx":342 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":342 * # 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 ) # <<<<<<<<<<<<<< @@ -4336,16 +4581,16 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_3 = (!__pyx_t_4); if (__pyx_t_3) { - __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_14), __pyx_v_end); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_10), __pyx_v_end); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __Pyx_GOTREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1)); __Pyx_GIVEREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_Raise(__pyx_t_1, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -4353,7 +4598,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P } __pyx_L14:; 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -4874,7 +5108,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_2_hasIndex(PyObject *__pyx_v_self, return __pyx_r; } -/* "csamtools.pyx":476 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":472 * return self.index != NULL * * def _open( self, # <<<<<<<<<<<<<< @@ -4882,9 +5116,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_2_hasIndex(PyObject *__pyx_v_self, * mode = None, */ -static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_3_open[] = "Samfile._open(self, char *filename, mode=None, Samfile template=None, referencenames=None, referencelengths=None, text=None, header=None, port=None, add_sq_text=True)\nopen a sam/bam file.\n\n If _open is called on an existing bamfile, the current file will be\n closed and a new file will be opened.\n "; -static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_9csamtools_7Samfile__open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_9csamtools_7Samfile__open[] = "Samfile._open(self, char *filename, mode=None, Samfile template=None, referencenames=None, referencelengths=None, text=None, header=None, port=None)\nopen a sam/bam file.\n\n If _open is called on an existing bamfile, the current file will be\n closed and a new file will be opened.\n "; +static PyObject *__pyx_pf_9csamtools_7Samfile__open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { char *__pyx_v_filename; PyObject *__pyx_v_mode = 0; struct __pyx_obj_9csamtools_Samfile *__pyx_v_template = 0; @@ -4893,7 +5127,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO PyObject *__pyx_v_text = 0; PyObject *__pyx_v_header = 0; PyObject *__pyx_v_port = 0; - PyObject *__pyx_v_add_sq_text = 0; PyObject *__pyx_v_msg; bam_header_t *__pyx_v_header_to_write; char *__pyx_v_ctext; @@ -4918,15 +5151,15 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO uint32_t __pyx_t_14; char *__pyx_t_15; int __pyx_t_16; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,&__pyx_n_s__template,&__pyx_n_s__referencenames,&__pyx_n_s__referencelengths,&__pyx_n_s__text,&__pyx_n_s__header,&__pyx_n_s__port,&__pyx_n_s__add_sq_text,0}; + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,&__pyx_n_s__template,&__pyx_n_s__referencenames,&__pyx_n_s__referencelengths,&__pyx_n_s__text,&__pyx_n_s__header,&__pyx_n_s__port,0}; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("_open"); - __Pyx_TraceCall("_open", __pyx_f[0], 476); + __Pyx_TraceCall("_open", __pyx_f[0], 472); if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args = PyDict_Size(__pyx_kwds); - PyObject* values[9] = {0,0,0,0,0,0,0,0,0}; + PyObject* values[8] = {0,0,0,0,0,0,0,0}; - /* "csamtools.pyx":478 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":474 * def _open( self, * char * filename, * mode = None, # <<<<<<<<<<<<<< @@ -4935,7 +5168,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO */ values[1] = ((PyObject *)Py_None); - /* "csamtools.pyx":479 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":475 * char * filename, * mode = None, * Samfile template = None, # <<<<<<<<<<<<<< @@ -4944,7 +5177,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO */ values[2] = (PyObject *)((struct __pyx_obj_9csamtools_Samfile *)Py_None); - /* "csamtools.pyx":480 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":476 * mode = None, * Samfile template = None, * referencenames = None, # <<<<<<<<<<<<<< @@ -4953,7 +5186,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO */ values[3] = ((PyObject *)Py_None); - /* "csamtools.pyx":481 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":477 * Samfile template = None, * referencenames = None, * referencelengths = None, # <<<<<<<<<<<<<< @@ -4962,7 +5195,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO */ values[4] = ((PyObject *)Py_None); - /* "csamtools.pyx":482 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":478 * referencenames = None, * referencelengths = None, * text = None, # <<<<<<<<<<<<<< @@ -4971,26 +5204,24 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO */ values[5] = ((PyObject *)Py_None); - /* "csamtools.pyx":483 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":479 * referencelengths = None, * text = None, * header = None, # <<<<<<<<<<<<<< * port = None, - * add_sq_text = True, + * ): */ values[6] = ((PyObject *)Py_None); - /* "csamtools.pyx":484 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":480 * text = None, * header = None, * port = None, # <<<<<<<<<<<<<< - * add_sq_text = True, * ): + * '''open a sam/bam file. */ values[7] = ((PyObject *)Py_None); - values[8] = __pyx_k_16; switch (PyTuple_GET_SIZE(__pyx_args)) { - case 9: values[8] = PyTuple_GET_ITEM(__pyx_args, 8); case 8: values[7] = PyTuple_GET_ITEM(__pyx_args, 7); case 7: values[6] = PyTuple_GET_ITEM(__pyx_args, 6); case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5); @@ -5042,16 +5273,11 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__port); if (value) { values[7] = value; kw_args--; } } - case 8: - if (kw_args > 0) { - PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__add_sq_text); - if (value) { values[8] = value; kw_args--; } - } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_open") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_open") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 472; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } - __pyx_v_filename = PyBytes_AsString(values[0]); if (unlikely((!__pyx_v_filename) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_filename = PyBytes_AsString(values[0]); if (unlikely((!__pyx_v_filename) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_mode = values[1]; __pyx_v_template = ((struct __pyx_obj_9csamtools_Samfile *)values[2]); __pyx_v_referencenames = values[3]; @@ -5059,10 +5285,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO __pyx_v_text = values[5]; __pyx_v_header = values[6]; __pyx_v_port = values[7]; - __pyx_v_add_sq_text = values[8]; } else { - /* "csamtools.pyx":478 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":474 * def _open( self, * char * filename, * mode = None, # <<<<<<<<<<<<<< @@ -5071,7 +5296,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO */ __pyx_v_mode = ((PyObject *)Py_None); - /* "csamtools.pyx":479 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":475 * char * filename, * mode = None, * Samfile template = None, # <<<<<<<<<<<<<< @@ -5080,7 +5305,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO */ __pyx_v_template = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); - /* "csamtools.pyx":480 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":476 * mode = None, * Samfile template = None, * referencenames = None, # <<<<<<<<<<<<<< @@ -5089,7 +5314,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO */ __pyx_v_referencenames = ((PyObject *)Py_None); - /* "csamtools.pyx":481 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":477 * Samfile template = None, * referencenames = None, * referencelengths = None, # <<<<<<<<<<<<<< @@ -5098,7 +5323,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO */ __pyx_v_referencelengths = ((PyObject *)Py_None); - /* "csamtools.pyx":482 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":478 * referencenames = None, * referencelengths = None, * text = None, # <<<<<<<<<<<<<< @@ -5107,26 +5332,24 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO */ __pyx_v_text = ((PyObject *)Py_None); - /* "csamtools.pyx":483 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":479 * referencelengths = None, * text = None, * header = None, # <<<<<<<<<<<<<< * port = None, - * add_sq_text = True, + * ): */ __pyx_v_header = ((PyObject *)Py_None); - /* "csamtools.pyx":484 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":480 * text = None, * header = None, * port = None, # <<<<<<<<<<<<<< - * add_sq_text = True, * ): + * '''open a sam/bam file. */ __pyx_v_port = ((PyObject *)Py_None); - __pyx_v_add_sq_text = __pyx_k_16; switch (PyTuple_GET_SIZE(__pyx_args)) { - case 9: __pyx_v_add_sq_text = PyTuple_GET_ITEM(__pyx_args, 8); case 8: __pyx_v_port = PyTuple_GET_ITEM(__pyx_args, 7); case 7: __pyx_v_header = PyTuple_GET_ITEM(__pyx_args, 6); case 6: __pyx_v_text = PyTuple_GET_ITEM(__pyx_args, 5); @@ -5134,42 +5357,41 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO case 4: __pyx_v_referencenames = PyTuple_GET_ITEM(__pyx_args, 3); case 3: __pyx_v_template = ((struct __pyx_obj_9csamtools_Samfile *)PyTuple_GET_ITEM(__pyx_args, 2)); case 2: __pyx_v_mode = PyTuple_GET_ITEM(__pyx_args, 1); - case 1: __pyx_v_filename = PyBytes_AsString(PyTuple_GET_ITEM(__pyx_args, 0)); if (unlikely((!__pyx_v_filename) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + case 1: __pyx_v_filename = PyBytes_AsString(PyTuple_GET_ITEM(__pyx_args, 0)); if (unlikely((!__pyx_v_filename) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L3_error;} break; default: goto __pyx_L5_argtuple_error; } } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("_open", 0, 1, 9, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_open", 0, 1, 8, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 472; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("csamtools.Samfile._open"); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __Pyx_INCREF(__pyx_v_text); __pyx_v_msg = Py_None; __Pyx_INCREF(Py_None); __pyx_v_n = Py_None; __Pyx_INCREF(Py_None); __pyx_v_x = Py_None; __Pyx_INCREF(Py_None); __pyx_v_name = Py_None; __Pyx_INCREF(Py_None); __pyx_v_store = Py_None; __Pyx_INCREF(Py_None); - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_template), __pyx_ptype_9csamtools_Samfile, 1, "template", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_template), __pyx_ptype_9csamtools_Samfile, 1, "template", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 475; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "csamtools.pyx":494 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":489 * * # read mode autodetection * if mode is None: # <<<<<<<<<<<<<< * try: - * self._open(filename, 'rb', template=template, + * self._open(filename, 'r', template=template, */ __pyx_t_1 = (__pyx_v_mode == Py_None); if (__pyx_t_1) { - /* "csamtools.pyx":495 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":490 * # read mode autodetection * if mode is None: * try: # <<<<<<<<<<<<<< - * self._open(filename, 'rb', template=template, + * self._open(filename, 'r', template=template, * referencenames=referencenames, */ { @@ -5180,65 +5402,65 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO __Pyx_XGOTREF(__pyx_save_exc_tb); /*try:*/ { - /* "csamtools.pyx":496 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":491 * if mode is None: * try: - * self._open(filename, 'rb', template=template, # <<<<<<<<<<<<<< + * self._open(filename, 'r', template=template, # <<<<<<<<<<<<<< * referencenames=referencenames, * referencelengths=referencelengths, */ - __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyBytes_FromString(__pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + __pyx_t_3 = PyBytes_FromString(__pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_3)); - __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L7_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_4)); + __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_3)); __Pyx_GIVEREF(((PyObject *)__pyx_t_3)); - __Pyx_INCREF(((PyObject *)__pyx_n_s__rb)); - PyTuple_SET_ITEM(__pyx_t_4, 1, ((PyObject *)__pyx_n_s__rb)); - __Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb)); + __Pyx_INCREF(((PyObject *)__pyx_n_s__r)); + PyTuple_SET_ITEM(__pyx_t_4, 1, ((PyObject *)__pyx_n_s__r)); + __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r)); __pyx_t_3 = 0; - __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_3)); - if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;} - /* "csamtools.pyx":497 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":492 * try: - * self._open(filename, 'rb', template=template, + * self._open(filename, 'r', template=template, * referencenames=referencenames, # <<<<<<<<<<<<<< * referencelengths=referencelengths, * text=text, header=header, port=port) */ - if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;} - /* "csamtools.pyx":498 - * self._open(filename, 'rb', template=template, + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":493 + * self._open(filename, 'r', template=template, * referencenames=referencenames, * referencelengths=referencelengths, # <<<<<<<<<<<<<< * text=text, header=header, port=port) * return */ - if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;} - /* "csamtools.pyx":499 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":494 * referencenames=referencenames, * referencelengths=referencelengths, * text=text, header=header, port=port) # <<<<<<<<<<<<<< * return * except ValueError, msg: */ - if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__text), __pyx_v_text) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L7_error;} - if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L7_error;} - if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L7_error;} - __pyx_t_5 = PyEval_CallObjectWithKeywords(__pyx_t_2, ((PyObject *)__pyx_t_4), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__text), __pyx_v_text) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + __pyx_t_5 = PyEval_CallObjectWithKeywords(__pyx_t_2, __pyx_t_4, ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "csamtools.pyx":500 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":495 * referencelengths=referencelengths, * text=text, header=header, port=port) * return # <<<<<<<<<<<<<< @@ -5265,17 +5487,17 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "csamtools.pyx":501 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":496 * text=text, header=header, port=port) * return * except ValueError, msg: # <<<<<<<<<<<<<< * pass - * + * self._open(filename, 'rb', template=template, */ __pyx_t_6 = PyErr_ExceptionMatches(__pyx_builtin_ValueError); if (__pyx_t_6) { __Pyx_AddTraceback("csamtools.Samfile._open"); - if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_3, &__pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 501; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;} + if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_3, &__pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GOTREF(__pyx_t_3); __Pyx_GOTREF(__pyx_t_4); @@ -5301,70 +5523,70 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO __pyx_L14_try_end:; } - /* "csamtools.pyx":504 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":498 + * except ValueError, msg: * pass - * - * self._open(filename, 'r', template=template, # <<<<<<<<<<<<<< + * self._open(filename, 'rb', template=template, # <<<<<<<<<<<<<< * referencenames=referencenames, * referencelengths=referencelengths, */ - __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = PyBytes_FromString(__pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyBytes_FromString(__pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_3)); - __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_5)); + __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_3)); __Pyx_GIVEREF(((PyObject *)__pyx_t_3)); - __Pyx_INCREF(((PyObject *)__pyx_n_s__r)); - PyTuple_SET_ITEM(__pyx_t_5, 1, ((PyObject *)__pyx_n_s__r)); - __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r)); + __Pyx_INCREF(((PyObject *)__pyx_n_s__rb)); + PyTuple_SET_ITEM(__pyx_t_5, 1, ((PyObject *)__pyx_n_s__rb)); + __Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb)); __pyx_t_3 = 0; - __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_3)); - if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "csamtools.pyx":505 - * - * self._open(filename, 'r', template=template, + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":499 + * pass + * self._open(filename, 'rb', template=template, * referencenames=referencenames, # <<<<<<<<<<<<<< * referencelengths=referencelengths, * text=text, header=header, port=port) */ - if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "csamtools.pyx":506 - * self._open(filename, 'r', template=template, + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":500 + * self._open(filename, 'rb', template=template, * referencenames=referencenames, * referencelengths=referencelengths, # <<<<<<<<<<<<<< * text=text, header=header, port=port) * return */ - if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; 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if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__w), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_8 = __pyx_t_1; __pyx_t_1 = __pyx_t_8; @@ -5399,9 +5621,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO __pyx_t_1 = __pyx_t_7; } if (!__pyx_t_1) { - __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__rb), Py_EQ); 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__pyx_lineno = 529; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_8) { - /* "csamtools.pyx":538 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":531 * if template: * # copy header from another file * header_to_write = template.samfile.header # <<<<<<<<<<<<<< @@ -5647,17 +5850,17 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO goto __pyx_L20; } - /* "csamtools.pyx":540 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":533 * header_to_write = template.samfile.header * * elif header: # <<<<<<<<<<<<<< * header_to_write = self._buildHeader( header ) * */ - __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_v_header); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 540; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_v_header); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 533; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_8) { - /* "csamtools.pyx":541 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":534 * * elif header: * header_to_write = self._buildHeader( header ) # <<<<<<<<<<<<<< @@ -5669,44 +5872,44 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO } /*else*/ { - /* "csamtools.pyx":545 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":538 * else: * # build header from a target names and lengths * assert referencenames and referencelengths, "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing" # <<<<<<<<<<<<<< * assert len(referencenames) == len(referencelengths), "unequal names and lengths of reference sequences" * */ - #ifndef CYTHON_WITHOUT_ASSERTIONS - __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_v_referencenames); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #ifndef PYREX_WITHOUT_ASSERTIONS + __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_v_referencenames); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_8) { - __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_v_referencelengths); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_1 = __pyx_t_7; + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_referencelengths); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __pyx_t_1; } else { - __pyx_t_1 = __pyx_t_8; + __pyx_t_7 = __pyx_t_8; } - if (unlikely(!__pyx_t_1)) { - PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_21)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_t_7)) { + PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_15)); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #endif - /* "csamtools.pyx":546 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":539 * # build header from a target names and lengths * assert referencenames and referencelengths, "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing" * assert len(referencenames) == len(referencelengths), "unequal names and lengths of reference sequences" # <<<<<<<<<<<<<< * * # allocate and fill header */ - #ifndef CYTHON_WITHOUT_ASSERTIONS - __pyx_t_9 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_10 = PyObject_Length(__pyx_v_referencelengths); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #ifndef PYREX_WITHOUT_ASSERTIONS + __pyx_t_9 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_Length(__pyx_v_referencelengths); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (unlikely(!(__pyx_t_9 == __pyx_t_10))) { - PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_22)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_16)); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #endif - /* "csamtools.pyx":549 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":542 * * # allocate and fill header * header_to_write = bam_header_init() # <<<<<<<<<<<<<< @@ -5715,17 +5918,17 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO */ __pyx_v_header_to_write = bam_header_init(); - /* "csamtools.pyx":550 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":543 * # allocate and fill header * header_to_write = bam_header_init() * header_to_write.n_targets = len(referencenames) # <<<<<<<<<<<<<< * n = 0 * for x in referencenames: n += len(x) + 1 */ - __pyx_t_10 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_header_to_write->n_targets = __pyx_t_10; - /* "csamtools.pyx":551 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":544 * header_to_write = bam_header_init() * header_to_write.n_targets = len(referencenames) * n = 0 # <<<<<<<<<<<<<< @@ -5736,7 +5939,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO __Pyx_DECREF(__pyx_v_n); __pyx_v_n = __pyx_int_0; - /* "csamtools.pyx":552 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":545 * header_to_write.n_targets = len(referencenames) * n = 0 * for x in referencenames: n += len(x) + 1 # <<<<<<<<<<<<<< @@ -5746,7 +5949,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO if (PyList_CheckExact(__pyx_v_referencenames) || PyTuple_CheckExact(__pyx_v_referencenames)) { __pyx_t_10 = 0; __pyx_t_3 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_3); } else { - __pyx_t_10 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); } for (;;) { @@ -5759,7 +5962,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO } else { __pyx_t_2 = PyIter_Next(__pyx_t_3); if (!__pyx_t_2) { - if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;} break; } __Pyx_GOTREF(__pyx_t_2); @@ -5767,10 +5970,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO __Pyx_DECREF(__pyx_v_x); __pyx_v_x = __pyx_t_2; __pyx_t_2 = 0; - __pyx_t_9 = PyObject_Length(__pyx_v_x); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_2 = PyInt_FromSsize_t((__pyx_t_9 + 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyObject_Length(__pyx_v_x); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyInt_FromSsize_t((__pyx_t_9 + 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_v_n, __pyx_t_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_v_n, __pyx_t_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_v_n); @@ -5779,27 +5982,27 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "csamtools.pyx":553 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":546 * n = 0 * for x in referencenames: n += len(x) + 1 * header_to_write.target_name = calloc(n, sizeof(char*)) # <<<<<<<<<<<<<< * header_to_write.target_len = calloc(n, sizeof(uint32_t)) * for x from 0 <= x < header_to_write.n_targets: */ - __pyx_t_11 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_11 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_11 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_header_to_write->target_name = ((char **)calloc(__pyx_t_11, (sizeof(char *)))); - /* "csamtools.pyx":554 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":547 * for x in referencenames: n += len(x) + 1 * header_to_write.target_name = calloc(n, sizeof(char*)) * header_to_write.target_len = calloc(n, sizeof(uint32_t)) # <<<<<<<<<<<<<< * for x from 0 <= x < header_to_write.n_targets: * header_to_write.target_len[x] = referencelengths[x] */ - __pyx_t_11 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_11 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_11 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_header_to_write->target_len = ((uint32_t *)calloc(__pyx_t_11, (sizeof(uint32_t)))); - /* "csamtools.pyx":555 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":548 * header_to_write.target_name = calloc(n, sizeof(char*)) * header_to_write.target_len = calloc(n, sizeof(uint32_t)) * for x from 0 <= x < header_to_write.n_targets: # <<<<<<<<<<<<<< @@ -5808,208 +6011,119 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO */ __pyx_t_12 = __pyx_v_header_to_write->n_targets; for (__pyx_t_13 = 0; __pyx_t_13 < __pyx_t_12; __pyx_t_13++) { - __pyx_t_3 = PyInt_FromLong(__pyx_t_13); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyInt_FromLong(__pyx_t_13); 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__pyx_lineno = 625; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_Call(__pyx_builtin_IOError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_Raise(__pyx_t_5, 0, 0); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 625; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L38; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L36; } - __pyx_L38:; - } - __pyx_L35:; - - /* "csamtools.pyx":627 - * raise IOError("error while opening index `%s` " % filename ) - * - * if not self.isstream: # <<<<<<<<<<<<<< - * self.start_offset = bam_tell( self.samfile.x.bam ) - * - */ - __pyx_t_1 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream); 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/*try:*/ { - /* "csamtools.pyx":683 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":665 * if start != None: * try: * rstart = start # <<<<<<<<<<<<<< * except OverflowError: * raise ValueError( 'start out of range (%i)' % start ) */ - __pyx_t_3 = __Pyx_PyInt_AsLongLong(__pyx_v_start); if (unlikely((__pyx_t_3 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 683; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + __pyx_t_3 = __Pyx_PyInt_AsLongLong(__pyx_v_start); if (unlikely((__pyx_t_3 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 665; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __pyx_v_rstart = __pyx_t_3; } __Pyx_XDECREF(__pyx_save_exc_type); __pyx_save_exc_type = 0; @@ -7120,7 +7263,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se __pyx_L7_error:; __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "csamtools.pyx":684 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":666 * try: * rstart = start * except OverflowError: # <<<<<<<<<<<<<< @@ -7130,31 +7273,31 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se __pyx_t_4 = PyErr_ExceptionMatches(__pyx_builtin_OverflowError); 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PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_6)); __Pyx_GIVEREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; - __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_1, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_Raise(__pyx_t_6, 0, 0); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L33; } __pyx_L33:; - /* "csamtools.pyx":704 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":686 * if rtid < 0: raise ValueError( "invalid reference `%s`" % reference ) * if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) ) * if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart ) # <<<<<<<<<<<<<< @@ -7512,27 +7669,27 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se } __pyx_t_2 = (!__pyx_t_10); 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} -/* "csamtools.pyx":738 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":713 * return bam_tell( self.samfile.x.bam ) * * def fetch( self, # <<<<<<<<<<<<<< @@ -7974,9 +8068,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_9tell(PyObject *__pyx_v_self, CYTH * start = None, */ -static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_10fetch[] = "Samfile.fetch(self, reference=None, start=None, end=None, region=None, callback=None, until_eof=False)\n\n fetch aligned reads in a :term:`region` using 0-based indexing. 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The reads will be returned\n ordered by reference sequence, which will not necessarily be the order within the file.\n If *until_eof* is given, all reads from the current file position will be returned\n *in order as they are within the file*. \n \n If only *reference* is set, all reads aligned to *reference* will be fetched.\n\n The method returns an iterator of type :class:`pysam.IteratorRow` unless\n a *callback is provided. If *callback* is given, the callback will be executed \n for each position within the :term:`region`. Note that callbacks currently work\n only, if *region* or *reference* is given.\n\n Note that a :term:`SAM` file does not allow random access. If *region* or *reference* are given,\n an exception is raised.\n "; +static PyObject *__pyx_pf_9csamtools_7Samfile_fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_reference = 0; PyObject *__pyx_v_start = 0; PyObject *__pyx_v_end = 0; @@ -7987,7 +8081,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py int __pyx_v_rstart; int __pyx_v_rend; int __pyx_v_has_coord; - int __pyx_v_reopen; PyObject *__pyx_r = NULL; PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; @@ -8006,12 +8099,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,&__pyx_n_s__until_eof,0}; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("fetch"); - __Pyx_TraceCall("fetch", __pyx_f[0], 738); + __Pyx_TraceCall("fetch", __pyx_f[0], 713); if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args = PyDict_Size(__pyx_kwds); 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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 782; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L12; + __Pyx_Raise(__pyx_t_7, 0, 0); + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L11; } - __pyx_L12:; + __pyx_L11:; - /* "csamtools.pyx":783 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":754 * if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) * if not self._hasIndex(): raise ValueError( "no index available for fetch" ) * return bam_fetch(self.samfile.x.bam, # <<<<<<<<<<<<<< @@ -8422,252 +8515,253 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py */ __Pyx_XDECREF(__pyx_r); - /* "csamtools.pyx":789 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":760 * rend, * callback, * fetch_callback ) # <<<<<<<<<<<<<< * else: * if has_coord: */ - __pyx_t_5 = PyInt_FromLong(bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)__pyx_v_callback), __pyx_f_9csamtools_fetch_callback)); 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__Pyx_INCREF(Py_None); goto __pyx_L0; @@ -8687,17 +8781,17 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py return __pyx_r; } -/* "csamtools.pyx":813 - * return IteratorRowAll( self, reopen=reopen ) +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":782 + * return IteratorRowAll( self ) * * def mate( self, # <<<<<<<<<<<<<< * AlignedRead read ): * '''return the mate of :class:`AlignedRead` *read*. */ -static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_11mate[] = "Samfile.mate(self, AlignedRead read)\nreturn the mate of :class:`AlignedRead` *read*.\n\n Throws a ValueError if read is unpaired or the mate\n is unmapped.\n\n .. note::\n Calling this method will change the file position.\n This might interfere with any iterators that have\n not re-opened the file.\n\n "; -static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read) { +static PyObject *__pyx_pf_9csamtools_7Samfile_mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/ +static char __pyx_doc_9csamtools_7Samfile_mate[] = "Samfile.mate(self, AlignedRead read)\nreturn the mate of :class:`AlignedRead` *read*.\n\n Throws a ValueError if read is unpaired or the mate\n is unmapped.\n\n .. note::\n Calling this method will change the file position.\n This might interfere with any iterators that have\n not re-opened the file.\n\n "; +static PyObject *__pyx_pf_9csamtools_7Samfile_mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read) { uint32_t __pyx_v_flag; __pyx_t_9csamtools_MateData __pyx_v_mate_data; int __pyx_v_x; @@ -8708,10 +8802,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyO PyObject *__pyx_t_3 = NULL; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("mate"); - __Pyx_TraceCall("mate", __pyx_f[0], 813); - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_TraceCall("mate", __pyx_f[0], 782); 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if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_read, __pyx_n_s__qname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_58), __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_36), __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_3)); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_3)); __Pyx_GIVEREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; - __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_Raise(__pyx_t_3, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L5; } __pyx_L5:; - /* "csamtools.pyx":830 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":799 * if flag & BAM_FPAIRED == 0: * raise ValueError( "read %s: is unpaired" % (read.qname)) * if flag & BAM_FMUNMAP != 0: # <<<<<<<<<<<<<< @@ -8767,34 +8861,34 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyO __pyx_t_1 = ((__pyx_v_flag & 8) != 0); if (__pyx_t_1) { - /* "csamtools.pyx":831 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":800 * raise ValueError( "read %s: is unpaired" % (read.qname)) * if flag & BAM_FMUNMAP != 0: * raise ValueError( "mate %s: is unmapped" % (read.qname)) # <<<<<<<<<<<<<< * * cdef MateData mate_data */ - __pyx_t_3 = PyObject_GetAttr(__pyx_v_read, __pyx_n_s__qname); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_GetAttr(__pyx_v_read, __pyx_n_s__qname); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_59), __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_37), __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_3)); + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2)); __Pyx_GIVEREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_Raise(__pyx_t_2, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L6; } __pyx_L6:; - /* "csamtools.pyx":835 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":804 * cdef MateData mate_data * * mate_data.name = bam1_qname(read._delegate) # <<<<<<<<<<<<<< @@ -8803,7 +8897,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyO */ __pyx_v_mate_data.name = bam1_qname(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate); - /* "csamtools.pyx":836 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":805 * * mate_data.name = bam1_qname(read._delegate) * mate_data.mate = NULL # <<<<<<<<<<<<<< @@ -8812,7 +8906,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyO */ __pyx_v_mate_data.mate = NULL; - /* "csamtools.pyx":838 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":807 * mate_data.mate = NULL * # xor flags to get the other mate * cdef int x = BAM_FREAD1 + BAM_FREAD2 # <<<<<<<<<<<<<< @@ -8821,7 +8915,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyO */ __pyx_v_x = 192; - /* "csamtools.pyx":839 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":808 * # xor flags to get the other mate * cdef int x = BAM_FREAD1 + BAM_FREAD2 * mate_data.flag = ( flag ^ x) & x # <<<<<<<<<<<<<< @@ -8830,7 +8924,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyO */ __pyx_v_mate_data.flag = ((__pyx_v_flag ^ __pyx_v_x) & __pyx_v_x); - /* "csamtools.pyx":847 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":816 * read._delegate.core.mpos + 1, * &mate_data, * mate_callback ) # <<<<<<<<<<<<<< @@ -8839,7 +8933,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyO */ bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mtid, ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mpos, (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mpos + 1), ((void *)(&__pyx_v_mate_data)), __pyx_f_9csamtools_mate_callback); - /* "csamtools.pyx":849 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":818 * mate_callback ) * * if mate_data.mate == NULL: # <<<<<<<<<<<<<< @@ -8849,36 +8943,42 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyO __pyx_t_1 = (__pyx_v_mate_data.mate == NULL); if (__pyx_t_1) { - /* "csamtools.pyx":850 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":819 * * if mate_data.mate == NULL: * raise ValueError( "mate not found" ) # <<<<<<<<<<<<<< * * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) */ - __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_61), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __Pyx_Raise(__pyx_t_2, 0, 0); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_38)); + PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_38)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_38)); + __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_Raise(__pyx_t_3, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L7; } __pyx_L7:; - /* "csamtools.pyx":852 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":821 * raise ValueError( "mate not found" ) * * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) # <<<<<<<<<<<<<< * dest._delegate = mate_data.mate * return dest */ - __pyx_t_2 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_AlignedRead)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - if (!(likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_9csamtools_AlignedRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_dest = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_t_2); - __pyx_t_2 = 0; + __pyx_t_3 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_AlignedRead)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + if (!(likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_9csamtools_AlignedRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_dest = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_t_3); + __pyx_t_3 = 0; - /* "csamtools.pyx":853 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":822 * * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) * dest._delegate = mate_data.mate # <<<<<<<<<<<<<< @@ -8887,7 +8987,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyO */ __pyx_v_dest->_delegate = __pyx_v_mate_data.mate; - /* "csamtools.pyx":854 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":823 * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) * dest._delegate = mate_data.mate * return dest # <<<<<<<<<<<<<< @@ -8914,7 +9014,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyO return __pyx_r; 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@@ -9377,7 +9507,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py return __pyx_r; } -/* "csamtools.pyx":900 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":869 * raise ValueError ("count for a region is not available for sam files" ) * * def pileup( self, # <<<<<<<<<<<<<< @@ -9385,9 +9515,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py * start = None, */ -static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_13pileup[] = "Samfile.pileup(self, reference=None, start=None, end=None, region=None, callback=None, **kwargs)\n\n perform a :term:`pileup` within a :term:`region`. The region is specified by\n :term:`reference`, *start* and *end* (using 0-based indexing). \n Alternatively, a samtools *region* string can be supplied.\n\n Without *reference* or *region* all reads will be used for the pileup. The reads will be returned\n ordered by :term:`reference` sequence, which will not necessarily be the order within the file.\n\n The method returns an iterator of type :class:`pysam.IteratorColumn` unless\n a *callback is provided. If a *callback* is given, the callback will be executed \n for each column within the :term:`region`. \n\n Note that :term:`SAM` formatted files do not allow random access. \n In these files, if a *region* or *reference* are given an exception is raised.\n \n Optional *kwargs* to the iterator:\n\n stepper\n The stepper controlls how the iterator advances. \n Possible options for the stepper are \n \n ``all``\n use all reads for pileup.\n ``samtools``\n same filter and read processing as in :term:`csamtools` pileup\n\n fastafile\n A :class:`FastaFile` object\n\n mask\n Skip all reads with bits set in mask.\n\n max_depth\n Maximum read depth permitted. The default limit is *8000*.\n\n .. note::\n\n *all* reads which overlap the region are returned. The first base returned will be the \n first base of the first read *not* necessarily the first base of the region used in the query.\n\n "; -static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_9csamtools_7Samfile_pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_9csamtools_7Samfile_pileup[] = "Samfile.pileup(self, reference=None, start=None, end=None, region=None, callback=None, **kwargs)\n\n perform a :term:`pileup` within a :term:`region`. The region is specified by\n :term:`reference`, *start* and *end* (using 0-based indexing). \n Alternatively, a samtools *region* string can be supplied.\n\n Without *reference* or *region* all reads will be used for the pileup. The reads will be returned\n ordered by :term:`reference` sequence, which will not necessarily be the order within the file.\n\n The method returns an iterator of type :class:`pysam.IteratorColumn` unless\n a *callback is provided. If a *callback* is given, the callback will be executed \n for each column within the :term:`region`. \n\n Note that :term:`SAM` formatted files do not allow random access. \n In these files, if a *region* or *reference* are given an exception is raised.\n \n Optional *kwargs* to the iterator:\n\n stepper\n The stepper controlls how the iterator advances. \n Possible options for the stepper are \n \n ``all``\n use all reads for pileup.\n ``samtools``\n same filter and read processing as in :term:`csamtools` pileup\n\n fastafile\n A :class:`FastaFile` object\n\n mask\n Skip all reads with bits set in mask.\n\n\n .. note::\n\n *all* reads which overlap the region are returned. The first base returned will be the \n first base of the first read *not* necessarily the first base of the region used in the query.\n\n The maximum number of reads considered for pileup is *8000*. This limit is set by\n :term:`csamtools`.\n\n "; +static PyObject *__pyx_pf_9csamtools_7Samfile_pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_reference = 0; PyObject *__pyx_v_start = 0; PyObject *__pyx_v_end = 0; @@ -9415,14 +9545,14 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,0}; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("pileup"); - __Pyx_TraceCall("pileup", __pyx_f[0], 900); + __Pyx_TraceCall("pileup", __pyx_f[0], 869); __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return NULL; __Pyx_GOTREF(__pyx_v_kwargs); if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args = PyDict_Size(__pyx_kwds); PyObject* values[5] = {0,0,0,0,0}; - /* "csamtools.pyx":901 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":870 * * def pileup( self, * reference = None, # <<<<<<<<<<<<<< @@ -9431,7 +9561,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P */ values[0] = ((PyObject *)Py_None); - /* "csamtools.pyx":902 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":871 * def pileup( self, * reference = None, * start = None, # <<<<<<<<<<<<<< @@ -9440,7 +9570,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P */ values[1] = ((PyObject *)Py_None); - /* "csamtools.pyx":903 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":872 * reference = None, * start = None, * end = None, # <<<<<<<<<<<<<< @@ -9449,7 +9579,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P */ values[2] = ((PyObject *)Py_None); - /* "csamtools.pyx":904 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":873 * start = None, * end = None, * region = None, # <<<<<<<<<<<<<< @@ -9458,7 +9588,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P */ values[3] = ((PyObject *)Py_None); - /* "csamtools.pyx":905 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":874 * end = None, * region = None, * callback = None, # <<<<<<<<<<<<<< @@ -9503,7 +9633,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "pileup") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 900; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "pileup") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } __pyx_v_reference = values[0]; __pyx_v_start = values[1]; @@ -9512,7 +9642,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P __pyx_v_callback = values[4]; } else { - /* "csamtools.pyx":901 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":870 * * def pileup( self, * reference = None, # <<<<<<<<<<<<<< @@ -9521,7 +9651,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P */ __pyx_v_reference = ((PyObject *)Py_None); - /* "csamtools.pyx":902 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":871 * def pileup( self, * reference = None, * start = None, # <<<<<<<<<<<<<< @@ -9530,7 +9660,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P */ __pyx_v_start = ((PyObject *)Py_None); 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__pyx_lineno = 900; __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 = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_DECREF(__pyx_v_kwargs); __Pyx_AddTraceback("csamtools.Samfile.pileup"); @@ -9576,79 +9706,85 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P return NULL; __pyx_L4_argument_unpacking_done:; - /* "csamtools.pyx":951 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":921 * cdef bam_plbuf_t *buf * * if not self._isOpen(): # <<<<<<<<<<<<<< * raise ValueError( "I/O operation on closed file" ) * */ - __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; 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/*proto*/ +static char __pyx_doc_9csamtools_7Samfile___enter__[] = "Samfile.__enter__(self)"; +static PyObject *__pyx_pf_9csamtools_7Samfile___enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { PyObject *__pyx_r = NULL; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__enter__"); - __Pyx_TraceCall("__enter__", __pyx_f[0], 1010); + __Pyx_TraceCall("__enter__", __pyx_f[0], 980); - /* "csamtools.pyx":1011 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":981 * * def __enter__(self): * return self # <<<<<<<<<<<<<< @@ -10224,7 +10378,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_17__enter__(PyObject *__pyx_v_self return __pyx_r; } -/* "csamtools.pyx":1013 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":983 * return self * * def __exit__(self, exc_type, exc_value, traceback): # <<<<<<<<<<<<<< @@ -10232,9 +10386,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_17__enter__(PyObject *__pyx_v_self * return False */ -static PyObject *__pyx_pf_9csamtools_7Samfile_18__exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); 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goto __pyx_L1_error;} + __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 = 984; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "csamtools.pyx":1015 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":985 * def __exit__(self, exc_type, exc_value, traceback): * self.close() * return False # <<<<<<<<<<<<<< @@ -10317,7 +10471,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18__exit__(PyObject *__pyx_v_self, * ############################################################### */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1015; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 985; __pyx_clineno = __LINE__; 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goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_4) { - /* "csamtools.pyx":1174 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1117 * data = new_header[record] * if type( data ) != type( ttype() ): * raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) ) # <<<<<<<<<<<<<< * if type( data ) == types.DictType: * lines.append( self._buildLine( data, record ) ) */ - __pyx_t_1 = PyObject_Call(__pyx_v_ttype, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1174; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(__pyx_v_ttype, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1117; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1174; __pyx_clineno = __LINE__; 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_5 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__DictType); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__DictType); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; 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__pyx_lineno = 1119; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); __Pyx_INCREF(__pyx_v_data); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_data); __Pyx_GIVEREF(__pyx_v_data); __Pyx_INCREF(__pyx_v_record); PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_record); __Pyx_GIVEREF(__pyx_v_record); - __pyx_t_6 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1176; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyObject_Call(__pyx_t_1, __pyx_t_5, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1119; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0; - __pyx_t_7 = PyList_Append(__pyx_v_lines, __pyx_t_6); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1176; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_5); 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if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Length(__pyx_v_text); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1127; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_dest->l_text = __pyx_t_2; - /* "csamtools.pyx":1185 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1128 * dest.text = calloc( len(text), sizeof(char)) * dest.l_text = len(text) * strncpy( dest.text, text, dest.l_text ) # <<<<<<<<<<<<<< * * # collect targets */ - __pyx_t_10 = PyBytes_AsString(__pyx_v_text); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1185; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyBytes_AsString(__pyx_v_text); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1128; __pyx_clineno = __LINE__; goto __pyx_L1_error;} strncpy(__pyx_v_dest->text, __pyx_t_10, __pyx_v_dest->l_text); - /* "csamtools.pyx":1188 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1131 * * # collect targets * if "SQ" in new_header: # <<<<<<<<<<<<<< * seqs = [] * for fields in new_header["SQ"]: */ - __pyx_t_4 = ((PySequence_Contains(__pyx_v_new_header, ((PyObject *)__pyx_n_s__SQ)))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = ((PySequence_Contains(__pyx_v_new_header, ((PyObject *)__pyx_n_s__SQ)))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1131; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_4) { - /* "csamtools.pyx":1189 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1132 * # collect targets * if "SQ" in new_header: * seqs = [] # <<<<<<<<<<<<<< * for fields in new_header["SQ"]: * try: */ - __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __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 = 1132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_5)); __Pyx_DECREF(((PyObject *)__pyx_v_seqs)); __pyx_v_seqs = __pyx_t_5; __pyx_t_5 = 0; - /* "csamtools.pyx":1190 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1133 * if "SQ" in new_header: * seqs = [] * for fields in new_header["SQ"]: # <<<<<<<<<<<<<< * try: * seqs.append( (fields["SN"], fields["LN"] ) ) */ - __pyx_t_5 = PyObject_GetItem(__pyx_v_new_header, ((PyObject *)__pyx_n_s__SQ)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_GetItem(__pyx_v_new_header, ((PyObject *)__pyx_n_s__SQ)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1133; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); if (PyList_CheckExact(__pyx_t_5) || PyTuple_CheckExact(__pyx_t_5)) { __pyx_t_2 = 0; __pyx_t_9 = __pyx_t_5; __Pyx_INCREF(__pyx_t_9); } else { - __pyx_t_2 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1133; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); } __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; @@ -12502,7 +12469,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_ } else { __pyx_t_5 = PyIter_Next(__pyx_t_9); if (!__pyx_t_5) { - if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1133; __pyx_clineno = __LINE__; goto __pyx_L1_error;} break; } __Pyx_GOTREF(__pyx_t_5); @@ -12511,7 +12478,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_ __pyx_v_fields = __pyx_t_5; __pyx_t_5 = 0; - /* "csamtools.pyx":1191 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1134 * seqs = [] * for fields in new_header["SQ"]: * try: # <<<<<<<<<<<<<< @@ -12526,7 +12493,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_ __Pyx_XGOTREF(__pyx_save_exc_tb); /*try:*/ { - /* "csamtools.pyx":1192 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1135 * for fields in new_header["SQ"]: * try: * seqs.append( (fields["SN"], fields["LN"] ) ) # <<<<<<<<<<<<<< @@ -12534,22 +12501,22 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_ * raise KeyError( "incomplete sequence information in '%s'" % str(fields)) */ if (unlikely(__pyx_v_seqs == Py_None)) { - PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L14_error;} + PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1135; __pyx_clineno = __LINE__; goto __pyx_L14_error;} } - __pyx_t_5 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__SN)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L14_error;} + __pyx_t_5 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__SN)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1135; __pyx_clineno = __LINE__; goto __pyx_L14_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_3 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__LN)); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L14_error;} + __pyx_t_3 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__LN)); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1135; __pyx_clineno = __LINE__; goto __pyx_L14_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L14_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_1)); + __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1135; __pyx_clineno = __LINE__; goto __pyx_L14_error;} + __Pyx_GOTREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_5 = 0; __pyx_t_3 = 0; - __pyx_t_7 = PyList_Append(__pyx_v_seqs, ((PyObject *)__pyx_t_1)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L14_error;} - __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; + __pyx_t_7 = PyList_Append(((PyObject *)__pyx_v_seqs), __pyx_t_1); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1135; __pyx_clineno = __LINE__; goto __pyx_L14_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } __Pyx_XDECREF(__pyx_save_exc_type); __pyx_save_exc_type = 0; __Pyx_XDECREF(__pyx_save_exc_value); __pyx_save_exc_value = 0; @@ -12561,7 +12528,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "csamtools.pyx":1193 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1136 * try: * seqs.append( (fields["SN"], fields["LN"] ) ) * except KeyError: # <<<<<<<<<<<<<< @@ -12571,40 +12538,40 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_ __pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_KeyError); if (__pyx_t_7) { __Pyx_AddTraceback("csamtools.Samfile._buildHeader"); - if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_3, &__pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1193; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;} + if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_3, &__pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_GOTREF(__pyx_t_3); __Pyx_GOTREF(__pyx_t_5); - /* "csamtools.pyx":1194 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1137 * seqs.append( (fields["SN"], fields["LN"] ) ) * except KeyError: * raise KeyError( "incomplete sequence information in '%s'" % str(fields)) # <<<<<<<<<<<<<< * * dest.n_targets = len(seqs) */ - __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1194; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_6)); + __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;} + __Pyx_GOTREF(__pyx_t_6); __Pyx_INCREF(__pyx_v_fields); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_fields); __Pyx_GIVEREF(__pyx_v_fields); - __pyx_t_11 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1194; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;} + __pyx_t_11 = PyObject_Call(((PyObject *)((PyObject*)&PyString_Type)), __pyx_t_6, NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;} __Pyx_GOTREF(__pyx_t_11); - __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; - __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_101), __pyx_t_11); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1194; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;} + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_53), __pyx_t_11); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_6)); __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; - __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1194; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_11)); + __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;} + __Pyx_GOTREF(__pyx_t_11); PyTuple_SET_ITEM(__pyx_t_11, 0, ((PyObject *)__pyx_t_6)); __Pyx_GIVEREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; - __pyx_t_6 = PyObject_Call(__pyx_builtin_KeyError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1194; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;} + __pyx_t_6 = PyObject_Call(__pyx_builtin_KeyError, __pyx_t_11, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;} __Pyx_GOTREF(__pyx_t_6); - __Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0; + __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; __Pyx_Raise(__pyx_t_6, 0, 0); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1194; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L16_except_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; @@ -12626,7 +12593,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_ } __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "csamtools.pyx":1196 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1139 * raise KeyError( "incomplete sequence information in '%s'" % str(fields)) * * dest.n_targets = len(seqs) # <<<<<<<<<<<<<< @@ -12634,12 +12601,12 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_ * dest.target_len = calloc( dest.n_targets, sizeof(uint32_t) ) */ if (unlikely(__pyx_v_seqs == Py_None)) { - PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_2 = PyList_GET_SIZE(((PyObject *)__pyx_v_seqs)); __pyx_v_dest->n_targets = __pyx_t_2; - /* "csamtools.pyx":1197 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1140 * * dest.n_targets = len(seqs) * dest.target_name = calloc( dest.n_targets, sizeof(char*) ) # <<<<<<<<<<<<<< @@ -12648,7 +12615,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_ */ __pyx_v_dest->target_name = ((char **)calloc(__pyx_v_dest->n_targets, (sizeof(char *)))); - /* "csamtools.pyx":1198 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1141 * dest.n_targets = len(seqs) * dest.target_name = calloc( dest.n_targets, sizeof(char*) ) * dest.target_len = calloc( dest.n_targets, sizeof(uint32_t) ) # <<<<<<<<<<<<<< @@ -12657,7 +12624,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_ */ __pyx_v_dest->target_len = ((uint32_t *)calloc(__pyx_v_dest->n_targets, (sizeof(uint32_t)))); - /* "csamtools.pyx":1200 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1143 * dest.target_len = calloc( dest.n_targets, sizeof(uint32_t) ) * * for x from 0 <= x < dest.n_targets: # <<<<<<<<<<<<<< @@ -12667,14 +12634,14 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_ __pyx_t_12 = __pyx_v_dest->n_targets; for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_12; __pyx_v_x++) { - /* "csamtools.pyx":1201 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1144 * * for x from 0 <= x < dest.n_targets: * seqname, seqlen = seqs[x] # <<<<<<<<<<<<<< * dest.target_name[x] = calloc( len( seqname ) + 1, sizeof(char) ) * strncpy( dest.target_name[x], seqname, len(seqname) + 1 ) */ - __pyx_t_9 = __Pyx_GetItemInt_List(((PyObject *)__pyx_v_seqs), __pyx_v_x, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_GetItemInt_List(((PyObject *)__pyx_v_seqs), __pyx_v_x, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); if (PyTuple_CheckExact(__pyx_t_9) && likely(PyTuple_GET_SIZE(__pyx_t_9) == 2)) { PyObject* tuple = __pyx_t_9; @@ -12688,14 +12655,14 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_ __pyx_v_seqlen = __pyx_t_3; __pyx_t_3 = 0; } else { - __pyx_t_1 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __pyx_t_5 = __Pyx_UnpackItem(__pyx_t_1, 0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_UnpackItem(__pyx_t_1, 0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_3 = __Pyx_UnpackItem(__pyx_t_1, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_UnpackItem(__pyx_t_1, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (__Pyx_EndUnpack(__pyx_t_1, 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_EndUnpack(__pyx_t_1, 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_v_seqname); __pyx_v_seqname = __pyx_t_5; @@ -12705,42 +12672,42 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_ __pyx_t_3 = 0; } - /* "csamtools.pyx":1202 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1145 * for x from 0 <= x < dest.n_targets: * seqname, seqlen = seqs[x] * dest.target_name[x] = calloc( len( seqname ) + 1, sizeof(char) ) # <<<<<<<<<<<<<< * strncpy( dest.target_name[x], seqname, len(seqname) + 1 ) * dest.target_len[x] = seqlen */ - __pyx_t_2 = PyObject_Length(__pyx_v_seqname); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Length(__pyx_v_seqname); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} (__pyx_v_dest->target_name[__pyx_v_x]) = ((char *)calloc((__pyx_t_2 + 1), (sizeof(char)))); - /* "csamtools.pyx":1203 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1146 * seqname, seqlen = seqs[x] * dest.target_name[x] = calloc( len( seqname ) + 1, sizeof(char) ) * strncpy( dest.target_name[x], seqname, len(seqname) + 1 ) # <<<<<<<<<<<<<< * dest.target_len[x] = seqlen * */ - __pyx_t_10 = PyBytes_AsString(__pyx_v_seqname); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1203; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_2 = PyObject_Length(__pyx_v_seqname); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1203; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyBytes_AsString(__pyx_v_seqname); if (unlikely((!__pyx_t_10) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1146; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Length(__pyx_v_seqname); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1146; __pyx_clineno = __LINE__; goto __pyx_L1_error;} strncpy((__pyx_v_dest->target_name[__pyx_v_x]), __pyx_t_10, (__pyx_t_2 + 1)); - /* "csamtools.pyx":1204 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1147 * dest.target_name[x] = calloc( len( seqname ) + 1, sizeof(char) ) * strncpy( dest.target_name[x], seqname, len(seqname) + 1 ) * dest.target_len[x] = seqlen # <<<<<<<<<<<<<< * * return dest */ - __pyx_t_13 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_seqlen); 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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1241; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1182; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_L5:; @@ -13022,7 +12962,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_21__next__(PyObject *__pyx_v_self) return __pyx_r; } -/* "csamtools.pyx":1293 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1234 * cdef int owns_samfile * * def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ): # <<<<<<<<<<<<<< @@ -13048,7 +12988,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_s static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__beg,&__pyx_n_s__end,&__pyx_n_s__reopen,0}; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__cinit__"); - __Pyx_TraceCall("__cinit__", __pyx_f[0], 1293); + __Pyx_TraceCall("__cinit__", __pyx_f[0], 1234); if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args = PyDict_Size(__pyx_kwds); PyObject* values[5] = {0,0,0,0,0}; @@ -13070,19 +13010,19 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_s values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid); if (likely(values[1])) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__beg); if (likely(values[2])) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end); if (likely(values[3])) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (kw_args > 0) { @@ -13091,14 +13031,14 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_s } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]); 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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 = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;} if (values[4]) { - __pyx_v_reopen = __Pyx_PyInt_AsInt(values[4]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_reopen = __Pyx_PyInt_AsInt(values[4]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else { __pyx_v_reopen = ((int)1); } @@ -13106,11 +13046,11 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_s __pyx_v_reopen = ((int)1); switch (PyTuple_GET_SIZE(__pyx_args)) { case 5: - __pyx_v_reopen = __Pyx_PyInt_AsInt(PyTuple_GET_ITEM(__pyx_args, 4)); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_GIVEREF(__pyx_t_1); __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter); __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter)); @@ -14247,7 +14211,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter(PyObject *__ return __pyx_r; } -/* "csamtools.pyx":1431 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1372 * self.rowiter = IteratorRowRegion(self.samfile, self.tid, 0, 1<<29) * * def __iter__(self): # <<<<<<<<<<<<<< @@ -14255,14 +14219,14 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter(PyObject *__ * */ -static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs___iter__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs___iter__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__iter__"); - __Pyx_TraceCall("__iter__", __pyx_f[0], 1431); + __Pyx_TraceCall("__iter__", __pyx_f[0], 1372); - /* "csamtools.pyx":1432 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1373 * * def __iter__(self): * return self # <<<<<<<<<<<<<< @@ -14282,7 +14246,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__(PyObject *__ return __pyx_r; } -/* "csamtools.pyx":1434 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1375 * return self * * def __next__(self): # <<<<<<<<<<<<<< @@ -14290,10 +14254,10 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__(PyObject *__ * */ -static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__pyx_v_self); 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if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1382; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1382; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_3 = (!__pyx_t_1); if (__pyx_t_3) { - /* "csamtools.pyx":1442 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1383 * if self.tid==-1: * if not self.samfile.nreferences: * raise StopIteration # <<<<<<<<<<<<<< @@ -14336,12 +14300,12 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__ * self.nextiter() */ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1442; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1383; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L6; } __pyx_L6:; - /* "csamtools.pyx":1443 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1384 * if not self.samfile.nreferences: * raise StopIteration * self.tid = 0 # <<<<<<<<<<<<<< @@ -14350,16 +14314,16 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__ */ ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid = 0; - /* "csamtools.pyx":1444 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1385 * raise StopIteration * self.tid = 0 * self.nextiter() # <<<<<<<<<<<<<< * * while 1: */ - __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__nextiter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1444; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__nextiter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1444; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -14367,7 +14331,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__ } __pyx_L5:; - /* "csamtools.pyx":1446 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1387 * self.nextiter() * * while 1: # <<<<<<<<<<<<<< @@ -14377,7 +14341,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__ while (1) { if (!1) break; - /* "csamtools.pyx":1447 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1388 * * while 1: * self.rowiter.cnext() # <<<<<<<<<<<<<< @@ -14386,7 +14350,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__ */ ((struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter); 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if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1456; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_RichCompare(__pyx_t_4, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1456; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_3) { - /* "csamtools.pyx":1457 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1398 * # Otherwise, proceed to next reference or stop * if self.tid 0) { @@ -14539,12 +14503,12 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_ } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; 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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1490; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #endif - /* "csamtools.pyx":1491 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1432 * store.release() * assert self.fp != NULL * self.owns_samfile = True # <<<<<<<<<<<<<< @@ -14738,7 +14714,7 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_ } /*else*/ { - /* "csamtools.pyx":1493 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1434 * self.owns_samfile = True * else: * self.fp = samfile.samfile # <<<<<<<<<<<<<< @@ -14747,7 +14723,7 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_ */ ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp = __pyx_v_samfile->samfile; - /* "csamtools.pyx":1494 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1435 * else: * self.fp = samfile.samfile * self.owns_samfile = False # <<<<<<<<<<<<<< @@ -14758,7 +14734,7 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_ } __pyx_L8:; 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- PyObject *__pyx_t_1 = NULL; - Py_ssize_t __pyx_t_2; - int __pyx_t_3; + Py_ssize_t __pyx_t_1; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; uint64_t __pyx_t_4; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("cnext"); - __Pyx_TraceCall("cnext", __pyx_f[0], 1508); + __Pyx_TraceCall("cnext", __pyx_f[0], 1449); - /* "csamtools.pyx":1512 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1453 * * # end iteration if out of positions * if self.current_pos >= len(self.positions): return -1 # <<<<<<<<<<<<<< * * bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 ) */ - __pyx_t_1 = __pyx_v_self->positions; - __Pyx_INCREF(__pyx_t_1); - __pyx_t_2 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1512; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_3 = (__pyx_v_self->current_pos >= __pyx_t_2); - if (__pyx_t_3) { + __pyx_t_1 = PyObject_Length(__pyx_v_self->positions); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1453; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = (__pyx_v_self->current_pos >= __pyx_t_1); + if (__pyx_t_2) { __pyx_r = -1; goto __pyx_L0; goto __pyx_L3; } __pyx_L3:; - /* "csamtools.pyx":1514 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1455 * if self.current_pos >= len(self.positions): return -1 * * bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 ) # <<<<<<<<<<<<<< * self.current_pos += 1 * return samread(self.fp, self.b) */ - __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_self->positions, __pyx_v_self->current_pos, sizeof(int), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1514; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __pyx_t_4 = __Pyx_PyInt_from_py_uint64_t(__pyx_t_1); if (unlikely((__pyx_t_4 == (uint64_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1514; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_self->positions, __pyx_v_self->current_pos, sizeof(int), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_4 = __Pyx_PyInt_from_py_uint64_t(__pyx_t_3); if (unlikely((__pyx_t_4 == (uint64_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; bam_seek(__pyx_v_self->fp->x.bam, __pyx_t_4, 0); - /* "csamtools.pyx":1515 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1456 * * bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 ) * self.current_pos += 1 # <<<<<<<<<<<<<< * return samread(self.fp, self.b) * */ - __pyx_v_self->current_pos = (__pyx_v_self->current_pos + 1); + __pyx_v_self->current_pos += 1; - /* "csamtools.pyx":1516 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1457 * bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 ) * self.current_pos += 1 * return samread(self.fp, self.b) # <<<<<<<<<<<<<< @@ -14942,7 +14915,7 @@ static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9cs __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; - __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_3); __Pyx_WriteUnraisable("csamtools.IteratorRowSelection.cnext"); __pyx_r = 0; __pyx_L0:; @@ -14951,7 +14924,7 @@ static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9cs return __pyx_r; } -/* "csamtools.pyx":1518 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1459 * return samread(self.fp, self.b) * * def __next__(self): # <<<<<<<<<<<<<< @@ -14959,19 +14932,19 @@ static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9cs * */ -static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_9csamtools_20IteratorRowSelection_2__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n "; -struct wrapperbase __pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__; -static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection___next__(PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_9csamtools_20IteratorRowSelection___next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n "; +struct wrapperbase __pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__; +static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection___next__(PyObject *__pyx_v_self) { int __pyx_v_ret; PyObject *__pyx_r = NULL; int __pyx_t_1; PyObject *__pyx_t_2 = NULL; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__next__"); - __Pyx_TraceCall("__next__", __pyx_f[0], 1518); + __Pyx_TraceCall("__next__", __pyx_f[0], 1459); - /* "csamtools.pyx":1524 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1465 * """ * * cdef int ret = self.cnext() # <<<<<<<<<<<<<< @@ -14980,7 +14953,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject * */ __pyx_v_ret = ((struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *)((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)); - /* "csamtools.pyx":1525 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1466 * * cdef int ret = self.cnext() * if (ret > 0): # <<<<<<<<<<<<<< @@ -14990,7 +14963,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject * __pyx_t_1 = (__pyx_v_ret > 0); if (__pyx_t_1) { - /* "csamtools.pyx":1526 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1467 * cdef int ret = self.cnext() * if (ret > 0): * return makeAlignedRead( self.b ) # <<<<<<<<<<<<<< @@ -14998,7 +14971,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject * * raise StopIteration */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1526; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; 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/*proto*/ -static void __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(PyObject *__pyx_v_self) { +static void __pyx_pf_9csamtools_20IteratorRowSelection___dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pf_9csamtools_20IteratorRowSelection___dealloc__(PyObject *__pyx_v_self) { __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__dealloc__"); - __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1530); + __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1471); - /* "csamtools.pyx":1531 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1472 * * def __dealloc__(self): * bam_destroy1(self.b) # <<<<<<<<<<<<<< @@ -15055,7 +15028,7 @@ static void __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(PyObject *__ */ bam_destroy1(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b); - /* "csamtools.pyx":1532 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1473 * def __dealloc__(self): * bam_destroy1(self.b) * if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<< @@ -15072,7 +15045,7 @@ static void __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(PyObject *__ __Pyx_RefNannyFinishContext(); 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} -/* "csamtools.pyx":1552 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1493 * return bam_iter_read( d.samfile.x.bam, d.iter, b ) * * cdef int __advance_snpcalls( void * data, bam1_t * b ): # <<<<<<<<<<<<<< @@ -15139,9 +15112,9 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__ long __pyx_t_7; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__advance_snpcalls"); - __Pyx_TraceCall("__advance_snpcalls", __pyx_f[0], 1552); + __Pyx_TraceCall("__advance_snpcalls", __pyx_f[0], 1493); - /* "csamtools.pyx":1557 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1498 * ''' * cdef __iterdata * d * d = <__iterdata*>data # <<<<<<<<<<<<<< @@ -15150,7 +15123,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__ */ __pyx_v_d = ((__pyx_t_9csamtools___iterdata *)__pyx_v_data); - /* "csamtools.pyx":1559 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1500 * d = <__iterdata*>data * * cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<< @@ -15159,7 +15132,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__ */ __pyx_v_ret = bam_iter_read(__pyx_v_d->samfile->x.bam, __pyx_v_d->iter, __pyx_v_b); - /* "csamtools.pyx":1560 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1501 * * cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b ) * cdef int skip = 0 # <<<<<<<<<<<<<< @@ -15168,7 +15141,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__ */ __pyx_v_skip = 0; - /* "csamtools.pyx":1562 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1503 * cdef int skip = 0 * cdef int q * cdef int is_cns = 1 # <<<<<<<<<<<<<< @@ -15177,7 +15150,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__ */ __pyx_v_is_cns = 1; - /* "csamtools.pyx":1563 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1504 * cdef int q * cdef int is_cns = 1 * cdef int is_nobaq = 0 # <<<<<<<<<<<<<< @@ -15186,7 +15159,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__ */ __pyx_v_is_nobaq = 0; - /* "csamtools.pyx":1564 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1505 * cdef int is_cns = 1 * cdef int is_nobaq = 0 * cdef int capQ_thres = 0 # <<<<<<<<<<<<<< @@ -15195,7 +15168,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__ */ __pyx_v_capQ_thres = 0; - /* "csamtools.pyx":1567 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1508 * * # reload sequence * if d.fastafile != NULL and b.core.tid != d.tid: # <<<<<<<<<<<<<< @@ -15211,7 +15184,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__ } if (__pyx_t_3) { - /* "csamtools.pyx":1568 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1509 * # reload sequence * if d.fastafile != NULL and b.core.tid != d.tid: * if d.seq != NULL: free(d.seq) # <<<<<<<<<<<<<< @@ -15225,7 +15198,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__ } __pyx_L4:; - /* "csamtools.pyx":1569 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1510 * if d.fastafile != NULL and b.core.tid != d.tid: * if d.seq != NULL: free(d.seq) * d.tid = b.core.tid # <<<<<<<<<<<<<< @@ -15234,7 +15207,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__ */ __pyx_v_d->tid = __pyx_v_b->core.tid; - /* "csamtools.pyx":1570 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1511 * if d.seq != NULL: free(d.seq) * d.tid = b.core.tid * d.seq = faidx_fetch_seq(d.fastafile, # <<<<<<<<<<<<<< @@ -15243,7 +15216,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__ */ __pyx_v_d->seq = faidx_fetch_seq(__pyx_v_d->fastafile, (__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid]), 0, __pyx_v_9csamtools_max_pos, (&__pyx_v_d->seq_len)); 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- /* "csamtools.pyx":1577 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1518 * raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \ * (d.samfile.header.target_name[d.tid], * d.tid)) # <<<<<<<<<<<<<< * * */ - __pyx_t_5 = PyInt_FromLong(__pyx_v_d->tid); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1577; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyInt_FromLong(__pyx_v_d->tid); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1518; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1576; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_6)); + __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1517; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_4)); __Pyx_GIVEREF(((PyObject *)__pyx_t_4)); PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_4 = 0; __pyx_t_5 = 0; - __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_113), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1575; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_56), __pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1516; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_5)); - __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; - __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1575; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_6)); + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1516; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_6); PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_5)); __Pyx_GIVEREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0; - __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1575; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_6, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1516; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_Raise(__pyx_t_5, 0, 0); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1575; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1516; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L5; } __pyx_L5:; @@ -15301,7 +15274,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__ } __pyx_L3:; 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/*proto*/ +static char __pyx_doc_9csamtools_14IteratorColumn_addReference[] = "IteratorColumn.addReference(self, Fastafile fastafile)\n\n add reference sequences in *fastafile* to iterator."; +static PyObject *__pyx_pf_9csamtools_14IteratorColumn_addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile) { PyObject *__pyx_r = NULL; int __pyx_t_1; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("addReference"); - __Pyx_TraceCall("addReference", __pyx_f[0], 1696); - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fastafile), __pyx_ptype_9csamtools_Fastafile, 1, "fastafile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1696; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_TraceCall("addReference", __pyx_f[0], 1634); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fastafile), __pyx_ptype_9csamtools_Fastafile, 1, "fastafile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1634; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "csamtools.pyx":1699 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1637 * ''' * add reference sequences in *fastafile* to iterator.''' * self.fastafile = fastafile # <<<<<<<<<<<<<< @@ -15852,7 +15809,7 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_2addReference(PyObject *__ __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile)); 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if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1774; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = PyObject_RichCompare(__pyx_t_2, __pyx_t_3, Py_LT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1774; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_4 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1774; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1774; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (__pyx_t_1) { - /* "csamtools.pyx":1840 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1775 * self.tid += 1 * if self.tid < self.samfile.nreferences: * self.setupIteratorData( self.tid, 0, max_pos, 0 ) # <<<<<<<<<<<<<< @@ -16962,14 +16912,14 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject */ __pyx_t_5.__pyx_n = 1; __pyx_t_5.reopen = 0; - __pyx_t_4 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid, 0, __pyx_v_9csamtools_max_pos, &__pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1840; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid, 0, __pyx_v_9csamtools_max_pos, &__pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1775; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; goto __pyx_L9; } /*else*/ { - /* "csamtools.pyx":1842 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1777 * self.setupIteratorData( self.tid, 0, max_pos, 0 ) * else: * raise StopIteration # <<<<<<<<<<<<<< @@ -16977,7 +16927,7 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject * ##------------------------------------------------------------------- */ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_L9:; } @@ -16997,7 +16947,7 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject return __pyx_r; } -/* "csamtools.pyx":1847 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1782 * ##------------------------------------------------------------------- * ##------------------------------------------------------------------- * cdef inline int32_t query_start(bam1_t *src) except -1: # <<<<<<<<<<<<<< @@ -17017,9 +16967,9 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) int __pyx_t_4; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("query_start"); - __Pyx_TraceCall("query_start", __pyx_f[0], 1847); + __Pyx_TraceCall("query_start", __pyx_f[0], 1782); - /* "csamtools.pyx":1850 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1785 * cdef uint32_t * cigar_p, op * cdef uint32_t k * cdef uint32_t start_offset = 0 # <<<<<<<<<<<<<< @@ -17028,7 +16978,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) */ __pyx_v_start_offset = 0; - /* "csamtools.pyx":1852 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1787 * cdef uint32_t start_offset = 0 * * if src.core.n_cigar: # <<<<<<<<<<<<<< @@ -17037,7 +16987,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) */ if (__pyx_v_src->core.n_cigar) { - /* "csamtools.pyx":1853 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1788 * * if src.core.n_cigar: * cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<< @@ -17046,7 +16996,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) */ __pyx_v_cigar_p = bam1_cigar(__pyx_v_src); - /* "csamtools.pyx":1854 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1789 * if src.core.n_cigar: * cigar_p = bam1_cigar(src); * for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<< @@ -17056,7 +17006,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) __pyx_t_1 = __pyx_v_src->core.n_cigar; for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_1; __pyx_v_k++) { - /* "csamtools.pyx":1855 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1790 * cigar_p = bam1_cigar(src); * for k from 0 <= k < src.core.n_cigar: * op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<< @@ -17065,25 +17015,17 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) */ __pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15); - /* "csamtools.pyx":1860 - * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') - * return -1 - * elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<< - * start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT - * else: - */ - switch (__pyx_v_op) { - - /* "csamtools.pyx":1856 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1791 * for k from 0 <= k < src.core.n_cigar: * op = cigar_p[k] & BAM_CIGAR_MASK * if op==BAM_CHARD_CLIP: # <<<<<<<<<<<<<< * if start_offset!=0 and start_offset!=src.core.l_qseq: * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') */ + switch (__pyx_v_op) { case 5: - /* "csamtools.pyx":1857 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1792 * op = cigar_p[k] & BAM_CIGAR_MASK * if op==BAM_CHARD_CLIP: * if start_offset!=0 and start_offset!=src.core.l_qseq: # <<<<<<<<<<<<<< @@ -17099,16 +17041,16 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) } if (__pyx_t_4) { - /* "csamtools.pyx":1858 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1793 * 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_119); + PyErr_SetString(__pyx_builtin_ValueError, __pyx_k_60); - /* "csamtools.pyx":1859 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1794 * if start_offset!=0 and start_offset!=src.core.l_qseq: * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') * return -1 # <<<<<<<<<<<<<< @@ -17122,7 +17064,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) __pyx_L6:; break; - /* "csamtools.pyx":1860 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1795 * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') * return -1 * elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<< @@ -17131,18 +17073,18 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) */ case 4: - /* "csamtools.pyx":1861 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1796 * return -1 * elif op==BAM_CSOFT_CLIP: * start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<< * else: * break */ - __pyx_v_start_offset = (__pyx_v_start_offset + ((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); + __pyx_v_start_offset += ((__pyx_v_cigar_p[__pyx_v_k]) >> 4); break; default: - /* "csamtools.pyx":1863 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1798 * start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT * else: * break # <<<<<<<<<<<<<< @@ -17158,7 +17100,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) } __pyx_L3:; - /* "csamtools.pyx":1865 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1800 * break * * return start_offset # <<<<<<<<<<<<<< @@ -17175,7 +17117,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) return __pyx_r; } -/* "csamtools.pyx":1870 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1805 * ##------------------------------------------------------------------- * ##------------------------------------------------------------------- * cdef inline int32_t query_end(bam1_t *src) except -1: # <<<<<<<<<<<<<< @@ -17194,9 +17136,9 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) { int __pyx_t_3; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("query_end"); - __Pyx_TraceCall("query_end", __pyx_f[0], 1870); + __Pyx_TraceCall("query_end", __pyx_f[0], 1805); - /* "csamtools.pyx":1873 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1808 * cdef uint32_t * cigar_p, op * cdef uint32_t k * cdef uint32_t end_offset = src.core.l_qseq # <<<<<<<<<<<<<< @@ -17205,7 +17147,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) { */ __pyx_v_end_offset = __pyx_v_src->core.l_qseq; - /* "csamtools.pyx":1875 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1810 * cdef uint32_t end_offset = src.core.l_qseq * * if src.core.n_cigar>1: # <<<<<<<<<<<<<< @@ -17215,7 +17157,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) { __pyx_t_1 = (__pyx_v_src->core.n_cigar > 1); if (__pyx_t_1) { - /* "csamtools.pyx":1876 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1811 * * if src.core.n_cigar>1: * cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<< @@ -17224,7 +17166,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) { */ __pyx_v_cigar_p = bam1_cigar(__pyx_v_src); - /* "csamtools.pyx":1877 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1812 * if src.core.n_cigar>1: * cigar_p = bam1_cigar(src); * for k from src.core.n_cigar > k >= 1: # <<<<<<<<<<<<<< @@ -17233,7 +17175,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) { */ for (__pyx_v_k = __pyx_v_src->core.n_cigar-1; __pyx_v_k >= 1; __pyx_v_k--) { - /* "csamtools.pyx":1878 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1813 * cigar_p = bam1_cigar(src); * for k from src.core.n_cigar > k >= 1: * op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<< @@ -17242,25 +17184,17 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) { */ __pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15); - /* "csamtools.pyx":1883 - * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') - * return -1 - * elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<< - * end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT - * else: - */ - switch (__pyx_v_op) { - - /* "csamtools.pyx":1879 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1814 * for k from src.core.n_cigar > k >= 1: * op = cigar_p[k] & BAM_CIGAR_MASK * if op==BAM_CHARD_CLIP: # <<<<<<<<<<<<<< * if end_offset!=0 and end_offset!=src.core.l_qseq: * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') */ + switch (__pyx_v_op) { case 5: - /* "csamtools.pyx":1880 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1815 * op = cigar_p[k] & BAM_CIGAR_MASK * if op==BAM_CHARD_CLIP: * if end_offset!=0 and end_offset!=src.core.l_qseq: # <<<<<<<<<<<<<< @@ -17276,16 +17210,16 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) { } if (__pyx_t_3) { - /* "csamtools.pyx":1881 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1816 * 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_119); + PyErr_SetString(__pyx_builtin_ValueError, __pyx_k_60); - /* "csamtools.pyx":1882 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1817 * if end_offset!=0 and end_offset!=src.core.l_qseq: * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') * return -1 # <<<<<<<<<<<<<< @@ -17299,7 +17233,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) { __pyx_L6:; break; - /* "csamtools.pyx":1883 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1818 * PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') * return -1 * elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<< @@ -17308,18 +17242,18 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) { */ case 4: - /* "csamtools.pyx":1884 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1819 * return -1 * elif op==BAM_CSOFT_CLIP: * end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<< * else: * break */ - __pyx_v_end_offset = (__pyx_v_end_offset - ((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); + __pyx_v_end_offset -= ((__pyx_v_cigar_p[__pyx_v_k]) >> 4); break; default: - /* "csamtools.pyx":1886 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1821 * end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT * else: * break # <<<<<<<<<<<<<< @@ -17335,7 +17269,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) { } __pyx_L3:; - /* "csamtools.pyx":1888 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1823 * break * * if end_offset==0: # <<<<<<<<<<<<<< @@ -17345,7 +17279,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) { __pyx_t_3 = (__pyx_v_end_offset == 0); if (__pyx_t_3) { - /* "csamtools.pyx":1889 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1824 * * if end_offset==0: * end_offset = src.core.l_qseq # <<<<<<<<<<<<<< @@ -17357,7 +17291,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) { } __pyx_L7:; - /* "csamtools.pyx":1891 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1826 * end_offset = src.core.l_qseq * * return end_offset # <<<<<<<<<<<<<< @@ -17374,7 +17308,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) { return __pyx_r; } -/* "csamtools.pyx":1894 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1829 * * * cdef inline object get_seq_range(bam1_t *src, uint32_t start, uint32_t end): # <<<<<<<<<<<<<< @@ -17393,10 +17327,10 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_ uint32_t __pyx_t_3; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("get_seq_range"); - __Pyx_TraceCall("get_seq_range", __pyx_f[0], 1894); + __Pyx_TraceCall("get_seq_range", __pyx_f[0], 1829); __pyx_v_seq = Py_None; __Pyx_INCREF(Py_None); - /* "csamtools.pyx":1899 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1834 * cdef char * s * * if not src.core.l_qseq: # <<<<<<<<<<<<<< @@ -17406,7 +17340,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_ __pyx_t_1 = (!__pyx_v_src->core.l_qseq); if (__pyx_t_1) { - /* "csamtools.pyx":1900 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1835 * * if not src.core.l_qseq: * return None # <<<<<<<<<<<<<< @@ -17421,20 +17355,20 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_ } __pyx_L3:; - /* "csamtools.pyx":1902 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1837 * return None * * seq = PyString_FromStringAndSize(NULL, end-start) # <<<<<<<<<<<<<< * s = PyString_AS_STRING(seq) * p = bam1_seq(src) */ - __pyx_t_2 = PyString_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1902; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyString_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_v_seq); __pyx_v_seq = __pyx_t_2; __pyx_t_2 = 0; - /* "csamtools.pyx":1903 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1838 * * seq = PyString_FromStringAndSize(NULL, end-start) * s = PyString_AS_STRING(seq) # <<<<<<<<<<<<<< @@ -17443,7 +17377,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_ */ __pyx_v_s = PyString_AS_STRING(__pyx_v_seq); - /* "csamtools.pyx":1904 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1839 * seq = PyString_FromStringAndSize(NULL, end-start) * s = PyString_AS_STRING(seq) * p = bam1_seq(src) # <<<<<<<<<<<<<< @@ -17452,7 +17386,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_ */ __pyx_v_p = bam1_seq(__pyx_v_src); - /* "csamtools.pyx":1906 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1841 * p = bam1_seq(src) * * for k from start <= k < end: # <<<<<<<<<<<<<< @@ -17462,7 +17396,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_ __pyx_t_3 = __pyx_v_end; for (__pyx_v_k = __pyx_v_start; __pyx_v_k < __pyx_t_3; __pyx_v_k++) { - /* "csamtools.pyx":1909 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1844 * # 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] # <<<<<<<<<<<<<< @@ -17472,7 +17406,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_ (__pyx_v_s[(__pyx_v_k - __pyx_v_start)]) = (__pyx_v_9csamtools_bam_nt16_rev_table[(((__pyx_v_p[__Pyx_div_long(__pyx_v_k, 2)]) >> (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2)))) & 0xf)]); } - /* "csamtools.pyx":1911 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1846 * s[k-start] = bam_nt16_rev_table[p[k/2] >> 4 * (1 - k%2) & 0xf] * * return seq # <<<<<<<<<<<<<< @@ -17498,7 +17432,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_ return __pyx_r; } -/* "csamtools.pyx":1914 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1849 * * * cdef inline object get_qual_range(bam1_t *src, uint32_t start, uint32_t end): # <<<<<<<<<<<<<< @@ -17517,10 +17451,10 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v uint32_t __pyx_t_3; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("get_qual_range"); - __Pyx_TraceCall("get_qual_range", __pyx_f[0], 1914); + __Pyx_TraceCall("get_qual_range", __pyx_f[0], 1849); __pyx_v_qual = Py_None; __Pyx_INCREF(Py_None); - /* "csamtools.pyx":1919 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1854 * cdef char * q * * p = bam1_qual(src) # <<<<<<<<<<<<<< @@ -17529,7 +17463,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v */ __pyx_v_p = bam1_qual(__pyx_v_src); - /* "csamtools.pyx":1920 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1855 * * p = bam1_qual(src) * if p[0] == 0xff: # <<<<<<<<<<<<<< @@ -17539,7 +17473,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v __pyx_t_1 = ((__pyx_v_p[0]) == 0xff); if (__pyx_t_1) { - /* "csamtools.pyx":1921 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1856 * p = bam1_qual(src) * if p[0] == 0xff: * return None # <<<<<<<<<<<<<< @@ -17554,20 +17488,20 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v } __pyx_L3:; - /* "csamtools.pyx":1923 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1858 * return None * * qual = PyString_FromStringAndSize(NULL, end-start) # <<<<<<<<<<<<<< * q = PyString_AS_STRING(qual) * */ - __pyx_t_2 = PyString_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1923; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyString_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start)); 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} - /* "csamtools.pyx":1930 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1865 * q[k-start] = p[k] + 33 * * return qual # <<<<<<<<<<<<<< @@ -17622,7 +17556,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v return __pyx_r; } -/* "csamtools.pyx":1955 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1890 * * # Now only called when instances are created from Python * def __init__(self): # <<<<<<<<<<<<<< @@ -17635,12 +17569,12 @@ static int __pyx_pf_9csamtools_11AlignedRead___init__(PyObject *__pyx_v_self, Py int __pyx_r; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__init__"); - __Pyx_TraceCall("__init__", __pyx_f[0], 1955); + __Pyx_TraceCall("__init__", __pyx_f[0], 1890); if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) { __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;} if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1; 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- /* "csamtools.pyx":1963 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1898 * self._delegate.m_data = 40 * self._delegate.data = calloc( self._delegate.m_data, 1 ) * self._delegate.data_len = 0 # <<<<<<<<<<<<<< @@ -17682,7 +17616,7 @@ static int __pyx_pf_9csamtools_11AlignedRead___init__(PyObject *__pyx_v_self, Py return __pyx_r; } -/* "csamtools.pyx":1965 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1900 * self._delegate.data_len = 0 * * def __dealloc__(self): # <<<<<<<<<<<<<< @@ -17690,13 +17624,13 @@ static int __pyx_pf_9csamtools_11AlignedRead___init__(PyObject *__pyx_v_self, Py * */ -static void __pyx_pf_9csamtools_11AlignedRead_1__dealloc__(PyObject *__pyx_v_self); /*proto*/ -static void __pyx_pf_9csamtools_11AlignedRead_1__dealloc__(PyObject *__pyx_v_self) { +static void __pyx_pf_9csamtools_11AlignedRead___dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pf_9csamtools_11AlignedRead___dealloc__(PyObject *__pyx_v_self) { __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__dealloc__"); 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/*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_5qname___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) { bam1_t *__pyx_v_src; int __pyx_v_l; char *__pyx_v_p; @@ -18244,21 +18178,21 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_s char *__pyx_t_6; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__set__"); - __Pyx_TraceCall("__set__", __pyx_f[0], 2034); + __Pyx_TraceCall("__set__", __pyx_f[0], 1969); - /* "csamtools.pyx":2035 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1970 * * def __set__(self, qname ): * if qname == None or len(qname) == 0: return # <<<<<<<<<<<<<< * cdef bam1_t * src * cdef int l */ - __pyx_t_1 = PyObject_RichCompare(__pyx_v_qname, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2035; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_v_qname, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1970; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2035; __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 = 1970; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (!__pyx_t_2) { - __pyx_t_3 = PyObject_Length(__pyx_v_qname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2035; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_Length(__pyx_v_qname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1970; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = (__pyx_t_3 == 0); __pyx_t_5 = __pyx_t_4; } else { @@ -18271,7 +18205,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_s } __pyx_L5:; - /* "csamtools.pyx":2040 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1975 * cdef char * p * * src = self._delegate # <<<<<<<<<<<<<< @@ -18280,7 +18214,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_s */ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; - /* "csamtools.pyx":2041 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1976 * * src = self._delegate * p = bam1_qname( src ) # <<<<<<<<<<<<<< @@ -18289,17 +18223,17 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_s */ __pyx_v_p = bam1_qname(__pyx_v_src); - /* "csamtools.pyx":2044 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1979 * * # the qname is \0 terminated * l = len(qname) + 1 # <<<<<<<<<<<<<< * pysam_bam_update( src, * src.core.l_qname, */ - __pyx_t_3 = PyObject_Length(__pyx_v_qname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2044; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_Length(__pyx_v_qname); 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- /* "csamtools.pyx":2056 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1991 * p = bam1_qname(src) * * strncpy( p, qname, l ) # <<<<<<<<<<<<<< * * property cigar: */ - __pyx_t_6 = PyBytes_AsString(__pyx_v_qname); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2056; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyBytes_AsString(__pyx_v_qname); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1991; __pyx_clineno = __LINE__; goto __pyx_L1_error;} strncpy(__pyx_v_p, __pyx_t_6, __pyx_v_l); __pyx_r = 0; @@ -18348,7 +18282,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_s return __pyx_r; } -/* "csamtools.pyx":2061 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1996 * """the :term:`cigar` alignment (None if not present). * """ * def __get__(self): # <<<<<<<<<<<<<< @@ -18371,12 +18305,12 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__py PyObject *__pyx_t_4 = NULL; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__get__"); - __Pyx_TraceCall("__get__", __pyx_f[0], 2061); + __Pyx_TraceCall("__get__", __pyx_f[0], 1996); __pyx_v_op = Py_None; __Pyx_INCREF(Py_None); __pyx_v_l = Py_None; __Pyx_INCREF(Py_None); __pyx_v_cigar = Py_None; __Pyx_INCREF(Py_None); - /* "csamtools.pyx":2067 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2002 * cdef int k * * src = self._delegate # <<<<<<<<<<<<<< @@ -18385,7 +18319,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__py */ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; - /* "csamtools.pyx":2068 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2003 * * src = self._delegate * if src.core.n_cigar == 0: return None # <<<<<<<<<<<<<< @@ -18402,20 +18336,20 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__py } __pyx_L5:; - /* "csamtools.pyx":2070 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2005 * if src.core.n_cigar == 0: return None * * cigar = [] # <<<<<<<<<<<<<< * cigar_p = bam1_cigar(src); 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if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2074; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2009; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_v_l); __pyx_v_l = __pyx_t_2; __pyx_t_2 = 0; - /* "csamtools.pyx":2075 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2010 * op = cigar_p[k] & BAM_CIGAR_MASK * l = cigar_p[k] >> BAM_CIGAR_SHIFT * cigar.append((op, l)) # <<<<<<<<<<<<<< * return cigar * */ - __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2075; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2010; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_v_op); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_op); __Pyx_GIVEREF(__pyx_v_op); __Pyx_INCREF(__pyx_v_l); PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_l); __Pyx_GIVEREF(__pyx_v_l); - __pyx_t_4 = __Pyx_PyObject_Append(__pyx_v_cigar, ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2075; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Append(__pyx_v_cigar, __pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2010; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; } - /* "csamtools.pyx":2076 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2011 * l = cigar_p[k] >> BAM_CIGAR_SHIFT * cigar.append((op, l)) * return cigar # <<<<<<<<<<<<<< @@ -18510,7 +18444,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__py return __pyx_r; } -/* "csamtools.pyx":2078 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2013 * return cigar * * def __set__(self, values ): # <<<<<<<<<<<<<< @@ -18518,8 +18452,8 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__py * cdef uint32_t * p */ -static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values); /*proto*/ -static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values) { +static int __pyx_pf_9csamtools_11AlignedRead_5cigar___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values); /*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_5cigar___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values) { uint32_t *__pyx_v_p; bam1_t *__pyx_v_src; PyObject *__pyx_v_op; @@ -18538,23 +18472,23 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s uint32_t __pyx_t_10; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__set__"); 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if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2014; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (!__pyx_t_2) { - __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2079; __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 = 2014; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = (__pyx_t_3 == 0); __pyx_t_5 = __pyx_t_4; } else { @@ -18567,7 +18501,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s } __pyx_L5:; - /* "csamtools.pyx":2085 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2020 * cdef int k * * k = 0 # <<<<<<<<<<<<<< @@ -18576,7 +18510,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s */ __pyx_v_k = 0; - /* "csamtools.pyx":2087 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2022 * k = 0 * * src = self._delegate # <<<<<<<<<<<<<< @@ -18585,7 +18519,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s */ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; 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- /* "csamtools.pyx":2099 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2034 * * # length is number of cigar operations, not bytes * src.core.n_cigar = len(values) # <<<<<<<<<<<<<< * * # re-acquire pointer to location in memory */ - __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2099; __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 = 2034; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_src->core.n_cigar = __pyx_t_3; - /* "csamtools.pyx":2103 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2038 * # re-acquire pointer to location in memory * # as it might have moved * p = bam1_cigar(src) # <<<<<<<<<<<<<< @@ -18631,7 +18565,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s */ __pyx_v_p = bam1_cigar(__pyx_v_src); - /* "csamtools.pyx":2106 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2041 * * # insert cigar operations * for op, l in values: # <<<<<<<<<<<<<< @@ -18641,7 +18575,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s if (PyList_CheckExact(__pyx_v_values) || PyTuple_CheckExact(__pyx_v_values)) { __pyx_t_3 = 0; 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if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2041; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); - if (__Pyx_EndUnpack(__pyx_t_9, 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2106; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_EndUnpack(__pyx_t_9, 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2041; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_v_op); __pyx_v_op = __pyx_t_7; @@ -18688,34 +18622,34 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s __pyx_t_8 = 0; } - /* "csamtools.pyx":2107 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2042 * # insert cigar operations * for op, l in values: * p[k] = l << BAM_CIGAR_SHIFT | op # <<<<<<<<<<<<<< * k += 1 * */ - __pyx_t_6 = PyNumber_Lshift(__pyx_v_l, __pyx_int_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2107; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyNumber_Lshift(__pyx_v_l, __pyx_int_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2042; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_8 = PyNumber_Or(__pyx_t_6, __pyx_v_op); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2107; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = PyNumber_Or(__pyx_t_6, __pyx_v_op); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2042; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_10 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_8); if (unlikely((__pyx_t_10 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2107; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_8); if (unlikely((__pyx_t_10 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2042; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; (__pyx_v_p[__pyx_v_k]) = __pyx_t_10; - /* "csamtools.pyx":2108 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2043 * for op, l in values: * p[k] = l << BAM_CIGAR_SHIFT | op * k += 1 # <<<<<<<<<<<<<< * * ## setting the cigar string also updates the "bin" attribute */ - __pyx_v_k = (__pyx_v_k + 1); + __pyx_v_k += 1; } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "csamtools.pyx":2111 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2046 * * ## setting the cigar string also updates the "bin" attribute * src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, p)) # <<<<<<<<<<<<<< @@ -18742,7 +18676,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s return __pyx_r; } -/* "csamtools.pyx":2115 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2050 * property seq: * """read sequence bases, including :term:`soft clipped` bases (None if not present)""" * def __get__(self): # <<<<<<<<<<<<<< @@ -18758,9 +18692,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_ PyObject *__pyx_t_2 = NULL; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__get__"); - __Pyx_TraceCall("__get__", __pyx_f[0], 2115); + __Pyx_TraceCall("__get__", __pyx_f[0], 2050); - /* "csamtools.pyx":2118 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2053 * cdef bam1_t * src * cdef char * s * src = self._delegate # <<<<<<<<<<<<<< @@ -18769,7 +18703,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_ */ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; - /* "csamtools.pyx":2120 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2055 * src = self._delegate * * if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<< @@ -18786,7 +18720,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_ } __pyx_L5:; - /* "csamtools.pyx":2122 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2057 * if src.core.l_qseq == 0: return None * * return get_seq_range(src, 0, src.core.l_qseq) # <<<<<<<<<<<<<< @@ -18794,7 +18728,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_ * def __set__(self,seq): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __pyx_f_9csamtools_get_seq_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2122; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __pyx_f_9csamtools_get_seq_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2057; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_r = __pyx_t_2; __pyx_t_2 = 0; @@ -18813,7 +18747,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_ return __pyx_r; } -/* "csamtools.pyx":2124 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2059 * return get_seq_range(src, 0, src.core.l_qseq) * * def __set__(self,seq): # <<<<<<<<<<<<<< @@ -18821,8 +18755,8 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_ * # if no quality information is present, the first byte says 0xff. */ -static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq); /*proto*/ -static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq) { +static int __pyx_pf_9csamtools_11AlignedRead_3seq___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq); /*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_3seq___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq) { bam1_t *__pyx_v_src; uint8_t *__pyx_v_p; char *__pyx_v_s; @@ -18838,24 +18772,23 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel int __pyx_t_5; int __pyx_t_6; char *__pyx_t_7; - long __pyx_t_8; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__set__"); - __Pyx_TraceCall("__set__", __pyx_f[0], 2124); + __Pyx_TraceCall("__set__", __pyx_f[0], 2059); - /* "csamtools.pyx":2128 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2063 * # if no quality information is present, the first byte says 0xff. * * if seq == None or len(seq) == 0: return # <<<<<<<<<<<<<< * cdef bam1_t * src * cdef uint8_t * p */ - __pyx_t_1 = PyObject_RichCompare(__pyx_v_seq, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2128; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_v_seq, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2063; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2128; __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 = 2063; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (!__pyx_t_2) { - __pyx_t_3 = PyObject_Length(__pyx_v_seq); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2128; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_Length(__pyx_v_seq); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2063; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = (__pyx_t_3 == 0); __pyx_t_5 = __pyx_t_4; } else { @@ -18868,7 +18801,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel } __pyx_L5:; - /* "csamtools.pyx":2134 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2069 * cdef int l, k, nbytes_new, nbytes_old * * src = self._delegate # <<<<<<<<<<<<<< @@ -18877,17 +18810,17 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel */ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; - /* "csamtools.pyx":2136 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2071 * src = self._delegate * * l = len(seq) # <<<<<<<<<<<<<< * * # as the sequence is stored in half-bytes, the total length (sequence */ - __pyx_t_3 = PyObject_Length(__pyx_v_seq); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2136; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_Length(__pyx_v_seq); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2071; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_l = __pyx_t_3; - /* "csamtools.pyx":2140 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2075 * # as the sequence is stored in half-bytes, the total length (sequence * # plus quality scores) is (l+1)/2 + l * nbytes_new = (l+1)/2 + l # <<<<<<<<<<<<<< @@ -18896,7 +18829,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel */ __pyx_v_nbytes_new = (__Pyx_div_long((__pyx_v_l + 1), 2) + __pyx_v_l); - /* "csamtools.pyx":2141 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2076 * # plus quality scores) is (l+1)/2 + l * nbytes_new = (l+1)/2 + l * nbytes_old = (src.core.l_qseq+1)/2 + src.core.l_qseq # <<<<<<<<<<<<<< @@ -18905,7 +18838,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel */ __pyx_v_nbytes_old = (__Pyx_div_long((__pyx_v_src->core.l_qseq + 1), 2) + __pyx_v_src->core.l_qseq); - /* "csamtools.pyx":2143 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2078 * nbytes_old = (src.core.l_qseq+1)/2 + src.core.l_qseq * # acquire pointer to location in memory * p = bam1_seq( src ) # <<<<<<<<<<<<<< @@ -18914,7 +18847,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel */ __pyx_v_p = bam1_seq(__pyx_v_src); - /* "csamtools.pyx":2144 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2079 * # acquire pointer to location in memory * p = bam1_seq( src ) * src.core.l_qseq = l # <<<<<<<<<<<<<< @@ -18923,7 +18856,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel */ __pyx_v_src->core.l_qseq = __pyx_v_l; - /* "csamtools.pyx":2149 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2084 * nbytes_old, * nbytes_new, * p) # <<<<<<<<<<<<<< @@ -18932,7 +18865,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel */ pysam_bam_update(__pyx_v_src, __pyx_v_nbytes_old, __pyx_v_nbytes_new, __pyx_v_p); - /* "csamtools.pyx":2152 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2087 * # re-acquire pointer to location in memory * # as it might have moved * p = bam1_seq( src ) # <<<<<<<<<<<<<< @@ -18941,7 +18874,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel */ __pyx_v_p = bam1_seq(__pyx_v_src); - /* "csamtools.pyx":2153 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2088 * # as it might have moved * p = bam1_seq( src ) * for k from 0 <= k < nbytes_new: p[k] = 0 # <<<<<<<<<<<<<< @@ -18953,17 +18886,17 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel (__pyx_v_p[__pyx_v_k]) = 0; } - /* "csamtools.pyx":2155 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2090 * for k from 0 <= k < nbytes_new: p[k] = 0 * # convert to C string * s = seq # <<<<<<<<<<<<<< * for k from 0 <= k < l: * p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2) */ - __pyx_t_7 = PyBytes_AsString(__pyx_v_seq); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyBytes_AsString(__pyx_v_seq); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2090; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_s = __pyx_t_7; - /* "csamtools.pyx":2156 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2091 * # convert to C string * s = seq * for k from 0 <= k < l: # <<<<<<<<<<<<<< @@ -18973,18 +18906,17 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel __pyx_t_6 = __pyx_v_l; for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_6; __pyx_v_k++) { - /* "csamtools.pyx":2157 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2092 * s = seq * for k from 0 <= k < l: * p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2) # <<<<<<<<<<<<<< * * # erase qualities */ - __pyx_t_8 = __Pyx_div_long(__pyx_v_k, 2); - (__pyx_v_p[__pyx_t_8]) = ((__pyx_v_p[__pyx_t_8]) | (pysam_translate_sequence((__pyx_v_s[__pyx_v_k])) << (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2))))); + (__pyx_v_p[__Pyx_div_long(__pyx_v_k, 2)]) |= (pysam_translate_sequence((__pyx_v_s[__pyx_v_k])) << (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2)))); } - /* "csamtools.pyx":2160 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2095 * * # erase qualities * p = bam1_qual( src ) # <<<<<<<<<<<<<< @@ -18993,7 +18925,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel */ __pyx_v_p = bam1_qual(__pyx_v_src); - /* "csamtools.pyx":2161 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2096 * # erase qualities * p = bam1_qual( src ) * p[0] = 0xff # <<<<<<<<<<<<<< @@ -19014,7 +18946,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel return __pyx_r; } -/* "csamtools.pyx":2166 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2101 * property qual: * """read sequence base qualities, including :term:`soft clipped` bases (None if not present)""" * def __get__(self): # <<<<<<<<<<<<<< @@ -19030,9 +18962,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx PyObject *__pyx_t_2 = NULL; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__get__"); - __Pyx_TraceCall("__get__", __pyx_f[0], 2166); + __Pyx_TraceCall("__get__", __pyx_f[0], 2101); - /* "csamtools.pyx":2171 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2106 * cdef char * q * * src = self._delegate # <<<<<<<<<<<<<< @@ -19041,7 +18973,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx */ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; - /* "csamtools.pyx":2173 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2108 * src = self._delegate * * if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<< @@ -19058,7 +18990,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx } __pyx_L5:; - /* "csamtools.pyx":2175 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2110 * if src.core.l_qseq == 0: return None * * return get_qual_range(src, 0, src.core.l_qseq) # <<<<<<<<<<<<<< @@ -19066,7 +18998,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx * def __set__(self,qual): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __pyx_f_9csamtools_get_qual_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2175; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __pyx_f_9csamtools_get_qual_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_r = __pyx_t_2; __pyx_t_2 = 0; @@ -19085,7 +19017,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx return __pyx_r; } -/* "csamtools.pyx":2177 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2112 * return get_qual_range(src, 0, src.core.l_qseq) * * def __set__(self,qual): # <<<<<<<<<<<<<< @@ -19093,8 +19025,8 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx * cdef bam1_t * src */ -static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/ -static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) { +static int __pyx_pf_9csamtools_11AlignedRead_4qual___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_4qual___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) { bam1_t *__pyx_v_src; uint8_t *__pyx_v_p; char *__pyx_v_q; @@ -19112,9 +19044,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se int __pyx_t_9; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__set__"); - __Pyx_TraceCall("__set__", __pyx_f[0], 2177); + __Pyx_TraceCall("__set__", __pyx_f[0], 2112); - /* "csamtools.pyx":2184 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2119 * cdef int k * * src = self._delegate # <<<<<<<<<<<<<< @@ -19123,7 +19055,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se */ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; - /* "csamtools.pyx":2185 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2120 * * src = self._delegate * p = bam1_qual( src ) # <<<<<<<<<<<<<< @@ -19132,19 +19064,19 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se */ __pyx_v_p = bam1_qual(__pyx_v_src); - /* "csamtools.pyx":2186 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2121 * src = self._delegate * p = bam1_qual( src ) * if qual == None or len(qual) == 0: # <<<<<<<<<<<<<< * # if absent - set to 0xff * p[0] = 0xff */ - __pyx_t_1 = PyObject_RichCompare(__pyx_v_qual, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2186; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_v_qual, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2186; __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 = 2121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (!__pyx_t_2) { - __pyx_t_3 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2186; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = (__pyx_t_3 == 0); __pyx_t_5 = __pyx_t_4; } else { @@ -19152,7 +19084,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se } if (__pyx_t_5) { - /* "csamtools.pyx":2188 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2123 * if qual == None or len(qual) == 0: * # if absent - set to 0xff * p[0] = 0xff # <<<<<<<<<<<<<< @@ -19161,7 +19093,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se */ (__pyx_v_p[0]) = 0xff; - /* "csamtools.pyx":2189 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2124 * # if absent - set to 0xff * p[0] = 0xff * return # <<<<<<<<<<<<<< @@ -19174,27 +19106,27 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se } __pyx_L5:; - /* "csamtools.pyx":2192 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2127 * cdef int l * # convert to C string * q = qual # <<<<<<<<<<<<<< * l = len(qual) * if src.core.l_qseq != l: */ - __pyx_t_6 = PyBytes_AsString(__pyx_v_qual); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2192; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyBytes_AsString(__pyx_v_qual); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2127; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_q = __pyx_t_6; - /* "csamtools.pyx":2193 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2128 * # convert to C string * q = qual * l = len(qual) # <<<<<<<<<<<<<< * if src.core.l_qseq != l: * raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq)) */ - __pyx_t_3 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2128; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_l = __pyx_t_3; - /* "csamtools.pyx":2194 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2129 * q = qual * l = len(qual) * if src.core.l_qseq != l: # <<<<<<<<<<<<<< @@ -19204,58 +19136,58 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se __pyx_t_5 = (__pyx_v_src->core.l_qseq != __pyx_v_l); if (__pyx_t_5) { - /* "csamtools.pyx":2195 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2130 * l = len(qual) * if src.core.l_qseq != l: * raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq)) # <<<<<<<<<<<<<< * assert src.core.l_qseq == l * for k from 0 <= k < l: */ - __pyx_t_1 = PyInt_FromLong(__pyx_v_l); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyInt_FromLong(__pyx_v_l); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2130; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_7 = __Pyx_PyInt_to_py_int32_t(__pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyInt_to_py_int32_t(__pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2130; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_8)); + __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2130; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); __pyx_t_1 = 0; __pyx_t_7 = 0; - __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_120), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_61), __pyx_t_8); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2130; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_7)); - __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; - __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_8)); + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2130; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_7)); __Pyx_GIVEREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; - __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, __pyx_t_8, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2130; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_Raise(__pyx_t_7, 0, 0); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2130; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L6; } __pyx_L6:; - /* "csamtools.pyx":2196 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2131 * if src.core.l_qseq != l: * raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq)) * assert src.core.l_qseq == l # <<<<<<<<<<<<<< * for k from 0 <= k < l: * p[k] = q[k] - 33 */ - #ifndef CYTHON_WITHOUT_ASSERTIONS + #ifndef PYREX_WITHOUT_ASSERTIONS if (unlikely(!(__pyx_v_src->core.l_qseq == __pyx_v_l))) { PyErr_SetNone(PyExc_AssertionError); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2131; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #endif - /* "csamtools.pyx":2197 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2132 * raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq)) * assert src.core.l_qseq == l * for k from 0 <= k < l: # <<<<<<<<<<<<<< @@ -19265,7 +19197,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se __pyx_t_9 = __pyx_v_l; 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__pyx_t_3 = 0; @@ -19624,8 +19556,8 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(PyObject *__pyx return __pyx_r; } -/* "csamtools.pyx":2272 - * multiple times. +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2204 + * * """ * def __get__(self): # <<<<<<<<<<<<<< * cdef char * ctag @@ -19651,40 +19583,38 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx int __pyx_t_8; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__get__"); - __Pyx_TraceCall("__get__", __pyx_f[0], 2272); - __pyx_v_result = ((PyObject*)Py_None); __Pyx_INCREF(Py_None); + __Pyx_TraceCall("__get__", __pyx_f[0], 2204); + __pyx_v_result = ((PyObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_v_value = Py_None; __Pyx_INCREF(Py_None); - /* "csamtools.pyx":2279 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2211 * cdef char auxtype * * src = self._delegate # <<<<<<<<<<<<<< - * if src.l_aux == 0: return [] + * if src.l_aux == 0: return None * */ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; - /* "csamtools.pyx":2280 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2212 * * src = self._delegate - * if src.l_aux == 0: return [] # <<<<<<<<<<<<<< + * if src.l_aux == 0: return None # <<<<<<<<<<<<<< * * s = bam1_aux( src ) */ __pyx_t_1 = (__pyx_v_src->l_aux == 0); if (__pyx_t_1) { __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); - __pyx_r = ((PyObject *)__pyx_t_2); - __pyx_t_2 = 0; + __Pyx_INCREF(Py_None); + __pyx_r = Py_None; goto __pyx_L0; goto __pyx_L5; } __pyx_L5:; - /* "csamtools.pyx":2282 - * if src.l_aux == 0: return [] + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2214 + * if src.l_aux == 0: return None * * s = bam1_aux( src ) # <<<<<<<<<<<<<< * result = [] @@ -19692,20 +19622,20 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx */ __pyx_v_s = bam1_aux(__pyx_v_src); - /* "csamtools.pyx":2283 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2215 * * s = bam1_aux( src ) * result = [] # <<<<<<<<<<<<<< * auxtag[2] = 0 * while s < (src.data + src.data_len): */ - __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __Pyx_DECREF(((PyObject *)__pyx_v_result)); __pyx_v_result = __pyx_t_2; __pyx_t_2 = 0; - /* "csamtools.pyx":2284 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2216 * s = bam1_aux( src ) * result = [] * auxtag[2] = 0 # <<<<<<<<<<<<<< @@ -19714,7 +19644,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx */ (__pyx_v_auxtag[2]) = 0; - /* "csamtools.pyx":2285 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2217 * result = [] * auxtag[2] = 0 * while s < (src.data + src.data_len): # <<<<<<<<<<<<<< @@ -19725,7 +19655,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx __pyx_t_1 = (__pyx_v_s < (__pyx_v_src->data + __pyx_v_src->data_len)); if (!__pyx_t_1) break; - /* "csamtools.pyx":2287 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2219 * while s < (src.data + src.data_len): * # get tag * auxtag[0] = s[0] # <<<<<<<<<<<<<< @@ -19734,7 +19664,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx */ (__pyx_v_auxtag[0]) = (__pyx_v_s[0]); - /* "csamtools.pyx":2288 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2220 * # get tag * auxtag[0] = s[0] * auxtag[1] = s[1] # <<<<<<<<<<<<<< @@ -19743,16 +19673,16 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx */ (__pyx_v_auxtag[1]) = (__pyx_v_s[1]); - /* "csamtools.pyx":2289 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2221 * auxtag[0] = s[0] * auxtag[1] = s[1] * s += 2 # <<<<<<<<<<<<<< * auxtype = s[0] * */ - __pyx_v_s = (__pyx_v_s + 2); + __pyx_v_s += 2; - /* "csamtools.pyx":2290 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2222 * auxtag[1] = s[1] * s += 2 * auxtype = s[0] # <<<<<<<<<<<<<< @@ -19761,7 +19691,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx */ __pyx_v_auxtype = (__pyx_v_s[0]); - /* "csamtools.pyx":2292 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2224 * auxtype = s[0] * * if auxtype in ('c', 'C'): # <<<<<<<<<<<<<< @@ -19779,31 +19709,31 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx __pyx_t_1 = __pyx_t_5; if (__pyx_t_1) { - /* "csamtools.pyx":2293 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2225 * * if auxtype in ('c', 'C'): * value = bam_aux2i(s) # <<<<<<<<<<<<<< * s += 1 * elif auxtype in ('s', 'S'): */ - __pyx_t_2 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2293; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2225; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_v_value); __pyx_v_value = __pyx_t_2; __pyx_t_2 = 0; - /* "csamtools.pyx":2294 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2226 * if auxtype in ('c', 'C'): * value = bam_aux2i(s) * s += 1 # <<<<<<<<<<<<<< * elif auxtype in ('s', 'S'): * value = bam_aux2i(s) */ - __pyx_v_s = (__pyx_v_s + 1); + __pyx_v_s += 1; goto __pyx_L8; } - /* "csamtools.pyx":2295 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2227 * value = bam_aux2i(s) * s += 1 * elif auxtype in ('s', 'S'): # <<<<<<<<<<<<<< @@ -19821,31 +19751,31 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx __pyx_t_1 = __pyx_t_4; if (__pyx_t_1) { - /* "csamtools.pyx":2296 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2228 * s += 1 * elif auxtype in ('s', 'S'): * value = bam_aux2i(s) # <<<<<<<<<<<<<< * s += 2 * elif auxtype in ('i', 'I'): */ - __pyx_t_2 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2228; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_v_value); __pyx_v_value = __pyx_t_2; __pyx_t_2 = 0; - /* "csamtools.pyx":2297 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2229 * elif auxtype in ('s', 'S'): * value = bam_aux2i(s) * s += 2 # <<<<<<<<<<<<<< * elif auxtype in ('i', 'I'): * value = bam_aux2i(s) */ - __pyx_v_s = (__pyx_v_s + 2); + __pyx_v_s += 2; goto __pyx_L8; } - /* "csamtools.pyx":2298 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2230 * value = bam_aux2i(s) * s += 2 * elif auxtype in ('i', 'I'): # <<<<<<<<<<<<<< @@ -19863,31 +19793,31 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx __pyx_t_1 = __pyx_t_5; if (__pyx_t_1) { - /* "csamtools.pyx":2299 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2231 * s += 2 * elif auxtype in ('i', 'I'): * value = bam_aux2i(s) # <<<<<<<<<<<<<< * s += 4 * elif auxtype == 'f': */ - __pyx_t_2 = PyFloat_FromDouble(((float)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2299; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyFloat_FromDouble(((float)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2231; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_v_value); __pyx_v_value = __pyx_t_2; __pyx_t_2 = 0; - /* "csamtools.pyx":2300 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2232 * elif auxtype in ('i', 'I'): * value = bam_aux2i(s) * s += 4 # <<<<<<<<<<<<<< * elif auxtype == 'f': * value = bam_aux2f(s) */ - __pyx_v_s = (__pyx_v_s + 4); + __pyx_v_s += 4; goto __pyx_L8; } - /* "csamtools.pyx":2301 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2233 * value = bam_aux2i(s) * s += 4 * elif auxtype == 'f': # <<<<<<<<<<<<<< @@ -19897,31 +19827,31 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx __pyx_t_1 = (__pyx_v_auxtype == 'f'); if (__pyx_t_1) { - /* "csamtools.pyx":2302 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2234 * s += 4 * elif auxtype == 'f': * value = bam_aux2f(s) # <<<<<<<<<<<<<< * s += 4 * elif auxtype == 'd': */ - __pyx_t_2 = PyFloat_FromDouble(bam_aux2f(__pyx_v_s)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2302; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyFloat_FromDouble(bam_aux2f(__pyx_v_s)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2234; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_v_value); __pyx_v_value = __pyx_t_2; __pyx_t_2 = 0; - /* "csamtools.pyx":2303 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2235 * elif auxtype == 'f': * value = bam_aux2f(s) * s += 4 # <<<<<<<<<<<<<< * elif auxtype == 'd': * value = bam_aux2d(s) */ - __pyx_v_s = (__pyx_v_s + 4); + __pyx_v_s += 4; goto __pyx_L8; } - /* "csamtools.pyx":2304 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2236 * value = bam_aux2f(s) * s += 4 * elif auxtype == 'd': # <<<<<<<<<<<<<< @@ -19931,31 +19861,31 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx __pyx_t_1 = (__pyx_v_auxtype == 'd'); if (__pyx_t_1) { - /* "csamtools.pyx":2305 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2237 * s += 4 * elif auxtype == 'd': * value = bam_aux2d(s) # <<<<<<<<<<<<<< * s += 8 * elif auxtype == 'A': */ - __pyx_t_2 = PyFloat_FromDouble(bam_aux2d(__pyx_v_s)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2305; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyFloat_FromDouble(bam_aux2d(__pyx_v_s)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2237; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_v_value); __pyx_v_value = __pyx_t_2; __pyx_t_2 = 0; - /* "csamtools.pyx":2306 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2238 * elif auxtype == 'd': * value = bam_aux2d(s) * s += 8 # <<<<<<<<<<<<<< * elif auxtype == 'A': * value = "%c" % bam_aux2A(s) */ - __pyx_v_s = (__pyx_v_s + 8); + __pyx_v_s += 8; goto __pyx_L8; } - /* "csamtools.pyx":2307 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2239 * value = bam_aux2d(s) * s += 8 * elif auxtype == 'A': # <<<<<<<<<<<<<< @@ -19965,34 +19895,34 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx __pyx_t_1 = (__pyx_v_auxtype == 'A'); if (__pyx_t_1) { - /* "csamtools.pyx":2308 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2240 * s += 8 * elif auxtype == 'A': * value = "%c" % bam_aux2A(s) # <<<<<<<<<<<<<< * s += 1 * elif auxtype in ('Z', 'H'): */ - __pyx_t_2 = PyInt_FromLong(bam_aux2A(__pyx_v_s)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2308; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyInt_FromLong(bam_aux2A(__pyx_v_s)); 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_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_121), __pyx_t_2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2308; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_62), __pyx_t_2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2240; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_6)); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_v_value); __pyx_v_value = ((PyObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "csamtools.pyx":2309 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2241 * elif auxtype == 'A': * value = "%c" % bam_aux2A(s) * s += 1 # <<<<<<<<<<<<<< * elif auxtype in ('Z', 'H'): * value = bam_aux2Z(s) */ - __pyx_v_s = (__pyx_v_s + 1); + __pyx_v_s += 1; goto __pyx_L8; } - /* "csamtools.pyx":2310 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2242 * value = "%c" % bam_aux2A(s) * s += 1 * elif auxtype in ('Z', 'H'): # <<<<<<<<<<<<<< @@ -20010,42 +19940,42 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx __pyx_t_1 = __pyx_t_4; if (__pyx_t_1) { - /* "csamtools.pyx":2311 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2243 * s += 1 * elif auxtype in ('Z', 'H'): * value = bam_aux2Z(s) # <<<<<<<<<<<<<< * # +1 for NULL terminated string * s += len(value) + 1 */ - __pyx_t_6 = PyBytes_FromString(bam_aux2Z(__pyx_v_s)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2311; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyBytes_FromString(bam_aux2Z(__pyx_v_s)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2243; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_6)); __Pyx_DECREF(__pyx_v_value); __pyx_v_value = ((PyObject *)__pyx_t_6); __pyx_t_6 = 0; - /* "csamtools.pyx":2313 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2245 * value = bam_aux2Z(s) * # +1 for NULL terminated string * s += len(value) + 1 # <<<<<<<<<<<<<< * # * s += 1 */ - __pyx_t_7 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2313; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_s = (__pyx_v_s + (__pyx_t_7 + 1)); + __pyx_t_7 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2245; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_s += (__pyx_t_7 + 1); goto __pyx_L8; } __pyx_L8:; - /* "csamtools.pyx":2315 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2247 * s += len(value) + 1 * # * s += 1 # <<<<<<<<<<<<<< * * result.append( (auxtag, value) ) */ - __pyx_v_s = (__pyx_v_s + 1); + __pyx_v_s += 1; - /* "csamtools.pyx":2317 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2249 * s += 1 * * result.append( (auxtag, value) ) # <<<<<<<<<<<<<< @@ -20053,23 +19983,23 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx * return result */ if (unlikely(__pyx_v_result == Py_None)) { - PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2249; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_6 = PyBytes_FromString(__pyx_v_auxtag); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyBytes_FromString(__pyx_v_auxtag); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2249; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_6)); - __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2249; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_6)); __Pyx_GIVEREF(((PyObject *)__pyx_t_6)); __Pyx_INCREF(__pyx_v_value); PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_value); __Pyx_GIVEREF(__pyx_v_value); __pyx_t_6 = 0; - __pyx_t_8 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __pyx_t_8 = PyList_Append(((PyObject *)__pyx_v_result), __pyx_t_2); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2249; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; } - /* "csamtools.pyx":2319 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2251 * result.append( (auxtag, value) ) * * return result # <<<<<<<<<<<<<< @@ -20097,7 +20027,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx return __pyx_r; 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/*proto*/ -static int __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) { +static int __pyx_pf_9csamtools_11AlignedRead_4mrnm___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_4mrnm___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) { int __pyx_r; int32_t __pyx_t_1; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__set__"); - __Pyx_TraceCall("__set__", __pyx_f[0], 2485); - __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mtid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2485; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_TraceCall("__set__", __pyx_f[0], 2411); + __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mtid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2411; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid = __pyx_t_1; 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/*proto*/ -static int __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) { +static int __pyx_pf_9csamtools_11AlignedRead_4mpos___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_4mpos___set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) { int __pyx_r; int32_t __pyx_t_1; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("__set__"); - __Pyx_TraceCall("__set__", __pyx_f[0], 2494); - __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mpos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2494; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_TraceCall("__set__", __pyx_f[0], 2415); + __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mpos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2415; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos = __pyx_t_1; 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2578; __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 = 2494; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_DECREF(((PyObject *)__pyx_v_result)); __pyx_v_result = __pyx_t_1; __pyx_t_1 = 0; - /* "csamtools.pyx":2579 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2495 * * result = [] * src = self._delegate # <<<<<<<<<<<<<< @@ -22981,7 +22725,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject * */ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; - /* "csamtools.pyx":2580 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2496 * result = [] * src = self._delegate * if src.core.n_cigar == 0: return [] # <<<<<<<<<<<<<< @@ -22991,7 +22735,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject * __pyx_t_2 = (__pyx_v_src->core.n_cigar == 0); if (__pyx_t_2) { __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2580; __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 = 2496; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __pyx_r = ((PyObject *)__pyx_t_1); __pyx_t_1 = 0; @@ -23000,7 +22744,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject * } __pyx_L5:; - /* "csamtools.pyx":2582 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2498 * if src.core.n_cigar == 0: return [] * * pos = src.core.pos # <<<<<<<<<<<<<< @@ -23009,7 +22753,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject * */ __pyx_v_pos = __pyx_v_src->core.pos; - /* "csamtools.pyx":2584 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2500 * pos = src.core.pos * * cigar_p = bam1_cigar(src) # <<<<<<<<<<<<<< @@ -23018,7 +22762,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject * */ __pyx_v_cigar_p = bam1_cigar(__pyx_v_src); - /* "csamtools.pyx":2585 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2501 * * cigar_p = bam1_cigar(src) * for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<< @@ -23028,7 +22772,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject * __pyx_t_3 = __pyx_v_src->core.n_cigar; for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_3; __pyx_v_k++) { - /* "csamtools.pyx":2586 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2502 * cigar_p = bam1_cigar(src) * for k from 0 <= k < src.core.n_cigar: * op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<< @@ -23037,20 +22781,20 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject * */ __pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15); - /* "csamtools.pyx":2587 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2503 * for k from 0 <= k < src.core.n_cigar: * op = cigar_p[k] & BAM_CIGAR_MASK * l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<< * if op == BAM_CMATCH: * for i from pos <= i < pos + l: */ - __pyx_t_1 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2587; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2503; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_v_l); __pyx_v_l = __pyx_t_1; __pyx_t_1 = 0; - /* "csamtools.pyx":2588 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2504 * op = cigar_p[k] & BAM_CIGAR_MASK * l = cigar_p[k] >> BAM_CIGAR_SHIFT * if op == BAM_CMATCH: # <<<<<<<<<<<<<< @@ -23060,23 +22804,23 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject * __pyx_t_2 = (__pyx_v_op == 0); if (__pyx_t_2) { - /* "csamtools.pyx":2589 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2505 * l = cigar_p[k] >> BAM_CIGAR_SHIFT * if op == BAM_CMATCH: * for i from pos <= i < pos + l: # <<<<<<<<<<<<<< * result.append( i ) * */ - __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2505; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_4 = PyNumber_Add(__pyx_t_1, __pyx_v_l); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyNumber_Add(__pyx_t_1, __pyx_v_l); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2505; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_4); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_4); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2505; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_5; __pyx_v_i++) { - /* "csamtools.pyx":2590 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2506 * if op == BAM_CMATCH: * for i from pos <= i < pos + l: * result.append( i ) # <<<<<<<<<<<<<< @@ -23084,18 +22828,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject * * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP: */ if (unlikely(__pyx_v_result == Py_None)) { - PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2506; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2506; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_6 = PyList_Append(__pyx_v_result, __pyx_t_4); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyList_Append(((PyObject *)__pyx_v_result), __pyx_t_4); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2506; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; } goto __pyx_L8; } __pyx_L8:; - /* "csamtools.pyx":2592 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2508 * result.append( i ) * * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP: # <<<<<<<<<<<<<< @@ -23107,31 +22851,25 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject * case 2: case 3: - /* "csamtools.pyx":2593 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2509 * * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP: * pos += l # <<<<<<<<<<<<<< * * return result */ - __pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_4); - __pyx_t_1 = PyNumber_InPlaceAdd(__pyx_t_4, __pyx_v_l); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_1); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_v_pos = __pyx_t_5; + __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_l); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_pos += __pyx_t_5; break; } } - /* "csamtools.pyx":2595 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2511 * pos += l * * return result # <<<<<<<<<<<<<< - * * def overlap( self, uint32_t start, uint32_t end ): + * """return number of bases on reference overlapping *start* and *end* */ __Pyx_XDECREF(__pyx_r); __Pyx_INCREF(((PyObject *)__pyx_v_result)); @@ -23154,17 +22892,17 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject * return __pyx_r; } -/* "csamtools.pyx":2597 - * return result +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2512 * + * return result * def overlap( self, uint32_t start, uint32_t end ): # <<<<<<<<<<<<<< - * """return number of aligned bases of read overlapping the interval *start* and *end* - * on the reference sequence. + * """return number of bases on reference overlapping *start* and *end* + * """ */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_9csamtools_11AlignedRead_5overlap[] = "AlignedRead.overlap(self, uint32_t start, uint32_t end)\nreturn number of aligned bases of read overlapping the interval *start* and *end*\n on the reference sequence.\n "; -static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_9csamtools_11AlignedRead_overlap[] = "AlignedRead.overlap(self, uint32_t start, uint32_t end)\nreturn number of bases on reference overlapping *start* and *end*\n "; +static PyObject *__pyx_pf_9csamtools_11AlignedRead_overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { uint32_t __pyx_v_start; uint32_t __pyx_v_end; uint32_t __pyx_v_k; @@ -23189,7 +22927,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__start,&__pyx_n_s__end,0}; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("overlap"); - __Pyx_TraceCall("overlap", __pyx_f[0], 2597); + __Pyx_TraceCall("overlap", __pyx_f[0], 2512); if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args = PyDict_Size(__pyx_kwds); PyObject* values[2] = {0,0}; @@ -23208,23 +22946,23 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end); if (likely(values[1])) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("overlap", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("overlap", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2512; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "overlap") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "overlap") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2512; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } - __pyx_v_start = __Pyx_PyInt_from_py_uint32_t(values[0]); if (unlikely((__pyx_v_start == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_end = __Pyx_PyInt_from_py_uint32_t(values[1]); if (unlikely((__pyx_v_end == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_start = __Pyx_PyInt_from_py_uint32_t(values[0]); if (unlikely((__pyx_v_start == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2512; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_end = __Pyx_PyInt_from_py_uint32_t(values[1]); if (unlikely((__pyx_v_end == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2512; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; } else { - __pyx_v_start = __Pyx_PyInt_from_py_uint32_t(PyTuple_GET_ITEM(__pyx_args, 0)); if (unlikely((__pyx_v_start == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_end = __Pyx_PyInt_from_py_uint32_t(PyTuple_GET_ITEM(__pyx_args, 1)); if (unlikely((__pyx_v_end == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_start = __Pyx_PyInt_from_py_uint32_t(PyTuple_GET_ITEM(__pyx_args, 0)); if (unlikely((__pyx_v_start == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2512; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_end = __Pyx_PyInt_from_py_uint32_t(PyTuple_GET_ITEM(__pyx_args, 1)); if (unlikely((__pyx_v_end == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2512; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("overlap", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("overlap", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2512; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("csamtools.AlignedRead.overlap"); __Pyx_RefNannyFinishContext(); @@ -23232,7 +22970,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se __pyx_L4_argument_unpacking_done:; __pyx_v_l = Py_None; __Pyx_INCREF(Py_None); - /* "csamtools.pyx":2606 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2520 * cdef bam1_t * src * * overlap = 0 # <<<<<<<<<<<<<< @@ -23241,7 +22979,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se */ __pyx_v_overlap = 0; - /* "csamtools.pyx":2608 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2522 * overlap = 0 * * src = self._delegate # <<<<<<<<<<<<<< @@ -23250,7 +22988,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se */ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; 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if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_7 = PyObject_RichCompare(__pyx_t_6, __pyx_t_5, Py_LT); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2619; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyObject_RichCompare(__pyx_t_6, __pyx_t_5, Py_LT); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2619; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; if (__pyx_t_1) { - __pyx_t_7 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_4); 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyNumber_Subtract(__pyx_t_3, __pyx_t_5); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2619; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_v_o = __pyx_t_10; - /* "csamtools.pyx":2620 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2534 * if op == BAM_CMATCH: * o = min( pos + l, end) - max( pos, start ) * if o > 0: overlap += o # <<<<<<<<<<<<<< @@ -23392,7 +23130,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se */ __pyx_t_1 = (__pyx_v_o > 0); 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if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2623; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); - __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - __pyx_t_9 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_5); if (unlikely((__pyx_t_9 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2623; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_v_pos = __pyx_t_9; + __pyx_t_9 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_l); if (unlikely((__pyx_t_9 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2537; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_pos += __pyx_t_9; break; } } - /* "csamtools.pyx":2625 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2539 * pos += l * * return overlap # <<<<<<<<<<<<<< @@ -23439,10 +23171,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se * def opt(self, tag): */ __Pyx_XDECREF(__pyx_r); 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/*proto*/ -static char __pyx_doc_9csamtools_11AlignedRead_6opt[] = "AlignedRead.opt(self, tag)\nretrieves optional data given a two-letter *tag*"; -static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag); /*proto*/ +static char __pyx_doc_9csamtools_11AlignedRead_opt[] = "AlignedRead.opt(self, tag)\nretrieves optional data given a two-letter *tag*"; +static PyObject *__pyx_pf_9csamtools_11AlignedRead_opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag) { uint8_t *__pyx_v_v; PyObject *__pyx_v_type; PyObject *__pyx_r = NULL; @@ -23486,20 +23218,20 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self, int __pyx_t_8; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("opt"); - __Pyx_TraceCall("opt", __pyx_f[0], 2627); + __Pyx_TraceCall("opt", __pyx_f[0], 2541); __pyx_v_type = Py_None; __Pyx_INCREF(Py_None); - /* "csamtools.pyx":2631 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2545 * #see bam_aux.c: bam_aux_get() and bam_aux2i() etc * cdef uint8_t * v * v = bam_aux_get(self._delegate, tag) # <<<<<<<<<<<<<< * if v == NULL: raise KeyError( "tag '%s' not present" % tag ) * type = chr(v[0]) */ - __pyx_t_1 = PyBytes_AsString(__pyx_v_tag); 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if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2646; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_RichCompare(__pyx_v_type, ((PyObject *)__pyx_n_s__Z), Py_EQ); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2560; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2646; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2560; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (__pyx_t_5) { - /* "csamtools.pyx":2647 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2561 * return '%c' % bam_aux2A(v) * elif type == 'Z': * return bam_aux2Z(v) # <<<<<<<<<<<<<< @@ -23769,7 +23501,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self, * def fancy_str (self): */ __Pyx_XDECREF(__pyx_r); 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-static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static char __pyx_doc_9csamtools_11AlignedRead_fancy_str[] = "AlignedRead.fancy_str(self)\nreturns list of fieldnames/values in pretty format for debugging\n "; +static PyObject *__pyx_pf_9csamtools_11AlignedRead_fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { PyObject *__pyx_v_ret_string; PyObject *__pyx_v_field_names; PyObject *__pyx_v_fields_names_in_order; @@ -23821,64 +23553,64 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_ int __pyx_t_10; __Pyx_TraceDeclarations __Pyx_RefNannySetupContext("fancy_str"); - __Pyx_TraceCall("fancy_str", __pyx_f[0], 2649); - __pyx_v_ret_string = ((PyObject*)Py_None); __Pyx_INCREF(Py_None); - __pyx_v_field_names = ((PyObject*)Py_None); __Pyx_INCREF(Py_None); 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__pyx_v_ret_string = __pyx_t_1; __pyx_t_1 = 0; - /* "csamtools.pyx":2653 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2567 * """ * ret_string = [] * field_names = { # <<<<<<<<<<<<<< * "tid": "Contig index", * "pos": "Mapped position on contig", */ - __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__tid), ((PyObject *)__pyx_kp_s_136)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__pos), ((PyObject *)__pyx_kp_s_137)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__mtid), ((PyObject *)__pyx_kp_s_138)) < 0) {__pyx_filename = __pyx_f[0]; 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qual), ((PyObject *)__pyx_kp_s_144)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__bin), ((PyObject *)__pyx_kp_s_145)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_qname), ((PyObject *)__pyx_kp_s_146)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qname), ((PyObject *)__pyx_kp_s_147)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_qseq), ((PyObject *)__pyx_kp_s_148)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qseq), ((PyObject *)__pyx_kp_s_149)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__bqual), ((PyObject *)__pyx_kp_s_150)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_aux), ((PyObject *)__pyx_kp_s_151)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__m_data), ((PyObject *)__pyx_kp_s_152)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__data_len), ((PyObject *)__pyx_kp_s_153)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__tid), ((PyObject *)__pyx_kp_s_76)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__pos), ((PyObject *)__pyx_kp_s_77)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__mtid), ((PyObject *)__pyx_kp_s_78)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__mpos), ((PyObject *)__pyx_kp_s_79)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__isize), ((PyObject *)__pyx_kp_s_80)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__flag), ((PyObject *)__pyx_kp_s_81)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__n_cigar), ((PyObject *)__pyx_kp_s_82)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__cigar), ((PyObject *)__pyx_kp_s_83)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qual), ((PyObject *)__pyx_kp_s_84)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__bin), ((PyObject *)__pyx_kp_s_85)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_qname), ((PyObject *)__pyx_kp_s_86)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qname), ((PyObject *)__pyx_kp_s_87)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_qseq), ((PyObject *)__pyx_kp_s_88)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qseq), ((PyObject *)__pyx_kp_s_89)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__bqual), ((PyObject *)__pyx_kp_s_90)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_aux), ((PyObject *)__pyx_kp_s_91)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__m_data), ((PyObject *)__pyx_kp_s_92)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__data_len), ((PyObject *)__pyx_kp_s_93)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2567; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_v_field_names)); __pyx_v_field_names = __pyx_t_1; __pyx_t_1 = 0; - /* "csamtools.pyx":2673 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2587 * "data_len": "Current data length", * } * fields_names_in_order = ["tid", "pos", "mtid", "mpos", "isize", "flag", # <<<<<<<<<<<<<< * "n_cigar", "cigar", "qual", "bin", "l_qname", "qname", * "l_qseq", "qseq", "bqual", "l_aux", "m_data", "data_len"] */ - __pyx_t_1 = PyList_New(18); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2673; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyList_New(18); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2587; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); 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__pyx_lineno = 2680; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_8)); + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7); @@ -24021,28 +23754,28 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_ __pyx_t_3 = 0; __pyx_t_7 = 0; __pyx_t_9 = 0; - __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_154), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2680; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_94), __pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_9)); 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2682; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____dict__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2596; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) { __pyx_t_2 = 0; __pyx_t_9 = __pyx_t_1; __Pyx_INCREF(__pyx_t_9); } else { - __pyx_t_2 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2682; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2596; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -24056,7 +23789,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_ } else { __pyx_t_1 = PyIter_Next(__pyx_t_9); 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } else { + __pyx_t_5 = ((PyDict_Contains(((PyObject *)__pyx_v_field_names), __pyx_v_f))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_5 = ((PyDict_Contains(((PyObject *)__pyx_v_field_names), __pyx_v_f))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2683; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = (!__pyx_t_5); if (__pyx_t_4) { - /* "csamtools.pyx":2684 + /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2598 * for f in self.__dict__: * if not f in field_names: * ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f))) # <<<<<<<<<<<<<< @@ -24087,34 +23821,34 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_ * */ if (unlikely(__pyx_v_ret_string == Py_None)) { - PyErr_SetString(PyExc_AttributeError, "'NoneType' object has no attribute 'append'"); 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__pyx_t_4 = 0; + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); @@ -25399,7 +25149,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs_2setfile(PyObject *__pyx_self, PyObje return __pyx_r; } -/* "csamtools.pyx":2801 +/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2715 * self.setfd(fd) * * def setfd(self, fd): # <<<<<<<<<<<<<< @@ -25407,10 +25157,10 @@ static PyObject *__pyx_pf_9csamtools_4Outs_2setfile(PyObject *__pyx_self, PyObje * self.streams.append(ofd) */ -static PyObject *__pyx_pf_9csamtools_4Outs_3setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_9csamtools_4Outs_3setfd[] = "Outs.setfd(self, fd)"; -static PyMethodDef __pyx_mdef_9csamtools_4Outs_3setfd = {__Pyx_NAMESTR("setfd"), (PyCFunction)__pyx_pf_9csamtools_4Outs_3setfd, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_3setfd)}; -static PyObject *__pyx_pf_9csamtools_4Outs_3setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pf_9csamtools_4Outs_setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); 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} else { __pyx_v_args = ((PyObject *)__pyx_empty_tuple); - __pyx_v_catch_stdout = __pyx_k_160; - __pyx_v_catch_stderr = __pyx_k_161; + __pyx_v_catch_stdout = __pyx_k_98; + __pyx_v_catch_stderr = __pyx_k_99; switch (PyTuple_GET_SIZE(__pyx_args)) { case 4: __pyx_v_catch_stderr = PyTuple_GET_ITEM(__pyx_args, 3); case 3: __pyx_v_catch_stdout = PyTuple_GET_ITEM(__pyx_args, 2); @@ -25889,7 +25638,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("_samtools_dispatch", 0, 1, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2820; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_samtools_dispatch", 0, 1, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2734; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("csamtools._samtools_dispatch"); __Pyx_RefNannyFinishContext(); 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goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2764; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_162), __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2850; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_100), __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2764; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_4)); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2850; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_3)); + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; 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+} + +static int __pyx_setprop_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v, void *x) { + if (v) { + return __pyx_pf_9csamtools_11AlignedRead_5isize___set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_paired(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(o); +} + +static int __pyx_setprop_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObject *v, void *x) { + if (v) { + return __pyx_pf_9csamtools_11AlignedRead_9is_paired___set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(o); +} + +static int __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, PyObject *v, void *x) { + if (v) { + return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(o); +} + +static int __pyx_setprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObject *v, void *x) { + if (v) { + return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(o); +} + +static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, PyObject *v, void *x) { + if (v) { + return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(o); +} + +static int __pyx_setprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObject *v, void *x) { + if (v) { + return __pyx_pf_9csamtools_11AlignedRead_10is_reverse___set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(o); +} + +static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, PyObject *v, void *x) { + if (v) { + return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read1(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(o); +} + +static int __pyx_setprop_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject *v, void *x) { + if (v) { + return __pyx_pf_9csamtools_11AlignedRead_8is_read1___set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read2(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(o); +} + +static int __pyx_setprop_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject *v, void *x) { + if (v) { + return __pyx_pf_9csamtools_11AlignedRead_8is_read2___set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(o); +} + +static int __pyx_setprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyObject *v, void *x) { + if (v) { + return __pyx_pf_9csamtools_11AlignedRead_12is_secondary___set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(o); +} + +static int __pyx_setprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObject *v, void *x) { + if (v) { + return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail___set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(o); +} + +static int __pyx_setprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyObject *v, void *x) { + if (v) { + return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_9csamtools_11AlignedRead_positions(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11AlignedRead_9positions___get__(o); +} + +static PyMethodDef __pyx_methods_9csamtools_AlignedRead[] = { + {__Pyx_NAMESTR("compare"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_compare, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_compare)}, + {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_overlap)}, + {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_opt, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_opt)}, + {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_fancy_str)}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_9csamtools_AlignedRead[] = { + {(char *)"qname", __pyx_getprop_9csamtools_11AlignedRead_qname, __pyx_setprop_9csamtools_11AlignedRead_qname, __Pyx_DOCSTR(__pyx_k_114), 0}, + {(char *)"cigar", __pyx_getprop_9csamtools_11AlignedRead_cigar, __pyx_setprop_9csamtools_11AlignedRead_cigar, __Pyx_DOCSTR(__pyx_k_115), 0}, + {(char *)"seq", __pyx_getprop_9csamtools_11AlignedRead_seq, __pyx_setprop_9csamtools_11AlignedRead_seq, __Pyx_DOCSTR(__pyx_k_116), 0}, + {(char *)"qual", __pyx_getprop_9csamtools_11AlignedRead_qual, __pyx_setprop_9csamtools_11AlignedRead_qual, __Pyx_DOCSTR(__pyx_k_117), 0}, + {(char *)"query", __pyx_getprop_9csamtools_11AlignedRead_query, 0, __Pyx_DOCSTR(__pyx_k_118), 0}, + {(char *)"qqual", __pyx_getprop_9csamtools_11AlignedRead_qqual, 0, __Pyx_DOCSTR(__pyx_k_119), 0}, + {(char *)"qstart", __pyx_getprop_9csamtools_11AlignedRead_qstart, 0, __Pyx_DOCSTR(__pyx_k_120), 0}, + {(char *)"qend", __pyx_getprop_9csamtools_11AlignedRead_qend, 0, __Pyx_DOCSTR(__pyx_k_121), 0}, + {(char *)"qlen", __pyx_getprop_9csamtools_11AlignedRead_qlen, 0, __Pyx_DOCSTR(__pyx_k_122), 0}, + {(char *)"tags", __pyx_getprop_9csamtools_11AlignedRead_tags, __pyx_setprop_9csamtools_11AlignedRead_tags, __Pyx_DOCSTR(__pyx_k_123), 0}, + {(char *)"flag", __pyx_getprop_9csamtools_11AlignedRead_flag, __pyx_setprop_9csamtools_11AlignedRead_flag, __Pyx_DOCSTR(__pyx_k_124), 0}, + {(char *)"rname", __pyx_getprop_9csamtools_11AlignedRead_rname, __pyx_setprop_9csamtools_11AlignedRead_rname, __Pyx_DOCSTR(__pyx_k_125), 0}, + {(char *)"tid", __pyx_getprop_9csamtools_11AlignedRead_tid, __pyx_setprop_9csamtools_11AlignedRead_tid, __Pyx_DOCSTR(__pyx_k_126), 0}, + {(char *)"pos", __pyx_getprop_9csamtools_11AlignedRead_pos, __pyx_setprop_9csamtools_11AlignedRead_pos, __Pyx_DOCSTR(__pyx_k_127), 0}, + {(char *)"bin", __pyx_getprop_9csamtools_11AlignedRead_bin, __pyx_setprop_9csamtools_11AlignedRead_bin, __Pyx_DOCSTR(__pyx_k_128), 0}, + {(char *)"rlen", __pyx_getprop_9csamtools_11AlignedRead_rlen, 0, __Pyx_DOCSTR(__pyx_k_129), 0}, + {(char *)"aend", __pyx_getprop_9csamtools_11AlignedRead_aend, 0, __Pyx_DOCSTR(__pyx_k_130), 0}, + {(char *)"alen", __pyx_getprop_9csamtools_11AlignedRead_alen, 0, __Pyx_DOCSTR(__pyx_k_131), 0}, + {(char *)"mapq", __pyx_getprop_9csamtools_11AlignedRead_mapq, __pyx_setprop_9csamtools_11AlignedRead_mapq, __Pyx_DOCSTR(__pyx_k_132), 0}, + {(char *)"mrnm", __pyx_getprop_9csamtools_11AlignedRead_mrnm, __pyx_setprop_9csamtools_11AlignedRead_mrnm, __Pyx_DOCSTR(__pyx_k_133), 0}, + {(char *)"mpos", __pyx_getprop_9csamtools_11AlignedRead_mpos, __pyx_setprop_9csamtools_11AlignedRead_mpos, __Pyx_DOCSTR(__pyx_k_134), 0}, + {(char *)"isize", __pyx_getprop_9csamtools_11AlignedRead_isize, __pyx_setprop_9csamtools_11AlignedRead_isize, __Pyx_DOCSTR(__pyx_k_135), 0}, + {(char *)"is_paired", __pyx_getprop_9csamtools_11AlignedRead_is_paired, __pyx_setprop_9csamtools_11AlignedRead_is_paired, __Pyx_DOCSTR(__pyx_k_136), 0}, + {(char *)"is_proper_pair", __pyx_getprop_9csamtools_11AlignedRead_is_proper_pair, __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair, __Pyx_DOCSTR(__pyx_k_137), 0}, + {(char *)"is_unmapped", __pyx_getprop_9csamtools_11AlignedRead_is_unmapped, __pyx_setprop_9csamtools_11AlignedRead_is_unmapped, __Pyx_DOCSTR(__pyx_k_138), 0}, + {(char *)"mate_is_unmapped", __pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped, __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped, __Pyx_DOCSTR(__pyx_k_139), 0}, + {(char *)"is_reverse", __pyx_getprop_9csamtools_11AlignedRead_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_is_reverse, __Pyx_DOCSTR(__pyx_k_140), 0}, + {(char *)"mate_is_reverse", __pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse, __Pyx_DOCSTR(__pyx_k_141), 0}, + {(char *)"is_read1", __pyx_getprop_9csamtools_11AlignedRead_is_read1, __pyx_setprop_9csamtools_11AlignedRead_is_read1, __Pyx_DOCSTR(__pyx_k_142), 0}, + {(char *)"is_read2", __pyx_getprop_9csamtools_11AlignedRead_is_read2, __pyx_setprop_9csamtools_11AlignedRead_is_read2, __Pyx_DOCSTR(__pyx_k_143), 0}, + {(char *)"is_secondary", __pyx_getprop_9csamtools_11AlignedRead_is_secondary, __pyx_setprop_9csamtools_11AlignedRead_is_secondary, __Pyx_DOCSTR(__pyx_k_144), 0}, + {(char *)"is_qcfail", __pyx_getprop_9csamtools_11AlignedRead_is_qcfail, __pyx_setprop_9csamtools_11AlignedRead_is_qcfail, __Pyx_DOCSTR(__pyx_k_145), 0}, + {(char *)"is_duplicate", __pyx_getprop_9csamtools_11AlignedRead_is_duplicate, __pyx_setprop_9csamtools_11AlignedRead_is_duplicate, __Pyx_DOCSTR(__pyx_k_146), 0}, + {(char *)"positions", __pyx_getprop_9csamtools_11AlignedRead_positions, 0, __Pyx_DOCSTR(__pyx_k_147), 0}, + {0, 0, 0, 0, 0} +}; + +static PyNumberMethods __pyx_tp_as_number_AlignedRead = { + 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_AlignedRead = { + 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_AlignedRead = { + 0, /*mp_length*/ + 0, /*mp_subscript*/ + 0, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_AlignedRead = { + #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 +}; + +PyTypeObject __pyx_type_9csamtools_AlignedRead = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("csamtools.AlignedRead"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_AlignedRead), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_9csamtools_AlignedRead, /*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_AlignedRead, /*tp_as_number*/ + &__pyx_tp_as_sequence_AlignedRead, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_AlignedRead, /*tp_as_mapping*/ + __pyx_pf_9csamtools_11AlignedRead___hash__, /*tp_hash*/ + 0, /*tp_call*/ + __pyx_pf_9csamtools_11AlignedRead___str__, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_AlignedRead, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/ + __Pyx_DOCSTR("AlignedRead()\n\n Class representing an aligned read. see SAM format specification for \n the meaning of fields (http://samtools.sourceforge.net/).\n\n This class stores a handle to the samtools C-structure representing\n an aligned read. Member read access is forwarded to the C-structure\n and converted into python objects. This implementation should be fast,\n as only the data needed is converted.\n\n For write access, the C-structure is updated in-place. This is\n not the most efficient way to build BAM entries, as the variable\n length data is concatenated and thus needs to resized if\n a field is updated. Furthermore, the BAM entry might be\n in an inconsistent state. The :meth:`~validate` method can\n be used to check if an entry is consistent.\n\n One issue to look out for is that the sequence should always\n be set *before* the quality scores. Setting the sequence will\n also erase any quality scores that were set previously.\n "), /*tp_doc*/ + 0, /*tp_traverse*/ + 0, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_9csamtools_AlignedRead, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_9csamtools_AlignedRead, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_pf_9csamtools_11AlignedRead___init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_9csamtools_AlignedRead, /*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 struct __pyx_vtabstruct_9csamtools_Samfile __pyx_vtable_9csamtools_Samfile; + +static PyObject *__pyx_tp_new_9csamtools_Samfile(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_9csamtools_Samfile *p; + PyObject *o = (*t->tp_alloc)(t, 0); + if (!o) return 0; + p = ((struct __pyx_obj_9csamtools_Samfile *)o); + p->__pyx_vtab = __pyx_vtabptr_9csamtools_Samfile; + if (__pyx_pf_9csamtools_7Samfile___cinit__(o, a, k) < 0) { + Py_DECREF(o); o = 0; + } + return o; +} + +static void __pyx_tp_dealloc_9csamtools_Samfile(PyObject *o) { + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_pf_9csamtools_7Samfile___dealloc__(o); + if (PyErr_Occurred()) PyErr_WriteUnraisable(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + (*Py_TYPE(o)->tp_free)(o); +} + +static PyObject *__pyx_getprop_9csamtools_7Samfile_filename(PyObject *o, void *x) { + return __pyx_pf_9csamtools_7Samfile_8filename___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_7Samfile_nreferences(PyObject *o, void *x) { + return __pyx_pf_9csamtools_7Samfile_11nreferences___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_7Samfile_references(PyObject *o, void *x) { + return __pyx_pf_9csamtools_7Samfile_10references___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_7Samfile_lengths(PyObject *o, void *x) { + return __pyx_pf_9csamtools_7Samfile_7lengths___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_7Samfile_text(PyObject *o, void *x) { + return __pyx_pf_9csamtools_7Samfile_4text___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_7Samfile_header(PyObject *o, void *x) { + return __pyx_pf_9csamtools_7Samfile_6header___get__(o); +} + +static PyMethodDef __pyx_methods_9csamtools_Samfile[] = { + {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__isOpen)}, + {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__hasIndex)}, + {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__open)}, + {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_gettid)}, + {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_getrname)}, + {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__parseRegion)}, + {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_seek)}, + {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_tell)}, + {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_fetch)}, + {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_mate, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_mate)}, + {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_count)}, + {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_pileup)}, + {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_close)}, + {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_write)}, + {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile___enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile___enter__)}, + {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile___exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile___exit__)}, + {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__buildLine)}, + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile___next__)}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_9csamtools_Samfile[] = { + {(char *)"filename", __pyx_getprop_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_148), 0}, + {(char *)"nreferences", __pyx_getprop_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_149), 0}, + {(char *)"references", __pyx_getprop_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_150), 0}, + {(char *)"lengths", __pyx_getprop_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_151), 0}, + {(char *)"text", __pyx_getprop_9csamtools_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_152), 0}, + {(char *)"header", __pyx_getprop_9csamtools_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_153), 0}, + {0, 0, 0, 0, 0} +}; + +static PyNumberMethods __pyx_tp_as_number_Samfile = { + 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_Samfile = { + 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_Samfile = { + 0, /*mp_length*/ + 0, /*mp_subscript*/ + 0, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_Samfile = { + #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 +}; + +PyTypeObject __pyx_type_9csamtools_Samfile = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("csamtools.Samfile"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_Samfile), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_9csamtools_Samfile, /*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_Samfile, /*tp_as_number*/ + &__pyx_tp_as_sequence_Samfile, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_Samfile, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_Samfile, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/ + __Pyx_DOCSTR("*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None)*\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 :term:`BAM` output. \n Use ``h`` to output header information in text (:term:`TAM`) mode.\n\n If ``b`` is present, it must immediately follow ``r`` or ``w``. \n Valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb`` and ``wbu``. For instance, to open \n a :term:`BAM` formatted file for reading, type::\n\n f = pysam.Samfile('ex1.bam','rb')\n\n If mode is not specified, we will try to auto-detect in the order 'r', 'rb', thus both the following\n should work::\n\n f1 = pysam.Samfile('ex1.bam' )\n f2 = pysam.Samfile('ex1.bam' )\n\n If an index for a BAM file exists (.bai), it will be opened automatically. Without an index random\n access to reads via :meth:`fetch` and :meth:`pileup` is disabled.\n\n For writing, the header of a :term:`SAM` file/:term:`BAM` file can be constituted from several\n sources (see also the samtools format specification):\n\n 1. If *template* is given, the header is copied from a another *Samfile* \n (*template* must be of type *Samfile*).\n\n 2. If *header* is given, the header is built from a multi-level dictionary. The first level \n are the four types ('HD', 'SQ', ...). The second level are a list of lines, with each line \n being a list of tag-value pairs.\n\n 3. If *text* is given, new header text is copied from raw text.\n\n 4. The names (*referencenames*) and lengths (*referencelengths*) are supplied directly as lists. \n\n "), /*tp_doc*/ + 0, /*tp_traverse*/ + 0, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + __pyx_pf_9csamtools_7Samfile___iter__, /*tp_iter*/ + __pyx_pf_9csamtools_7Samfile___next__, /*tp_iternext*/ + __pyx_methods_9csamtools_Samfile, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_9csamtools_Samfile, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_9csamtools_Samfile, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + #if PY_VERSION_HEX >= 0x02060000 + 0, /*tp_version_tag*/ + #endif +}; + +static PyObject *__pyx_tp_new_9csamtools_PileupProxy(PyTypeObject *t, PyObject *a, PyObject *k) { + PyObject *o = (*t->tp_alloc)(t, 0); + if (!o) return 0; + return o; +} + +static void __pyx_tp_dealloc_9csamtools_PileupProxy(PyObject *o) { + (*Py_TYPE(o)->tp_free)(o); +} + +static PyObject *__pyx_getprop_9csamtools_11PileupProxy_tid(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11PileupProxy_3tid___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_11PileupProxy_n(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11PileupProxy_1n___get__(o); +} + +static int __pyx_setprop_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, void *x) { + if (v) { + return __pyx_pf_9csamtools_11PileupProxy_1n___set__(o, v); + } + else { + PyErr_SetString(PyExc_NotImplementedError, "__del__"); + return -1; + } +} + +static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pos(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11PileupProxy_3pos___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pileups(PyObject *o, void *x) { + return __pyx_pf_9csamtools_11PileupProxy_7pileups___get__(o); +} + +static PyMethodDef __pyx_methods_9csamtools_PileupProxy[] = { + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_9csamtools_PileupProxy[] = { + {(char *)"tid", __pyx_getprop_9csamtools_11PileupProxy_tid, 0, __Pyx_DOCSTR(__pyx_k_154), 0}, + {(char *)"n", __pyx_getprop_9csamtools_11PileupProxy_n, __pyx_setprop_9csamtools_11PileupProxy_n, __Pyx_DOCSTR(__pyx_k_155), 0}, + {(char *)"pos", __pyx_getprop_9csamtools_11PileupProxy_pos, 0, 0, 0}, + {(char *)"pileups", __pyx_getprop_9csamtools_11PileupProxy_pileups, 0, __Pyx_DOCSTR(__pyx_k_156), 0}, + {0, 0, 0, 0, 0} +}; + +static PyNumberMethods __pyx_tp_as_number_PileupProxy = { + 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_PileupProxy = { + 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_PileupProxy = { + 0, /*mp_length*/ + 0, /*mp_subscript*/ + 0, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_PileupProxy = { + #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 +}; + +PyTypeObject __pyx_type_9csamtools_PileupProxy = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("csamtools.PileupProxy"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_PileupProxy), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_9csamtools_PileupProxy, /*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_PileupProxy, /*tp_as_number*/ + &__pyx_tp_as_sequence_PileupProxy, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_PileupProxy, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + __pyx_pf_9csamtools_11PileupProxy___str__, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_PileupProxy, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/ + __Pyx_DOCSTR("PileupProxy()\nA pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column \n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n\n This class is a proxy for results returned by the samtools pileup engine.\n If the underlying engine iterator advances, the results of this column\n will change.\n "), /*tp_doc*/ + 0, /*tp_traverse*/ + 0, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_9csamtools_PileupProxy, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_9csamtools_PileupProxy, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_pf_9csamtools_11PileupProxy___init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_9csamtools_PileupProxy, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + #if PY_VERSION_HEX >= 0x02060000 + 0, /*tp_version_tag*/ + #endif +}; + +static PyObject *__pyx_tp_new_9csamtools_PileupRead(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_9csamtools_PileupRead *p; + PyObject *o = (*t->tp_alloc)(t, 0); + if (!o) return 0; + p = ((struct __pyx_obj_9csamtools_PileupRead *)o); + p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None); + return o; +} + +static void __pyx_tp_dealloc_9csamtools_PileupRead(PyObject *o) { + struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o; + Py_XDECREF(((PyObject *)p->_alignment)); + (*Py_TYPE(o)->tp_free)(o); +} + +static int __pyx_tp_traverse_9csamtools_PileupRead(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o; + if (p->_alignment) { + e = (*v)(((PyObject*)p->_alignment), a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_9csamtools_PileupRead(PyObject *o) { + struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o; + PyObject* tmp; + tmp = ((PyObject*)p->_alignment); + p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyObject *__pyx_getprop_9csamtools_10PileupRead_alignment(PyObject *o, void *x) { + return __pyx_pf_9csamtools_10PileupRead_9alignment___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_10PileupRead_qpos(PyObject *o, void *x) { + return __pyx_pf_9csamtools_10PileupRead_4qpos___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_10PileupRead_indel(PyObject *o, void *x) { + return __pyx_pf_9csamtools_10PileupRead_5indel___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_del(PyObject *o, void *x) { + return __pyx_pf_9csamtools_10PileupRead_6is_del___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_head(PyObject *o, void *x) { + return __pyx_pf_9csamtools_10PileupRead_7is_head___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_tail(PyObject *o, void *x) { + return __pyx_pf_9csamtools_10PileupRead_7is_tail___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_10PileupRead_level(PyObject *o, void *x) { + return __pyx_pf_9csamtools_10PileupRead_5level___get__(o); +} + +static PyMethodDef __pyx_methods_9csamtools_PileupRead[] = { + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_9csamtools_PileupRead[] = { + {(char *)"alignment", __pyx_getprop_9csamtools_10PileupRead_alignment, 0, __Pyx_DOCSTR(__pyx_k_157), 0}, + {(char *)"qpos", __pyx_getprop_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_158), 0}, + {(char *)"indel", __pyx_getprop_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_159), 0}, + {(char *)"is_del", __pyx_getprop_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_160), 0}, + {(char *)"is_head", __pyx_getprop_9csamtools_10PileupRead_is_head, 0, 0, 0}, + {(char *)"is_tail", __pyx_getprop_9csamtools_10PileupRead_is_tail, 0, 0, 0}, + {(char *)"level", __pyx_getprop_9csamtools_10PileupRead_level, 0, 0, 0}, + {0, 0, 0, 0, 0} +}; + +static PyNumberMethods __pyx_tp_as_number_PileupRead = { + 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_PileupRead = { + 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_PileupRead = { + 0, /*mp_length*/ + 0, /*mp_subscript*/ + 0, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_PileupRead = { + #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 +}; + +PyTypeObject __pyx_type_9csamtools_PileupRead = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("csamtools.PileupRead"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_PileupRead), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_9csamtools_PileupRead, /*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_PileupRead, /*tp_as_number*/ + &__pyx_tp_as_sequence_PileupRead, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_PileupRead, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + __pyx_pf_9csamtools_10PileupRead___str__, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_PileupRead, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + __Pyx_DOCSTR("PileupRead()\nA read aligned to a column.\n "), /*tp_doc*/ + __pyx_tp_traverse_9csamtools_PileupRead, /*tp_traverse*/ + __pyx_tp_clear_9csamtools_PileupRead, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_9csamtools_PileupRead, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_9csamtools_PileupRead, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_pf_9csamtools_10PileupRead___init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_9csamtools_PileupRead, /*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 struct __pyx_vtabstruct_9csamtools_Fastafile __pyx_vtable_9csamtools_Fastafile; + +static PyObject *__pyx_tp_new_9csamtools_Fastafile(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_9csamtools_Fastafile *p; + PyObject *o = (*t->tp_alloc)(t, 0); + if (!o) return 0; + p = ((struct __pyx_obj_9csamtools_Fastafile *)o); + p->__pyx_vtab = __pyx_vtabptr_9csamtools_Fastafile; + if (__pyx_pf_9csamtools_9Fastafile___cinit__(o, a, k) < 0) { + Py_DECREF(o); o = 0; + } + return o; +} + +static void __pyx_tp_dealloc_9csamtools_Fastafile(PyObject *o) { + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_pf_9csamtools_9Fastafile___dealloc__(o); + if (PyErr_Occurred()) PyErr_WriteUnraisable(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + (*Py_TYPE(o)->tp_free)(o); +} + +static PyObject *__pyx_getprop_9csamtools_9Fastafile_filename(PyObject *o, void *x) { + return __pyx_pf_9csamtools_9Fastafile_8filename___get__(o); +} + +static PyMethodDef __pyx_methods_9csamtools_Fastafile[] = { + {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile__isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile__isOpen)}, + {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile__open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile__open)}, + {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_close)}, + {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_fetch)}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_9csamtools_Fastafile[] = { + {(char *)"filename", __pyx_getprop_9csamtools_9Fastafile_filename, 0, __Pyx_DOCSTR(__pyx_k_148), 0}, + {0, 0, 0, 0, 0} +}; + +static PyNumberMethods __pyx_tp_as_number_Fastafile = { + 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_Fastafile = { + __pyx_pf_9csamtools_9Fastafile___len__, /*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_Fastafile = { + __pyx_pf_9csamtools_9Fastafile___len__, /*mp_length*/ + 0, /*mp_subscript*/ + 0, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_Fastafile = { + #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 +}; + +PyTypeObject __pyx_type_9csamtools_Fastafile = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("csamtools.Fastafile"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_Fastafile), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_9csamtools_Fastafile, /*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_Fastafile, /*tp_as_number*/ + &__pyx_tp_as_sequence_Fastafile, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_Fastafile, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_Fastafile, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*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*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_9csamtools_Fastafile, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_9csamtools_Fastafile, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_9csamtools_Fastafile, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + #if PY_VERSION_HEX >= 0x02060000 + 0, /*tp_version_tag*/ + #endif +}; + +static PyObject *__pyx_tp_new_9csamtools_IteratorRow(PyTypeObject *t, PyObject *a, PyObject *k) { + PyObject *o = (*t->tp_alloc)(t, 0); + if (!o) return 0; + return o; +} + +static void __pyx_tp_dealloc_9csamtools_IteratorRow(PyObject *o) { + (*Py_TYPE(o)->tp_free)(o); +} + +static PyMethodDef __pyx_methods_9csamtools_IteratorRow[] = { + {0, 0, 0, 0} +}; + +static PyNumberMethods __pyx_tp_as_number_IteratorRow = { + 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_IteratorRow = { + 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_IteratorRow = { + 0, /*mp_length*/ + 0, /*mp_subscript*/ + 0, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_IteratorRow = { + #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 +}; + +PyTypeObject __pyx_type_9csamtools_IteratorRow = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("csamtools.IteratorRow"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_IteratorRow), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_9csamtools_IteratorRow, /*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_IteratorRow, /*tp_as_number*/ + &__pyx_tp_as_sequence_IteratorRow, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_IteratorRow, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_IteratorRow, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/ + __Pyx_DOCSTR("abstract base class for iterators over mapped reads.\n\n Various iterators implement different behaviours for wrapping around\n contig boundaries. Examples include:\n\n :class:`pysam.IteratorRowRegion`\n iterate within a single contig and a defined region.\n\n :class:`pysam.IteratorRowAll`\n iterate until EOF. This iterator will also include unmapped reads.\n\n :class:`pysam.IteratorRowAllRefs`\n iterate over all reads in all reference sequences.\n \n The method :meth:`Samfile.fetch` returns an IteratorRow.\n "), /*tp_doc*/ + 0, /*tp_traverse*/ + 0, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_9csamtools_IteratorRow, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_9csamtools_IteratorRow, /*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 struct __pyx_vtabstruct_9csamtools_IteratorRowRegion __pyx_vtable_9csamtools_IteratorRowRegion; + +static PyObject *__pyx_tp_new_9csamtools_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_9csamtools_IteratorRowRegion *p; + PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k); + if (!o) return 0; + p = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)o); + p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowRegion; + p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); + if (__pyx_pf_9csamtools_17IteratorRowRegion___cinit__(o, a, k) < 0) { + Py_DECREF(o); o = 0; + } + return o; +} + +static void __pyx_tp_dealloc_9csamtools_IteratorRowRegion(PyObject *o) { + struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o; + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_pf_9csamtools_17IteratorRowRegion___dealloc__(o); + if (PyErr_Occurred()) PyErr_WriteUnraisable(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_XDECREF(((PyObject *)p->samfile)); + __pyx_tp_dealloc_9csamtools_IteratorRow(o); +} + +static int __pyx_tp_traverse_9csamtools_IteratorRowRegion(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o; + if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) { + e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e; + } + if (p->samfile) { + e = (*v)(((PyObject*)p->samfile), a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_9csamtools_IteratorRowRegion(PyObject *o) { + struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o; + PyObject* tmp; + if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) { + __pyx_ptype_9csamtools_IteratorRow->tp_clear(o); + } + tmp = ((PyObject*)p->samfile); + p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyMethodDef __pyx_methods_9csamtools_IteratorRowRegion[] = { + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_17IteratorRowRegion___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_17IteratorRowRegion___next__)}, + {0, 0, 0, 0} +}; + +static PyNumberMethods __pyx_tp_as_number_IteratorRowRegion = { + 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_IteratorRowRegion = { + 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_IteratorRowRegion = { + 0, /*mp_length*/ + 0, /*mp_subscript*/ + 0, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_IteratorRowRegion = { + #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 +}; + +PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("csamtools.IteratorRowRegion"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_IteratorRowRegion), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_9csamtools_IteratorRowRegion, /*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_IteratorRowRegion, /*tp_as_number*/ + &__pyx_tp_as_sequence_IteratorRowRegion, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_IteratorRowRegion, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_IteratorRowRegion, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + __Pyx_DOCSTR("*(Samfile samfile, int tid, int beg, int end, int reopen = True )*\n\n iterate over mapped reads in a region.\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n\n The samtools iterators assume that the file\n position between iterations do not change.\n As a consequence, no two iterators can work\n on the same file. To permit this, each iterator\n creates its own file handle by re-opening the\n file.\n\n Note that the index will be shared between \n samfile and the iterator.\n "), /*tp_doc*/ + __pyx_tp_traverse_9csamtools_IteratorRowRegion, /*tp_traverse*/ + __pyx_tp_clear_9csamtools_IteratorRowRegion, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + __pyx_pf_9csamtools_17IteratorRowRegion___iter__, /*tp_iter*/ + __pyx_pf_9csamtools_17IteratorRowRegion___next__, /*tp_iternext*/ + __pyx_methods_9csamtools_IteratorRowRegion, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_9csamtools_IteratorRowRegion, /*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 struct __pyx_vtabstruct_9csamtools_IteratorRowAll __pyx_vtable_9csamtools_IteratorRowAll; + +static PyObject *__pyx_tp_new_9csamtools_IteratorRowAll(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_9csamtools_IteratorRowAll *p; + PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k); + if (!o) return 0; + p = ((struct __pyx_obj_9csamtools_IteratorRowAll *)o); + p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowAll; + if (__pyx_pf_9csamtools_14IteratorRowAll___cinit__(o, a, k) < 0) { + Py_DECREF(o); o = 0; + } + return o; +} + +static void __pyx_tp_dealloc_9csamtools_IteratorRowAll(PyObject *o) { + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_pf_9csamtools_14IteratorRowAll___dealloc__(o); + if (PyErr_Occurred()) PyErr_WriteUnraisable(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + __pyx_tp_dealloc_9csamtools_IteratorRow(o); +} + +static PyMethodDef __pyx_methods_9csamtools_IteratorRowAll[] = { + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_14IteratorRowAll___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorRowAll___next__)}, + {0, 0, 0, 0} +}; + +static PyNumberMethods __pyx_tp_as_number_IteratorRowAll = { + 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_IteratorRowAll = { + 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_IteratorRowAll = { + 0, /*mp_length*/ + 0, /*mp_subscript*/ + 0, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAll = { + #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 +}; + +PyTypeObject __pyx_type_9csamtools_IteratorRowAll = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("csamtools.IteratorRowAll"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_IteratorRowAll), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_9csamtools_IteratorRowAll, /*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_IteratorRowAll, /*tp_as_number*/ + &__pyx_tp_as_sequence_IteratorRowAll, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_IteratorRowAll, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_IteratorRowAll, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/ + __Pyx_DOCSTR("*(Samfile samfile, int reopen = True)*\n\n iterate over all reads in *samfile*\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n "), /*tp_doc*/ + 0, /*tp_traverse*/ + 0, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + __pyx_pf_9csamtools_14IteratorRowAll___iter__, /*tp_iter*/ + __pyx_pf_9csamtools_14IteratorRowAll___next__, /*tp_iternext*/ + __pyx_methods_9csamtools_IteratorRowAll, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_9csamtools_IteratorRowAll, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + #if PY_VERSION_HEX >= 0x02060000 + 0, /*tp_version_tag*/ + #endif +}; + +static PyObject *__pyx_tp_new_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_9csamtools_IteratorRowAllRefs *p; + PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k); + if (!o) return 0; + p = ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o); + p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); + p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); + if (__pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(o, a, k) < 0) { + Py_DECREF(o); o = 0; + } + return o; +} + +static void __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs(PyObject *o) { + struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o; + Py_XDECREF(((PyObject *)p->samfile)); + Py_XDECREF(((PyObject *)p->rowiter)); + __pyx_tp_dealloc_9csamtools_IteratorRow(o); +} + +static int __pyx_tp_traverse_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o; + if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) { + e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e; + } + if (p->samfile) { + e = (*v)(((PyObject*)p->samfile), a); if (e) return e; + } + if (p->rowiter) { + e = (*v)(((PyObject*)p->rowiter), a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_9csamtools_IteratorRowAllRefs(PyObject *o) { + struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o; + PyObject* tmp; + if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) { + __pyx_ptype_9csamtools_IteratorRow->tp_clear(o); + } + tmp = ((PyObject*)p->samfile); + p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->rowiter); + p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyMethodDef __pyx_methods_9csamtools_IteratorRowAllRefs[] = { + {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_nextiter)}, + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs___next__)}, + {0, 0, 0, 0} +}; + +static PyNumberMethods __pyx_tp_as_number_IteratorRowAllRefs = { + 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_IteratorRowAllRefs = { + 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_IteratorRowAllRefs = { + 0, /*mp_length*/ + 0, /*mp_subscript*/ + 0, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = { + #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 +}; + +PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("csamtools.IteratorRowAllRefs"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs, /*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_IteratorRowAllRefs, /*tp_as_number*/ + &__pyx_tp_as_sequence_IteratorRowAllRefs, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_IteratorRowAllRefs, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_IteratorRowAllRefs, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + __Pyx_DOCSTR("iterates over all mapped reads by chaining iterators over each reference\n "), /*tp_doc*/ + __pyx_tp_traverse_9csamtools_IteratorRowAllRefs, /*tp_traverse*/ + __pyx_tp_clear_9csamtools_IteratorRowAllRefs, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + __pyx_pf_9csamtools_18IteratorRowAllRefs___iter__, /*tp_iter*/ + __pyx_pf_9csamtools_18IteratorRowAllRefs___next__, /*tp_iternext*/ + __pyx_methods_9csamtools_IteratorRowAllRefs, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_9csamtools_IteratorRowAllRefs, /*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 struct __pyx_vtabstruct_9csamtools_IteratorRowSelection __pyx_vtable_9csamtools_IteratorRowSelection; + +static PyObject *__pyx_tp_new_9csamtools_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_9csamtools_IteratorRowSelection *p; + PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k); + if (!o) return 0; + p = ((struct __pyx_obj_9csamtools_IteratorRowSelection *)o); + p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowSelection; + p->positions = Py_None; Py_INCREF(Py_None); + if (__pyx_pf_9csamtools_20IteratorRowSelection___cinit__(o, a, k) < 0) { + Py_DECREF(o); o = 0; + } + return o; +} + +static void __pyx_tp_dealloc_9csamtools_IteratorRowSelection(PyObject *o) { + struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o; + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_pf_9csamtools_20IteratorRowSelection___dealloc__(o); + if (PyErr_Occurred()) PyErr_WriteUnraisable(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_XDECREF(p->positions); + __pyx_tp_dealloc_9csamtools_IteratorRow(o); +} + +static int __pyx_tp_traverse_9csamtools_IteratorRowSelection(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o; + if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) { + e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e; + } + if (p->positions) { + e = (*v)(p->positions, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_9csamtools_IteratorRowSelection(PyObject *o) { + struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o; + PyObject* tmp; + if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) { + __pyx_ptype_9csamtools_IteratorRow->tp_clear(o); + } + tmp = ((PyObject*)p->positions); + p->positions = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyMethodDef __pyx_methods_9csamtools_IteratorRowSelection[] = { + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorRowSelection___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorRowSelection___next__)}, + {0, 0, 0, 0} +}; + +static PyNumberMethods __pyx_tp_as_number_IteratorRowSelection = { + 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_IteratorRowSelection = { + 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_IteratorRowSelection = { + 0, /*mp_length*/ + 0, /*mp_subscript*/ + 0, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_IteratorRowSelection = { + #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 +}; + +PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("csamtools.IteratorRowSelection"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_IteratorRowSelection), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_9csamtools_IteratorRowSelection, /*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_IteratorRowSelection, /*tp_as_number*/ + &__pyx_tp_as_sequence_IteratorRowSelection, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_IteratorRowSelection, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_IteratorRowSelection, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + __Pyx_DOCSTR("*(Samfile samfile)*\n\n iterate over reads in *samfile* at a given list of file positions.\n "), /*tp_doc*/ + __pyx_tp_traverse_9csamtools_IteratorRowSelection, /*tp_traverse*/ + __pyx_tp_clear_9csamtools_IteratorRowSelection, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + __pyx_pf_9csamtools_20IteratorRowSelection___iter__, /*tp_iter*/ + __pyx_pf_9csamtools_20IteratorRowSelection___next__, /*tp_iternext*/ + __pyx_methods_9csamtools_IteratorRowSelection, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_9csamtools_IteratorRowSelection, /*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 struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_vtable_9csamtools_IteratorColumn; + +static PyObject *__pyx_tp_new_9csamtools_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_9csamtools_IteratorColumn *p; + PyObject *o = (*t->tp_alloc)(t, 0); + if (!o) return 0; + p = ((struct __pyx_obj_9csamtools_IteratorColumn *)o); + p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorColumn; + p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); + p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); + p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None); + p->stepper = Py_None; Py_INCREF(Py_None); + if (__pyx_pf_9csamtools_14IteratorColumn___cinit__(o, a, k) < 0) { + Py_DECREF(o); o = 0; + } + return o; +} + +static void __pyx_tp_dealloc_9csamtools_IteratorColumn(PyObject *o) { + struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o; + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_pf_9csamtools_14IteratorColumn___dealloc__(o); + if (PyErr_Occurred()) PyErr_WriteUnraisable(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_XDECREF(((PyObject *)p->iter)); + Py_XDECREF(((PyObject *)p->samfile)); + Py_XDECREF(((PyObject *)p->fastafile)); + Py_XDECREF(p->stepper); + (*Py_TYPE(o)->tp_free)(o); +} + +static int __pyx_tp_traverse_9csamtools_IteratorColumn(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o; + if (p->iter) { + e = (*v)(((PyObject*)p->iter), a); if (e) return e; + } + if (p->samfile) { + e = (*v)(((PyObject*)p->samfile), a); if (e) return e; + } + if (p->fastafile) { + e = (*v)(((PyObject*)p->fastafile), a); if (e) return e; + } + if (p->stepper) { + e = (*v)(p->stepper, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_9csamtools_IteratorColumn(PyObject *o) { + struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o; + PyObject* tmp; + tmp = ((PyObject*)p->iter); + p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->samfile); + p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->fastafile); + p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->stepper); + p->stepper = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyObject *__pyx_getprop_9csamtools_14IteratorColumn_seq_len(PyObject *o, void *x) { + return __pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(o); +} + +static PyMethodDef __pyx_methods_9csamtools_IteratorColumn[] = { + {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_addReference)}, + {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_hasReference)}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_9csamtools_IteratorColumn[] = { + {(char *)"seq_len", __pyx_getprop_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_161), 0}, {0, 0, 0, 0, 0} }; -static PyNumberMethods __pyx_tp_as_number_PileupProxy = { +static PyNumberMethods __pyx_tp_as_number_IteratorColumn = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ @@ -28930,7 +33384,7 @@ static PyNumberMethods __pyx_tp_as_number_PileupProxy = { #endif }; -static PySequenceMethods __pyx_tp_as_sequence_PileupProxy = { +static PySequenceMethods __pyx_tp_as_sequence_IteratorColumn = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ @@ -28943,13 +33397,13 @@ static PySequenceMethods __pyx_tp_as_sequence_PileupProxy = { 0, /*sq_inplace_repeat*/ }; -static PyMappingMethods __pyx_tp_as_mapping_PileupProxy = { +static PyMappingMethods __pyx_tp_as_mapping_IteratorColumn = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; -static PyBufferProcs __pyx_tp_as_buffer_PileupProxy = { +static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif @@ -28970,12 +33424,12 @@ static PyBufferProcs __pyx_tp_as_buffer_PileupProxy = { #endif }; -static PyTypeObject __pyx_type_9csamtools_PileupProxy = { +PyTypeObject __pyx_type_9csamtools_IteratorColumn = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("csamtools.PileupProxy"), /*tp_name*/ - sizeof(struct __pyx_obj_9csamtools_PileupProxy), /*tp_basicsize*/ + __Pyx_NAMESTR("csamtools.IteratorColumn"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_IteratorColumn), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_9csamtools_PileupProxy, /*tp_dealloc*/ + __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -28985,34 +33439,34 @@ static PyTypeObject __pyx_type_9csamtools_PileupProxy = { 0, /*reserved*/ #endif 0, /*tp_repr*/ - &__pyx_tp_as_number_PileupProxy, /*tp_as_number*/ - &__pyx_tp_as_sequence_PileupProxy, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_PileupProxy, /*tp_as_mapping*/ + &__pyx_tp_as_number_IteratorColumn, /*tp_as_number*/ + &__pyx_tp_as_sequence_IteratorColumn, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_IteratorColumn, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ - __pyx_pf_9csamtools_11PileupProxy_1__str__, /*tp_str*/ + 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ - &__pyx_tp_as_buffer_PileupProxy, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ - __Pyx_DOCSTR("PileupProxy()\nA pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column \n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n\n This class is a proxy for results returned by the samtools pileup engine.\n If the underlying engine iterator advances, the results of this column\n will change.\n "), /*tp_doc*/ - 0, /*tp_traverse*/ - 0, /*tp_clear*/ + &__pyx_tp_as_buffer_IteratorColumn, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + __Pyx_DOCSTR("abstract base class for iterators over columns.\n\n IteratorColumn objects wrap the pileup functionality of samtools.\n \n For reasons of efficiency, the iterator points to the current \n pileup buffer. The pileup buffer is updated at every iteration.\n This might cause some unexpected behavious. For example,\n consider the conversion to a list::\n \n f = Samfile(\"file.bam\", \"rb\")\n result = list( f.pileup() )\n\n Here, ``result`` will contain ``n`` objects of type :class:`PileupProxy` for ``n`` columns, \n but each object in ``result`` will contain the same information.\n \n The desired behaviour can be achieved by list comprehension::\n\n result = [ x.pileups() for x in f.pileup() ]\n\n ``result`` will be a list of ``n`` lists of objects of type :class:`PileupRead`.\n\n If the iterator is associated with a :class:`Fastafile` using the :meth:`addReference`\n method, then the iterator will export the current sequence via the methods :meth:`getSequence`\n and :meth:`seq_len`.\n\n Optional kwargs to the iterator\n\n stepper\n The stepper controlls how the iterator advances. \n Possible options for the stepper are \n \n all\n use all reads for pileup.\n samtools\n same filter and read processing as in :term:`csamtools` pileup\n fastafile\n A :class:`FastaFile` object\n mask\n Skip all reads with bits set in mask.\n \n \n "), /*tp_doc*/ + __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/ + __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - 0, /*tp_iter*/ + __pyx_pf_9csamtools_14IteratorColumn___iter__, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_9csamtools_PileupProxy, /*tp_methods*/ + __pyx_methods_9csamtools_IteratorColumn, /*tp_methods*/ 0, /*tp_members*/ - __pyx_getsets_9csamtools_PileupProxy, /*tp_getset*/ + __pyx_getsets_9csamtools_IteratorColumn, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ - __pyx_pf_9csamtools_11PileupProxy___init__, /*tp_init*/ + 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_9csamtools_PileupProxy, /*tp_new*/ + __pyx_tp_new_9csamtools_IteratorColumn, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -29025,84 +33479,198 @@ static PyTypeObject __pyx_type_9csamtools_PileupProxy = { 0, /*tp_version_tag*/ #endif }; +static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion __pyx_vtable_9csamtools_IteratorColumnRegion; -static PyObject *__pyx_tp_new_9csamtools_PileupRead(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_9csamtools_PileupRead *p; - PyObject *o = (*t->tp_alloc)(t, 0); +static PyObject *__pyx_tp_new_9csamtools_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_9csamtools_IteratorColumnRegion *p; + PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k); if (!o) return 0; - p = ((struct __pyx_obj_9csamtools_PileupRead *)o); - p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None); - return o; -} - -static void __pyx_tp_dealloc_9csamtools_PileupRead(PyObject *o) { - struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o; - Py_XDECREF(((PyObject *)p->_alignment)); - (*Py_TYPE(o)->tp_free)(o); -} - -static int __pyx_tp_traverse_9csamtools_PileupRead(PyObject *o, visitproc v, void *a) { - int e; - struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o; - if (p->_alignment) { - e = (*v)(((PyObject*)p->_alignment), a); if (e) return e; + p = ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)o); + p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnRegion; + if (__pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(o, a, k) < 0) { + Py_DECREF(o); o = 0; } - return 0; -} - -static int __pyx_tp_clear_9csamtools_PileupRead(PyObject *o) { - struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o; - PyObject* tmp; - tmp = ((PyObject*)p->_alignment); - p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None); - Py_XDECREF(tmp); - return 0; + return o; } -static PyObject *__pyx_getprop_9csamtools_10PileupRead_alignment(PyObject *o, void *x) { - return __pyx_pf_9csamtools_10PileupRead_9alignment___get__(o); -} +static PyMethodDef __pyx_methods_9csamtools_IteratorColumnRegion[] = { + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorColumnRegion___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorColumnRegion___next__)}, + {0, 0, 0, 0} +}; -static PyObject *__pyx_getprop_9csamtools_10PileupRead_qpos(PyObject *o, void *x) { - return __pyx_pf_9csamtools_10PileupRead_4qpos___get__(o); -} +static PyNumberMethods __pyx_tp_as_number_IteratorColumnRegion = { + 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 PyObject *__pyx_getprop_9csamtools_10PileupRead_indel(PyObject *o, void *x) { - return __pyx_pf_9csamtools_10PileupRead_5indel___get__(o); -} +static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnRegion = { + 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 PyObject *__pyx_getprop_9csamtools_10PileupRead_is_del(PyObject *o, void *x) { - return __pyx_pf_9csamtools_10PileupRead_6is_del___get__(o); -} +static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnRegion = { + 0, /*mp_length*/ + 0, /*mp_subscript*/ + 0, /*mp_ass_subscript*/ +}; -static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_head(PyObject *o, void *x) { - return __pyx_pf_9csamtools_10PileupRead_7is_head___get__(o); -} +static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnRegion = { + #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 PyObject *__pyx_getprop_9csamtools_10PileupRead_is_tail(PyObject *o, void *x) { - return __pyx_pf_9csamtools_10PileupRead_7is_tail___get__(o); -} +PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("csamtools.IteratorColumnRegion"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_IteratorColumnRegion), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_9csamtools_IteratorColumn, /*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_IteratorColumnRegion, /*tp_as_number*/ + &__pyx_tp_as_sequence_IteratorColumnRegion, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_IteratorColumnRegion, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_IteratorColumnRegion, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + __Pyx_DOCSTR("iterates over a region only.\n "), /*tp_doc*/ + __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/ + __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + __pyx_pf_9csamtools_20IteratorColumnRegion___next__, /*tp_iternext*/ + __pyx_methods_9csamtools_IteratorColumnRegion, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_9csamtools_IteratorColumnRegion, /*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 struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs __pyx_vtable_9csamtools_IteratorColumnAllRefs; -static PyObject *__pyx_getprop_9csamtools_10PileupRead_level(PyObject *o, void *x) { - return __pyx_pf_9csamtools_10PileupRead_5level___get__(o); +static PyObject *__pyx_tp_new_9csamtools_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_9csamtools_IteratorColumnAllRefs *p; + PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k); + if (!o) return 0; + p = ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)o); + p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnAllRefs; + if (__pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(o, a, k) < 0) { + Py_DECREF(o); o = 0; + } + return o; } -static PyMethodDef __pyx_methods_9csamtools_PileupRead[] = { +static PyMethodDef __pyx_methods_9csamtools_IteratorColumnAllRefs[] = { + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_21IteratorColumnAllRefs___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs___next__)}, {0, 0, 0, 0} }; -static struct PyGetSetDef __pyx_getsets_9csamtools_PileupRead[] = { - {(char *)"alignment", __pyx_getprop_9csamtools_10PileupRead_alignment, 0, __Pyx_DOCSTR(__pyx_k_217), 0}, - {(char *)"qpos", __pyx_getprop_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_218), 0}, - {(char *)"indel", __pyx_getprop_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_219), 0}, - {(char *)"is_del", __pyx_getprop_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_220), 0}, - {(char *)"is_head", __pyx_getprop_9csamtools_10PileupRead_is_head, 0, 0, 0}, - {(char *)"is_tail", __pyx_getprop_9csamtools_10PileupRead_is_tail, 0, 0, 0}, - {(char *)"level", __pyx_getprop_9csamtools_10PileupRead_level, 0, 0, 0}, - {0, 0, 0, 0, 0} -}; - -static PyNumberMethods __pyx_tp_as_number_PileupRead = { +static PyNumberMethods __pyx_tp_as_number_IteratorColumnAllRefs = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ @@ -29160,7 +33728,7 @@ static PyNumberMethods __pyx_tp_as_number_PileupRead = { #endif }; -static PySequenceMethods __pyx_tp_as_sequence_PileupRead = { +static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnAllRefs = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ @@ -29173,13 +33741,13 @@ static PySequenceMethods __pyx_tp_as_sequence_PileupRead = { 0, /*sq_inplace_repeat*/ }; -static PyMappingMethods __pyx_tp_as_mapping_PileupRead = { +static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnAllRefs = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; -static PyBufferProcs __pyx_tp_as_buffer_PileupRead = { +static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif @@ -29200,12 +33768,12 @@ static PyBufferProcs __pyx_tp_as_buffer_PileupRead = { #endif }; -static PyTypeObject __pyx_type_9csamtools_PileupRead = { +PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("csamtools.PileupRead"), /*tp_name*/ - sizeof(struct __pyx_obj_9csamtools_PileupRead), /*tp_basicsize*/ + __Pyx_NAMESTR("csamtools.IteratorColumnAllRefs"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_IteratorColumnAllRefs), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_9csamtools_PileupRead, /*tp_dealloc*/ + __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -29215,34 +33783,34 @@ static PyTypeObject __pyx_type_9csamtools_PileupRead = { 0, /*reserved*/ #endif 0, /*tp_repr*/ - &__pyx_tp_as_number_PileupRead, /*tp_as_number*/ - &__pyx_tp_as_sequence_PileupRead, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_PileupRead, /*tp_as_mapping*/ + &__pyx_tp_as_number_IteratorColumnAllRefs, /*tp_as_number*/ + &__pyx_tp_as_sequence_IteratorColumnAllRefs, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_IteratorColumnAllRefs, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ - __pyx_pf_9csamtools_10PileupRead_1__str__, /*tp_str*/ + 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ - &__pyx_tp_as_buffer_PileupRead, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - __Pyx_DOCSTR("PileupRead()\nA read aligned to a column.\n "), /*tp_doc*/ - __pyx_tp_traverse_9csamtools_PileupRead, /*tp_traverse*/ - __pyx_tp_clear_9csamtools_PileupRead, /*tp_clear*/ + &__pyx_tp_as_buffer_IteratorColumnAllRefs, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + __Pyx_DOCSTR("iterates over all columns by chaining iterators over each reference\n "), /*tp_doc*/ + __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/ + __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ - 0, /*tp_iternext*/ - __pyx_methods_9csamtools_PileupRead, /*tp_methods*/ + __pyx_pf_9csamtools_21IteratorColumnAllRefs___next__, /*tp_iternext*/ + __pyx_methods_9csamtools_IteratorColumnAllRefs, /*tp_methods*/ 0, /*tp_members*/ - __pyx_getsets_9csamtools_PileupRead, /*tp_getset*/ + 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ - __pyx_pf_9csamtools_10PileupRead___init__, /*tp_init*/ + 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_9csamtools_PileupRead, /*tp_new*/ + __pyx_tp_new_9csamtools_IteratorColumnAllRefs, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -29255,51 +33823,66 @@ static PyTypeObject __pyx_type_9csamtools_PileupRead = { 0, /*tp_version_tag*/ #endif }; -static struct __pyx_vtabstruct_9csamtools_Fastafile __pyx_vtable_9csamtools_Fastafile; -static PyObject *__pyx_tp_new_9csamtools_Fastafile(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_9csamtools_Fastafile *p; +static PyObject *__pyx_tp_new_9csamtools_SNPCall(PyTypeObject *t, PyObject *a, PyObject *k) { PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; - p = ((struct __pyx_obj_9csamtools_Fastafile *)o); - p->__pyx_vtab = __pyx_vtabptr_9csamtools_Fastafile; - if (__pyx_pf_9csamtools_9Fastafile___cinit__(o, a, k) < 0) { - Py_DECREF(o); o = 0; - } return o; } -static void __pyx_tp_dealloc_9csamtools_Fastafile(PyObject *o) { - { - PyObject *etype, *eval, *etb; - PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); - __pyx_pf_9csamtools_9Fastafile_5__dealloc__(o); - if (PyErr_Occurred()) PyErr_WriteUnraisable(o); - --Py_REFCNT(o); - PyErr_Restore(etype, eval, etb); - } +static void __pyx_tp_dealloc_9csamtools_SNPCall(PyObject *o) { (*Py_TYPE(o)->tp_free)(o); } -static PyObject *__pyx_getprop_9csamtools_9Fastafile_filename(PyObject *o, void *x) { - return __pyx_pf_9csamtools_9Fastafile_8filename___get__(o); +static PyObject *__pyx_getprop_9csamtools_7SNPCall_tid(PyObject *o, void *x) { + return __pyx_pf_9csamtools_7SNPCall_3tid___get__(o); } -static PyMethodDef __pyx_methods_9csamtools_Fastafile[] = { - {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_1_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_1_isOpen)}, - {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_3_open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_3_open)}, - {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_4close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_4close)}, - {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_6fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_6fetch)}, +static PyObject *__pyx_getprop_9csamtools_7SNPCall_pos(PyObject *o, void *x) { + return __pyx_pf_9csamtools_7SNPCall_3pos___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_7SNPCall_reference_base(PyObject *o, void *x) { + return __pyx_pf_9csamtools_7SNPCall_14reference_base___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_7SNPCall_genotype(PyObject *o, void *x) { + return __pyx_pf_9csamtools_7SNPCall_8genotype___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_7SNPCall_consensus_quality(PyObject *o, void *x) { + return __pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_7SNPCall_snp_quality(PyObject *o, void *x) { + return __pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_7SNPCall_mapping_quality(PyObject *o, void *x) { + return __pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_7SNPCall_coverage(PyObject *o, void *x) { + return __pyx_pf_9csamtools_7SNPCall_8coverage___get__(o); +} + +static PyMethodDef __pyx_methods_9csamtools_SNPCall[] = { {0, 0, 0, 0} }; -static struct PyGetSetDef __pyx_getsets_9csamtools_Fastafile[] = { - {(char *)"filename", __pyx_getprop_9csamtools_9Fastafile_filename, 0, __Pyx_DOCSTR(__pyx_k_206), 0}, +static struct PyGetSetDef __pyx_getsets_9csamtools_SNPCall[] = { + {(char *)"tid", __pyx_getprop_9csamtools_7SNPCall_tid, 0, __Pyx_DOCSTR(__pyx_k_154), 0}, + {(char *)"pos", __pyx_getprop_9csamtools_7SNPCall_pos, 0, __Pyx_DOCSTR(__pyx_k_162), 0}, + {(char *)"reference_base", __pyx_getprop_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_163), 0}, + {(char *)"genotype", __pyx_getprop_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_164), 0}, + {(char *)"consensus_quality", __pyx_getprop_9csamtools_7SNPCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_165), 0}, + {(char *)"snp_quality", __pyx_getprop_9csamtools_7SNPCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_166), 0}, + {(char *)"mapping_quality", __pyx_getprop_9csamtools_7SNPCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_167), 0}, + {(char *)"coverage", __pyx_getprop_9csamtools_7SNPCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_168), 0}, {0, 0, 0, 0, 0} }; -static PyNumberMethods __pyx_tp_as_number_Fastafile = { +static PyNumberMethods __pyx_tp_as_number_SNPCall = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ @@ -29357,8 +33940,8 @@ static PyNumberMethods __pyx_tp_as_number_Fastafile = { #endif }; -static PySequenceMethods __pyx_tp_as_sequence_Fastafile = { - __pyx_pf_9csamtools_9Fastafile_2__len__, /*sq_length*/ +static PySequenceMethods __pyx_tp_as_sequence_SNPCall = { + 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ @@ -29370,13 +33953,13 @@ static PySequenceMethods __pyx_tp_as_sequence_Fastafile = { 0, /*sq_inplace_repeat*/ }; -static PyMappingMethods __pyx_tp_as_mapping_Fastafile = { - __pyx_pf_9csamtools_9Fastafile_2__len__, /*mp_length*/ +static PyMappingMethods __pyx_tp_as_mapping_SNPCall = { + 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; -static PyBufferProcs __pyx_tp_as_buffer_Fastafile = { +static PyBufferProcs __pyx_tp_as_buffer_SNPCall = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif @@ -29397,12 +33980,12 @@ static PyBufferProcs __pyx_tp_as_buffer_Fastafile = { #endif }; -static PyTypeObject __pyx_type_9csamtools_Fastafile = { +PyTypeObject __pyx_type_9csamtools_SNPCall = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("csamtools.Fastafile"), /*tp_name*/ - sizeof(struct __pyx_obj_9csamtools_Fastafile), /*tp_basicsize*/ + __Pyx_NAMESTR("csamtools.SNPCall"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_SNPCall), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_9csamtools_Fastafile, /*tp_dealloc*/ + __pyx_tp_dealloc_9csamtools_SNPCall, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -29412,26 +33995,26 @@ static PyTypeObject __pyx_type_9csamtools_Fastafile = { 0, /*reserved*/ #endif 0, /*tp_repr*/ - &__pyx_tp_as_number_Fastafile, /*tp_as_number*/ - &__pyx_tp_as_sequence_Fastafile, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_Fastafile, /*tp_as_mapping*/ + &__pyx_tp_as_number_SNPCall, /*tp_as_number*/ + &__pyx_tp_as_sequence_SNPCall, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_SNPCall, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ - 0, /*tp_str*/ + __pyx_pf_9csamtools_7SNPCall___str__, /*tp_str*/ 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*/ - __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*/ + &__pyx_tp_as_buffer_SNPCall, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/ + __Pyx_DOCSTR("the results of a SNP call."), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_9csamtools_Fastafile, /*tp_methods*/ + __pyx_methods_9csamtools_SNPCall, /*tp_methods*/ 0, /*tp_members*/ - __pyx_getsets_9csamtools_Fastafile, /*tp_getset*/ + __pyx_getsets_9csamtools_SNPCall, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ @@ -29439,7 +34022,7 @@ static PyTypeObject __pyx_type_9csamtools_Fastafile = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_9csamtools_Fastafile, /*tp_new*/ + __pyx_tp_new_9csamtools_SNPCall, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -29452,66 +34035,59 @@ static PyTypeObject __pyx_type_9csamtools_Fastafile = { 0, /*tp_version_tag*/ #endif }; -static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion __pyx_vtable_9csamtools_IteratorRowRegion; +static struct __pyx_vtabstruct_9csamtools_SNPCallerBase __pyx_vtable_9csamtools_SNPCallerBase; -static PyObject *__pyx_tp_new_9csamtools_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_9csamtools_IteratorRowRegion *p; - PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k); +static PyObject *__pyx_tp_new_9csamtools_SNPCallerBase(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_9csamtools_SNPCallerBase *p; + PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; - p = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)o); - p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowRegion; - p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); - if (__pyx_pf_9csamtools_17IteratorRowRegion___cinit__(o, a, k) < 0) { + p = ((struct __pyx_obj_9csamtools_SNPCallerBase *)o); + p->__pyx_vtab = __pyx_vtabptr_9csamtools_SNPCallerBase; + p->iter = ((struct __pyx_obj_9csamtools_IteratorColumn *)Py_None); Py_INCREF(Py_None); + if (__pyx_pf_9csamtools_13SNPCallerBase___cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } -static void __pyx_tp_dealloc_9csamtools_IteratorRowRegion(PyObject *o) { - struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o; +static void __pyx_tp_dealloc_9csamtools_SNPCallerBase(PyObject *o) { + struct __pyx_obj_9csamtools_SNPCallerBase *p = (struct __pyx_obj_9csamtools_SNPCallerBase *)o; { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pf_9csamtools_17IteratorRowRegion_3__dealloc__(o); + __pyx_pf_9csamtools_13SNPCallerBase___dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } - Py_XDECREF(((PyObject *)p->samfile)); - __pyx_tp_dealloc_9csamtools_IteratorRow(o); + Py_XDECREF(((PyObject *)p->iter)); + (*Py_TYPE(o)->tp_free)(o); } -static int __pyx_tp_traverse_9csamtools_IteratorRowRegion(PyObject *o, visitproc v, void *a) { +static int __pyx_tp_traverse_9csamtools_SNPCallerBase(PyObject *o, visitproc v, void *a) { int e; - struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o; - if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) { - e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e; - } - if (p->samfile) { - e = (*v)(((PyObject*)p->samfile), a); if (e) return e; + struct __pyx_obj_9csamtools_SNPCallerBase *p = (struct __pyx_obj_9csamtools_SNPCallerBase *)o; + if (p->iter) { + e = (*v)(((PyObject*)p->iter), a); if (e) return e; } return 0; } -static int __pyx_tp_clear_9csamtools_IteratorRowRegion(PyObject *o) { - struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o; +static int __pyx_tp_clear_9csamtools_SNPCallerBase(PyObject *o) { + struct __pyx_obj_9csamtools_SNPCallerBase *p = (struct __pyx_obj_9csamtools_SNPCallerBase *)o; PyObject* tmp; - if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) { - __pyx_ptype_9csamtools_IteratorRow->tp_clear(o); - } - tmp = ((PyObject*)p->samfile); - p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); + tmp = ((PyObject*)p->iter); + p->iter = ((struct __pyx_obj_9csamtools_IteratorColumn *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } -static PyMethodDef __pyx_methods_9csamtools_IteratorRowRegion[] = { - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_17IteratorRowRegion_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_17IteratorRowRegion_2__next__)}, +static PyMethodDef __pyx_methods_9csamtools_SNPCallerBase[] = { {0, 0, 0, 0} }; -static PyNumberMethods __pyx_tp_as_number_IteratorRowRegion = { +static PyNumberMethods __pyx_tp_as_number_SNPCallerBase = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ @@ -29569,7 +34145,7 @@ static PyNumberMethods __pyx_tp_as_number_IteratorRowRegion = { #endif }; -static PySequenceMethods __pyx_tp_as_sequence_IteratorRowRegion = { +static PySequenceMethods __pyx_tp_as_sequence_SNPCallerBase = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ @@ -29582,13 +34158,13 @@ static PySequenceMethods __pyx_tp_as_sequence_IteratorRowRegion = { 0, /*sq_inplace_repeat*/ }; -static PyMappingMethods __pyx_tp_as_mapping_IteratorRowRegion = { +static PyMappingMethods __pyx_tp_as_mapping_SNPCallerBase = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; -static PyBufferProcs __pyx_tp_as_buffer_IteratorRowRegion = { +static PyBufferProcs __pyx_tp_as_buffer_SNPCallerBase = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif @@ -29609,12 +34185,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorRowRegion = { #endif }; -static PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = { +PyTypeObject __pyx_type_9csamtools_SNPCallerBase = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("csamtools.IteratorRowRegion"), /*tp_name*/ - sizeof(struct __pyx_obj_9csamtools_IteratorRowRegion), /*tp_basicsize*/ + __Pyx_NAMESTR("csamtools.SNPCallerBase"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_SNPCallerBase), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_9csamtools_IteratorRowRegion, /*tp_dealloc*/ + __pyx_tp_dealloc_9csamtools_SNPCallerBase, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -29624,24 +34200,24 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = { 0, /*reserved*/ #endif 0, /*tp_repr*/ - &__pyx_tp_as_number_IteratorRowRegion, /*tp_as_number*/ - &__pyx_tp_as_sequence_IteratorRowRegion, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_IteratorRowRegion, /*tp_as_mapping*/ + &__pyx_tp_as_number_SNPCallerBase, /*tp_as_number*/ + &__pyx_tp_as_sequence_SNPCallerBase, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_SNPCallerBase, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ - &__pyx_tp_as_buffer_IteratorRowRegion, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - __Pyx_DOCSTR("*(Samfile samfile, int tid, int beg, int end, int reopen = True )*\n\n iterate over mapped reads in a region.\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n\n The samtools iterators assume that the file\n position between iterations do not change.\n As a consequence, no two iterators can work\n on the same file. To permit this, each iterator\n creates its own file handle by re-opening the\n file.\n\n Note that the index will be shared between \n samfile and the iterator.\n "), /*tp_doc*/ - __pyx_tp_traverse_9csamtools_IteratorRowRegion, /*tp_traverse*/ - __pyx_tp_clear_9csamtools_IteratorRowRegion, /*tp_clear*/ + &__pyx_tp_as_buffer_SNPCallerBase, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + __Pyx_DOCSTR("Base class for SNP callers.\n\n *min_baseQ*\n minimum base quality (possibly capped by BAQ)\n *capQ_threshold*\n coefficient for adjusting mapQ of poor mappings\n *theta*\n theta in maq consensus calling model\n *n_haplotypes*\n number of haplotypes in the sample\n *het_rate*\n prior of a difference between two haplotypes\n "), /*tp_doc*/ + __pyx_tp_traverse_9csamtools_SNPCallerBase, /*tp_traverse*/ + __pyx_tp_clear_9csamtools_SNPCallerBase, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pf_9csamtools_17IteratorRowRegion_1__iter__, /*tp_iter*/ - __pyx_pf_9csamtools_17IteratorRowRegion_2__next__, /*tp_iternext*/ - __pyx_methods_9csamtools_IteratorRowRegion, /*tp_methods*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_9csamtools_SNPCallerBase, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -29651,7 +34227,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_9csamtools_IteratorRowRegion, /*tp_new*/ + __pyx_tp_new_9csamtools_SNPCallerBase, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -29664,64 +34240,26 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = { 0, /*tp_version_tag*/ #endif }; - -static PyObject *__pyx_tp_new_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_9csamtools_IteratorRowAllRefs *p; - PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k); - if (!o) return 0; - p = ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o); - p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); - p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); - if (__pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(o, a, k) < 0) { - Py_DECREF(o); o = 0; - } - return o; -} - -static void __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs(PyObject *o) { - struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o; - Py_XDECREF(((PyObject *)p->samfile)); - Py_XDECREF(((PyObject *)p->rowiter)); - __pyx_tp_dealloc_9csamtools_IteratorRow(o); -} - -static int __pyx_tp_traverse_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) { - int e; - struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o; - if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) { - e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e; - } - if (p->samfile) { - e = (*v)(((PyObject*)p->samfile), a); if (e) return e; - } - if (p->rowiter) { - e = (*v)(((PyObject*)p->rowiter), a); if (e) return e; - } - return 0; -} - -static int __pyx_tp_clear_9csamtools_IteratorRowAllRefs(PyObject *o) { - struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o; - PyObject* tmp; - if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) { - __pyx_ptype_9csamtools_IteratorRow->tp_clear(o); +static struct __pyx_vtabstruct_9csamtools_IteratorSNPCalls __pyx_vtable_9csamtools_IteratorSNPCalls; + +static PyObject *__pyx_tp_new_9csamtools_IteratorSNPCalls(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_9csamtools_IteratorSNPCalls *p; + PyObject *o = __pyx_tp_new_9csamtools_SNPCallerBase(t, a, k); + if (!o) return 0; + p = ((struct __pyx_obj_9csamtools_IteratorSNPCalls *)o); + p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_SNPCallerBase*)__pyx_vtabptr_9csamtools_IteratorSNPCalls; + if (__pyx_pf_9csamtools_16IteratorSNPCalls___cinit__(o, a, k) < 0) { + Py_DECREF(o); o = 0; } - tmp = ((PyObject*)p->samfile); - p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); - Py_XDECREF(tmp); - tmp = ((PyObject*)p->rowiter); - p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); - Py_XDECREF(tmp); - return 0; + return o; } -static PyMethodDef __pyx_methods_9csamtools_IteratorRowAllRefs[] = { - {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_1nextiter)}, - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__)}, +static PyMethodDef __pyx_methods_9csamtools_IteratorSNPCalls[] = { + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_16IteratorSNPCalls___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_16IteratorSNPCalls___next__)}, {0, 0, 0, 0} }; -static PyNumberMethods __pyx_tp_as_number_IteratorRowAllRefs = { +static PyNumberMethods __pyx_tp_as_number_IteratorSNPCalls = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ @@ -29779,7 +34317,7 @@ static PyNumberMethods __pyx_tp_as_number_IteratorRowAllRefs = { #endif }; -static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAllRefs = { +static PySequenceMethods __pyx_tp_as_sequence_IteratorSNPCalls = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ @@ -29792,13 +34330,13 @@ static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAllRefs = { 0, /*sq_inplace_repeat*/ }; -static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAllRefs = { +static PyMappingMethods __pyx_tp_as_mapping_IteratorSNPCalls = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; -static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = { +static PyBufferProcs __pyx_tp_as_buffer_IteratorSNPCalls = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif @@ -29819,12 +34357,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = { #endif }; -static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = { +PyTypeObject __pyx_type_9csamtools_IteratorSNPCalls = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("csamtools.IteratorRowAllRefs"), /*tp_name*/ - sizeof(struct __pyx_obj_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/ + __Pyx_NAMESTR("csamtools.IteratorSNPCalls"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_IteratorSNPCalls), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs, /*tp_dealloc*/ + __pyx_tp_dealloc_9csamtools_SNPCallerBase, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -29834,24 +34372,24 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = { 0, /*reserved*/ #endif 0, /*tp_repr*/ - &__pyx_tp_as_number_IteratorRowAllRefs, /*tp_as_number*/ - &__pyx_tp_as_sequence_IteratorRowAllRefs, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_IteratorRowAllRefs, /*tp_as_mapping*/ + &__pyx_tp_as_number_IteratorSNPCalls, /*tp_as_number*/ + &__pyx_tp_as_sequence_IteratorSNPCalls, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_IteratorSNPCalls, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ - &__pyx_tp_as_buffer_IteratorRowAllRefs, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - __Pyx_DOCSTR("iterates over all mapped reads by chaining iterators over each reference\n "), /*tp_doc*/ - __pyx_tp_traverse_9csamtools_IteratorRowAllRefs, /*tp_traverse*/ - __pyx_tp_clear_9csamtools_IteratorRowAllRefs, /*tp_clear*/ + &__pyx_tp_as_buffer_IteratorSNPCalls, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + __Pyx_DOCSTR("*(IteratorColumn iterator)*\n\n call SNPs within a region.\n\n *iterator* is a pileup iterator. SNPs will be called\n on all positions returned by this iterator.\n\n This caller is fast if SNPs are called over large continuous\n regions. It is slow, if instantiated frequently and in random\n order as the sequence will have to be reloaded.\n\n "), /*tp_doc*/ + __pyx_tp_traverse_9csamtools_SNPCallerBase, /*tp_traverse*/ + __pyx_tp_clear_9csamtools_SNPCallerBase, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__, /*tp_iter*/ - __pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, /*tp_iternext*/ - __pyx_methods_9csamtools_IteratorRowAllRefs, /*tp_methods*/ + __pyx_pf_9csamtools_16IteratorSNPCalls___iter__, /*tp_iter*/ + __pyx_pf_9csamtools_16IteratorSNPCalls___next__, /*tp_iternext*/ + __pyx_methods_9csamtools_IteratorSNPCalls, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -29861,7 +34399,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_9csamtools_IteratorRowAllRefs, /*tp_new*/ + __pyx_tp_new_9csamtools_IteratorSNPCalls, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -29874,66 +34412,26 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = { 0, /*tp_version_tag*/ #endif }; -static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection __pyx_vtable_9csamtools_IteratorRowSelection; +static struct __pyx_vtabstruct_9csamtools_SNPCaller __pyx_vtable_9csamtools_SNPCaller; -static PyObject *__pyx_tp_new_9csamtools_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_9csamtools_IteratorRowSelection *p; - PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k); +static PyObject *__pyx_tp_new_9csamtools_SNPCaller(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_9csamtools_SNPCaller *p; + PyObject *o = __pyx_tp_new_9csamtools_SNPCallerBase(t, a, k); if (!o) return 0; - p = ((struct __pyx_obj_9csamtools_IteratorRowSelection *)o); - p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowSelection; - p->positions = Py_None; Py_INCREF(Py_None); - if (__pyx_pf_9csamtools_20IteratorRowSelection___cinit__(o, a, k) < 0) { + p = ((struct __pyx_obj_9csamtools_SNPCaller *)o); + p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_SNPCallerBase*)__pyx_vtabptr_9csamtools_SNPCaller; + if (__pyx_pf_9csamtools_9SNPCaller___cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } -static void __pyx_tp_dealloc_9csamtools_IteratorRowSelection(PyObject *o) { - struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o; - { - PyObject *etype, *eval, *etb; - PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); - __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(o); - if (PyErr_Occurred()) PyErr_WriteUnraisable(o); - --Py_REFCNT(o); - PyErr_Restore(etype, eval, etb); - } - Py_XDECREF(p->positions); - __pyx_tp_dealloc_9csamtools_IteratorRow(o); -} - -static int __pyx_tp_traverse_9csamtools_IteratorRowSelection(PyObject *o, visitproc v, void *a) { - int e; - struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o; - if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) { - e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e; - } - if (p->positions) { - e = (*v)(p->positions, a); if (e) return e; - } - return 0; -} - -static int __pyx_tp_clear_9csamtools_IteratorRowSelection(PyObject *o) { - struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o; - PyObject* tmp; - if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) { - __pyx_ptype_9csamtools_IteratorRow->tp_clear(o); - } - tmp = ((PyObject*)p->positions); - p->positions = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - return 0; -} - -static PyMethodDef __pyx_methods_9csamtools_IteratorRowSelection[] = { - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorRowSelection_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorRowSelection_2__next__)}, +static PyMethodDef __pyx_methods_9csamtools_SNPCaller[] = { + {__Pyx_NAMESTR("call"), (PyCFunction)__pyx_pf_9csamtools_9SNPCaller_call, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9SNPCaller_call)}, {0, 0, 0, 0} }; -static PyNumberMethods __pyx_tp_as_number_IteratorRowSelection = { +static PyNumberMethods __pyx_tp_as_number_SNPCaller = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ @@ -29991,7 +34489,7 @@ static PyNumberMethods __pyx_tp_as_number_IteratorRowSelection = { #endif }; -static PySequenceMethods __pyx_tp_as_sequence_IteratorRowSelection = { +static PySequenceMethods __pyx_tp_as_sequence_SNPCaller = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ @@ -30004,13 +34502,13 @@ static PySequenceMethods __pyx_tp_as_sequence_IteratorRowSelection = { 0, /*sq_inplace_repeat*/ }; -static PyMappingMethods __pyx_tp_as_mapping_IteratorRowSelection = { +static PyMappingMethods __pyx_tp_as_mapping_SNPCaller = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; -static PyBufferProcs __pyx_tp_as_buffer_IteratorRowSelection = { +static PyBufferProcs __pyx_tp_as_buffer_SNPCaller = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif @@ -30031,12 +34529,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorRowSelection = { #endif }; -static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = { +PyTypeObject __pyx_type_9csamtools_SNPCaller = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("csamtools.IteratorRowSelection"), /*tp_name*/ - sizeof(struct __pyx_obj_9csamtools_IteratorRowSelection), /*tp_basicsize*/ + __Pyx_NAMESTR("csamtools.SNPCaller"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_SNPCaller), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_9csamtools_IteratorRowSelection, /*tp_dealloc*/ + __pyx_tp_dealloc_9csamtools_SNPCallerBase, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -30046,24 +34544,24 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = { 0, /*reserved*/ #endif 0, /*tp_repr*/ - &__pyx_tp_as_number_IteratorRowSelection, /*tp_as_number*/ - &__pyx_tp_as_sequence_IteratorRowSelection, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_IteratorRowSelection, /*tp_as_mapping*/ + &__pyx_tp_as_number_SNPCaller, /*tp_as_number*/ + &__pyx_tp_as_sequence_SNPCaller, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_SNPCaller, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ - &__pyx_tp_as_buffer_IteratorRowSelection, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - __Pyx_DOCSTR("*(Samfile samfile)*\n\n iterate over reads in *samfile* at a given list of file positions.\n "), /*tp_doc*/ - __pyx_tp_traverse_9csamtools_IteratorRowSelection, /*tp_traverse*/ - __pyx_tp_clear_9csamtools_IteratorRowSelection, /*tp_clear*/ + &__pyx_tp_as_buffer_SNPCaller, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + __Pyx_DOCSTR("*(IteratorColumn iterator_column )*\n\n The samtools SNP caller.\n\n This object will call SNPs in *samfile* against the reference\n sequence in *fasta*.\n\n This caller is fast for calling few SNPs in selected regions.\n\n It is slow, if called over large genomic regions.\n "), /*tp_doc*/ + __pyx_tp_traverse_9csamtools_SNPCallerBase, /*tp_traverse*/ + __pyx_tp_clear_9csamtools_SNPCallerBase, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pf_9csamtools_20IteratorRowSelection_1__iter__, /*tp_iter*/ - __pyx_pf_9csamtools_20IteratorRowSelection_2__next__, /*tp_iternext*/ - __pyx_methods_9csamtools_IteratorRowSelection, /*tp_methods*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_9csamtools_SNPCaller, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -30073,7 +34571,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_9csamtools_IteratorRowSelection, /*tp_new*/ + __pyx_tp_new_9csamtools_SNPCaller, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -30086,94 +34584,98 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = { 0, /*tp_version_tag*/ #endif }; -static struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_vtable_9csamtools_IteratorColumn; -static PyObject *__pyx_tp_new_9csamtools_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_9csamtools_IteratorColumn *p; +static PyObject *__pyx_tp_new_9csamtools_IndelCall(PyTypeObject *t, PyObject *a, PyObject *k) { PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; - p = ((struct __pyx_obj_9csamtools_IteratorColumn *)o); - p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorColumn; - p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); - p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); - p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None); - p->stepper = Py_None; Py_INCREF(Py_None); - if (__pyx_pf_9csamtools_14IteratorColumn___cinit__(o, a, k) < 0) { + if (__pyx_pf_9csamtools_9IndelCall___cinit__(o, __pyx_empty_tuple, NULL) < 0) { Py_DECREF(o); o = 0; } return o; } -static void __pyx_tp_dealloc_9csamtools_IteratorColumn(PyObject *o) { - struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o; +static void __pyx_tp_dealloc_9csamtools_IndelCall(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pf_9csamtools_14IteratorColumn_4__dealloc__(o); + __pyx_pf_9csamtools_9IndelCall___dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } - Py_XDECREF(((PyObject *)p->iter)); - Py_XDECREF(((PyObject *)p->samfile)); - Py_XDECREF(((PyObject *)p->fastafile)); - Py_XDECREF(p->stepper); (*Py_TYPE(o)->tp_free)(o); } -static int __pyx_tp_traverse_9csamtools_IteratorColumn(PyObject *o, visitproc v, void *a) { - int e; - struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o; - if (p->iter) { - e = (*v)(((PyObject*)p->iter), a); if (e) return e; - } - if (p->samfile) { - e = (*v)(((PyObject*)p->samfile), a); if (e) return e; - } - if (p->fastafile) { - e = (*v)(((PyObject*)p->fastafile), a); if (e) return e; - } - if (p->stepper) { - e = (*v)(p->stepper, a); if (e) return e; - } - return 0; +static PyObject *__pyx_getprop_9csamtools_9IndelCall_tid(PyObject *o, void *x) { + return __pyx_pf_9csamtools_9IndelCall_3tid___get__(o); } -static int __pyx_tp_clear_9csamtools_IteratorColumn(PyObject *o) { - struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o; - PyObject* tmp; - tmp = ((PyObject*)p->iter); - p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); - Py_XDECREF(tmp); - tmp = ((PyObject*)p->samfile); - p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); - Py_XDECREF(tmp); - tmp = ((PyObject*)p->fastafile); - p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None); - Py_XDECREF(tmp); - tmp = ((PyObject*)p->stepper); - p->stepper = Py_None; Py_INCREF(Py_None); - Py_XDECREF(tmp); - return 0; +static PyObject *__pyx_getprop_9csamtools_9IndelCall_pos(PyObject *o, void *x) { + return __pyx_pf_9csamtools_9IndelCall_3pos___get__(o); } -static PyObject *__pyx_getprop_9csamtools_14IteratorColumn_seq_len(PyObject *o, void *x) { - return __pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(o); +static PyObject *__pyx_getprop_9csamtools_9IndelCall_genotype(PyObject *o, void *x) { + return __pyx_pf_9csamtools_9IndelCall_8genotype___get__(o); } -static PyMethodDef __pyx_methods_9csamtools_IteratorColumn[] = { - {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_2addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_2addReference)}, - {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_3hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_3hasReference)}, +static PyObject *__pyx_getprop_9csamtools_9IndelCall_consensus_quality(PyObject *o, void *x) { + return __pyx_pf_9csamtools_9IndelCall_17consensus_quality___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_9IndelCall_snp_quality(PyObject *o, void *x) { + return __pyx_pf_9csamtools_9IndelCall_11snp_quality___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_9IndelCall_mapping_quality(PyObject *o, void *x) { + return __pyx_pf_9csamtools_9IndelCall_15mapping_quality___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_9IndelCall_coverage(PyObject *o, void *x) { + return __pyx_pf_9csamtools_9IndelCall_8coverage___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_9IndelCall_first_allele(PyObject *o, void *x) { + return __pyx_pf_9csamtools_9IndelCall_12first_allele___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_9IndelCall_second_allele(PyObject *o, void *x) { + return __pyx_pf_9csamtools_9IndelCall_13second_allele___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_9IndelCall_reads_first(PyObject *o, void *x) { + return __pyx_pf_9csamtools_9IndelCall_11reads_first___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_9IndelCall_reads_second(PyObject *o, void *x) { + return __pyx_pf_9csamtools_9IndelCall_12reads_second___get__(o); +} + +static PyObject *__pyx_getprop_9csamtools_9IndelCall_reads_diff(PyObject *o, void *x) { + return __pyx_pf_9csamtools_9IndelCall_10reads_diff___get__(o); +} + +static PyMethodDef __pyx_methods_9csamtools_IndelCall[] = { {0, 0, 0, 0} }; -static struct PyGetSetDef __pyx_getsets_9csamtools_IteratorColumn[] = { - {(char *)"seq_len", __pyx_getprop_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_221), 0}, +static struct PyGetSetDef __pyx_getsets_9csamtools_IndelCall[] = { + {(char *)"tid", __pyx_getprop_9csamtools_9IndelCall_tid, 0, __Pyx_DOCSTR(__pyx_k_154), 0}, + {(char *)"pos", __pyx_getprop_9csamtools_9IndelCall_pos, 0, __Pyx_DOCSTR(__pyx_k_162), 0}, + {(char *)"genotype", __pyx_getprop_9csamtools_9IndelCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_164), 0}, + {(char *)"consensus_quality", __pyx_getprop_9csamtools_9IndelCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_165), 0}, + {(char *)"snp_quality", __pyx_getprop_9csamtools_9IndelCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_166), 0}, + {(char *)"mapping_quality", __pyx_getprop_9csamtools_9IndelCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_167), 0}, + {(char *)"coverage", __pyx_getprop_9csamtools_9IndelCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_168), 0}, + {(char *)"first_allele", __pyx_getprop_9csamtools_9IndelCall_first_allele, 0, __Pyx_DOCSTR(__pyx_k_169), 0}, + {(char *)"second_allele", __pyx_getprop_9csamtools_9IndelCall_second_allele, 0, __Pyx_DOCSTR(__pyx_k_170), 0}, + {(char *)"reads_first", __pyx_getprop_9csamtools_9IndelCall_reads_first, 0, __Pyx_DOCSTR(__pyx_k_171), 0}, + {(char *)"reads_second", __pyx_getprop_9csamtools_9IndelCall_reads_second, 0, __Pyx_DOCSTR(__pyx_k_171), 0}, + {(char *)"reads_diff", __pyx_getprop_9csamtools_9IndelCall_reads_diff, 0, __Pyx_DOCSTR(__pyx_k_171), 0}, {0, 0, 0, 0, 0} }; -static PyNumberMethods __pyx_tp_as_number_IteratorColumn = { +static PyNumberMethods __pyx_tp_as_number_IndelCall = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ @@ -30231,7 +34733,7 @@ static PyNumberMethods __pyx_tp_as_number_IteratorColumn = { #endif }; -static PySequenceMethods __pyx_tp_as_sequence_IteratorColumn = { +static PySequenceMethods __pyx_tp_as_sequence_IndelCall = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ @@ -30244,13 +34746,13 @@ static PySequenceMethods __pyx_tp_as_sequence_IteratorColumn = { 0, /*sq_inplace_repeat*/ }; -static PyMappingMethods __pyx_tp_as_mapping_IteratorColumn = { +static PyMappingMethods __pyx_tp_as_mapping_IndelCall = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; -static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = { +static PyBufferProcs __pyx_tp_as_buffer_IndelCall = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif @@ -30271,12 +34773,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = { #endif }; -static PyTypeObject __pyx_type_9csamtools_IteratorColumn = { +PyTypeObject __pyx_type_9csamtools_IndelCall = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("csamtools.IteratorColumn"), /*tp_name*/ - sizeof(struct __pyx_obj_9csamtools_IteratorColumn), /*tp_basicsize*/ + __Pyx_NAMESTR("csamtools.IndelCall"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_IndelCall), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/ + __pyx_tp_dealloc_9csamtools_IndelCall, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -30286,26 +34788,26 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumn = { 0, /*reserved*/ #endif 0, /*tp_repr*/ - &__pyx_tp_as_number_IteratorColumn, /*tp_as_number*/ - &__pyx_tp_as_sequence_IteratorColumn, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_IteratorColumn, /*tp_as_mapping*/ + &__pyx_tp_as_number_IndelCall, /*tp_as_number*/ + &__pyx_tp_as_sequence_IndelCall, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_IndelCall, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ - 0, /*tp_str*/ + __pyx_pf_9csamtools_9IndelCall___str__, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ - &__pyx_tp_as_buffer_IteratorColumn, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - __Pyx_DOCSTR("abstract base class for iterators over columns.\n\n IteratorColumn objects wrap the pileup functionality of samtools.\n \n For reasons of efficiency, the iterator points to the current \n pileup buffer. The pileup buffer is updated at every iteration.\n This might cause some unexpected behavious. For example,\n consider the conversion to a list::\n \n f = Samfile(\"file.bam\", \"rb\")\n result = list( f.pileup() )\n\n Here, ``result`` will contain ``n`` objects of type :class:`PileupProxy` for ``n`` columns, \n but each object in ``result`` will contain the same information.\n \n The desired behaviour can be achieved by list comprehension::\n\n result = [ x.pileups() for x in f.pileup() ]\n\n ``result`` will be a list of ``n`` lists of objects of type :class:`PileupRead`.\n\n If the iterator is associated with a :class:`Fastafile` using the :meth:`addReference`\n method, then the iterator will export the current sequence via the methods :meth:`getSequence`\n and :meth:`seq_len`.\n\n Optional kwargs to the iterator\n\n stepper\n The stepper controlls how the iterator advances. \n Possible options for the stepper are \n \n all\n use all reads for pileup.\n samtools\n same filter and read processing as in :term:`csamtools` pileup\n fastafile\n A :class:`FastaFile` object\n mask\n Skip all reads with bits set in mask.\n max_depth\n maximum read depth. The default is 8000.\n "), /*tp_doc*/ - __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/ - __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/ + &__pyx_tp_as_buffer_IndelCall, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/ + __Pyx_DOCSTR("the results of an indel call."), /*tp_doc*/ + 0, /*tp_traverse*/ + 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pf_9csamtools_14IteratorColumn_1__iter__, /*tp_iter*/ + 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_9csamtools_IteratorColumn, /*tp_methods*/ + __pyx_methods_9csamtools_IndelCall, /*tp_methods*/ 0, /*tp_members*/ - __pyx_getsets_9csamtools_IteratorColumn, /*tp_getset*/ + __pyx_getsets_9csamtools_IndelCall, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ @@ -30313,7 +34815,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumn = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_9csamtools_IteratorColumn, /*tp_new*/ + __pyx_tp_new_9csamtools_IndelCall, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -30326,26 +34828,58 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumn = { 0, /*tp_version_tag*/ #endif }; -static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion __pyx_vtable_9csamtools_IteratorColumnRegion; -static PyObject *__pyx_tp_new_9csamtools_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_9csamtools_IteratorColumnRegion *p; - PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k); +static PyObject *__pyx_tp_new_9csamtools_IndelCallerBase(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_9csamtools_IndelCallerBase *p; + PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; - p = ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)o); - p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnRegion; - if (__pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(o, a, k) < 0) { + p = ((struct __pyx_obj_9csamtools_IndelCallerBase *)o); + p->iter = ((struct __pyx_obj_9csamtools_IteratorColumn *)Py_None); Py_INCREF(Py_None); + if (__pyx_pf_9csamtools_15IndelCallerBase___cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } -static PyMethodDef __pyx_methods_9csamtools_IteratorColumnRegion[] = { - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorColumnRegion_1__next__)}, +static void __pyx_tp_dealloc_9csamtools_IndelCallerBase(PyObject *o) { + struct __pyx_obj_9csamtools_IndelCallerBase *p = (struct __pyx_obj_9csamtools_IndelCallerBase *)o; + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_pf_9csamtools_15IndelCallerBase___dealloc__(o); + if (PyErr_Occurred()) PyErr_WriteUnraisable(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_XDECREF(((PyObject *)p->iter)); + (*Py_TYPE(o)->tp_free)(o); +} + +static int __pyx_tp_traverse_9csamtools_IndelCallerBase(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_obj_9csamtools_IndelCallerBase *p = (struct __pyx_obj_9csamtools_IndelCallerBase *)o; + if (p->iter) { + e = (*v)(((PyObject*)p->iter), a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_9csamtools_IndelCallerBase(PyObject *o) { + struct __pyx_obj_9csamtools_IndelCallerBase *p = (struct __pyx_obj_9csamtools_IndelCallerBase *)o; + PyObject* tmp; + tmp = ((PyObject*)p->iter); + p->iter = ((struct __pyx_obj_9csamtools_IteratorColumn *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyMethodDef __pyx_methods_9csamtools_IndelCallerBase[] = { + {__Pyx_NAMESTR("_call"), (PyCFunction)__pyx_pf_9csamtools_15IndelCallerBase__call, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_15IndelCallerBase__call)}, {0, 0, 0, 0} }; -static PyNumberMethods __pyx_tp_as_number_IteratorColumnRegion = { +static PyNumberMethods __pyx_tp_as_number_IndelCallerBase = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ @@ -30403,7 +34937,7 @@ static PyNumberMethods __pyx_tp_as_number_IteratorColumnRegion = { #endif }; -static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnRegion = { +static PySequenceMethods __pyx_tp_as_sequence_IndelCallerBase = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ @@ -30416,13 +34950,13 @@ static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnRegion = { 0, /*sq_inplace_repeat*/ }; -static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnRegion = { +static PyMappingMethods __pyx_tp_as_mapping_IndelCallerBase = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; -static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnRegion = { +static PyBufferProcs __pyx_tp_as_buffer_IndelCallerBase = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif @@ -30443,12 +34977,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnRegion = { #endif }; -static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = { +PyTypeObject __pyx_type_9csamtools_IndelCallerBase = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("csamtools.IteratorColumnRegion"), /*tp_name*/ - sizeof(struct __pyx_obj_9csamtools_IteratorColumnRegion), /*tp_basicsize*/ + __Pyx_NAMESTR("csamtools.IndelCallerBase"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_IndelCallerBase), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/ + __pyx_tp_dealloc_9csamtools_IndelCallerBase, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -30458,24 +34992,24 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = { 0, /*reserved*/ #endif 0, /*tp_repr*/ - &__pyx_tp_as_number_IteratorColumnRegion, /*tp_as_number*/ - &__pyx_tp_as_sequence_IteratorColumnRegion, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_IteratorColumnRegion, /*tp_as_mapping*/ + &__pyx_tp_as_number_IndelCallerBase, /*tp_as_number*/ + &__pyx_tp_as_sequence_IndelCallerBase, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_IndelCallerBase, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ - &__pyx_tp_as_buffer_IteratorColumnRegion, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - __Pyx_DOCSTR("iterates over a region only.\n "), /*tp_doc*/ - __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/ - __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/ + &__pyx_tp_as_buffer_IndelCallerBase, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + __Pyx_DOCSTR("Base class for SNP callers.\n\n *min_baseQ*\n minimum base quality (possibly capped by BAQ)\n *capQ_threshold*\n coefficient for adjusting mapQ of poor mappings\n *theta*\n theta in maq consensus calling model\n *n_haplotypes*\n number of haplotypes in the sample\n *het_rate*\n prior of a difference between two haplotypes\n "), /*tp_doc*/ + __pyx_tp_traverse_9csamtools_IndelCallerBase, /*tp_traverse*/ + __pyx_tp_clear_9csamtools_IndelCallerBase, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ - __pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, /*tp_iternext*/ - __pyx_methods_9csamtools_IteratorColumnRegion, /*tp_methods*/ + 0, /*tp_iternext*/ + __pyx_methods_9csamtools_IndelCallerBase, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -30485,7 +35019,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_9csamtools_IteratorColumnRegion, /*tp_new*/ + __pyx_tp_new_9csamtools_IndelCallerBase, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -30498,26 +35032,22 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = { 0, /*tp_version_tag*/ #endif }; -static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs __pyx_vtable_9csamtools_IteratorColumnAllRefs; -static PyObject *__pyx_tp_new_9csamtools_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_9csamtools_IteratorColumnAllRefs *p; - PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k); +static PyObject *__pyx_tp_new_9csamtools_IndelCaller(PyTypeObject *t, PyObject *a, PyObject *k) { + PyObject *o = __pyx_tp_new_9csamtools_IndelCallerBase(t, a, k); if (!o) return 0; - p = ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)o); - p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnAllRefs; - if (__pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(o, a, k) < 0) { + if (__pyx_pf_9csamtools_11IndelCaller___cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } -static PyMethodDef __pyx_methods_9csamtools_IteratorColumnAllRefs[] = { - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__)}, +static PyMethodDef __pyx_methods_9csamtools_IndelCaller[] = { + {__Pyx_NAMESTR("call"), (PyCFunction)__pyx_pf_9csamtools_11IndelCaller_call, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11IndelCaller_call)}, {0, 0, 0, 0} }; -static PyNumberMethods __pyx_tp_as_number_IteratorColumnAllRefs = { +static PyNumberMethods __pyx_tp_as_number_IndelCaller = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ @@ -30575,7 +35105,7 @@ static PyNumberMethods __pyx_tp_as_number_IteratorColumnAllRefs = { #endif }; -static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnAllRefs = { +static PySequenceMethods __pyx_tp_as_sequence_IndelCaller = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ @@ -30588,13 +35118,13 @@ static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnAllRefs = { 0, /*sq_inplace_repeat*/ }; -static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnAllRefs = { +static PyMappingMethods __pyx_tp_as_mapping_IndelCaller = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; -static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = { +static PyBufferProcs __pyx_tp_as_buffer_IndelCaller = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif @@ -30615,12 +35145,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = { #endif }; -static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = { +PyTypeObject __pyx_type_9csamtools_IndelCaller = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("csamtools.IteratorColumnAllRefs"), /*tp_name*/ - sizeof(struct __pyx_obj_9csamtools_IteratorColumnAllRefs), /*tp_basicsize*/ + __Pyx_NAMESTR("csamtools.IndelCaller"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_IndelCaller), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/ + __pyx_tp_dealloc_9csamtools_IndelCallerBase, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -30630,24 +35160,24 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = { 0, /*reserved*/ #endif 0, /*tp_repr*/ - &__pyx_tp_as_number_IteratorColumnAllRefs, /*tp_as_number*/ - &__pyx_tp_as_sequence_IteratorColumnAllRefs, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_IteratorColumnAllRefs, /*tp_as_mapping*/ + &__pyx_tp_as_number_IndelCaller, /*tp_as_number*/ + &__pyx_tp_as_sequence_IndelCaller, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_IndelCaller, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ - &__pyx_tp_as_buffer_IteratorColumnAllRefs, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - __Pyx_DOCSTR("iterates over all columns by chaining iterators over each reference\n "), /*tp_doc*/ - __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/ - __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/ + &__pyx_tp_as_buffer_IndelCaller, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + __Pyx_DOCSTR("*(IteratorColumn iterator_column )*\n\n The samtools SNP caller.\n\n This object will call SNPs in *samfile* against the reference\n sequence in *fasta*.\n\n This caller is fast for calling few SNPs in selected regions.\n\n It is slow, if called over large genomic regions.\n "), /*tp_doc*/ + __pyx_tp_traverse_9csamtools_IndelCallerBase, /*tp_traverse*/ + __pyx_tp_clear_9csamtools_IndelCallerBase, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ - __pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, /*tp_iternext*/ - __pyx_methods_9csamtools_IteratorColumnAllRefs, /*tp_methods*/ + 0, /*tp_iternext*/ + __pyx_methods_9csamtools_IndelCaller, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -30657,7 +35187,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_9csamtools_IteratorColumnAllRefs, /*tp_new*/ + __pyx_tp_new_9csamtools_IndelCaller, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -30671,65 +35201,21 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = { #endif }; -static PyObject *__pyx_tp_new_9csamtools_SNPCall(PyTypeObject *t, PyObject *a, PyObject *k) { - PyObject *o = (*t->tp_alloc)(t, 0); +static PyObject *__pyx_tp_new_9csamtools_IteratorIndelCalls(PyTypeObject *t, PyObject *a, PyObject *k) { + PyObject *o = __pyx_tp_new_9csamtools_IndelCallerBase(t, a, k); if (!o) return 0; + if (__pyx_pf_9csamtools_18IteratorIndelCalls___cinit__(o, a, k) < 0) { + Py_DECREF(o); o = 0; + } return o; } -static void __pyx_tp_dealloc_9csamtools_SNPCall(PyObject *o) { - (*Py_TYPE(o)->tp_free)(o); -} - -static PyObject *__pyx_getprop_9csamtools_7SNPCall_tid(PyObject *o, void *x) { - return __pyx_pf_9csamtools_7SNPCall_3tid___get__(o); -} - -static PyObject *__pyx_getprop_9csamtools_7SNPCall_pos(PyObject *o, void *x) { - return __pyx_pf_9csamtools_7SNPCall_3pos___get__(o); -} - -static PyObject *__pyx_getprop_9csamtools_7SNPCall_reference_base(PyObject *o, void *x) { - return __pyx_pf_9csamtools_7SNPCall_14reference_base___get__(o); -} - -static PyObject *__pyx_getprop_9csamtools_7SNPCall_genotype(PyObject *o, void *x) { - return __pyx_pf_9csamtools_7SNPCall_8genotype___get__(o); -} - -static PyObject *__pyx_getprop_9csamtools_7SNPCall_consensus_quality(PyObject *o, void *x) { - return __pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(o); -} - -static PyObject *__pyx_getprop_9csamtools_7SNPCall_snp_quality(PyObject *o, void *x) { - return __pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(o); -} - -static PyObject *__pyx_getprop_9csamtools_7SNPCall_mapping_quality(PyObject *o, void *x) { - return __pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(o); -} - -static PyObject *__pyx_getprop_9csamtools_7SNPCall_coverage(PyObject *o, void *x) { - return __pyx_pf_9csamtools_7SNPCall_8coverage___get__(o); -} - -static PyMethodDef __pyx_methods_9csamtools_SNPCall[] = { +static PyMethodDef __pyx_methods_9csamtools_IteratorIndelCalls[] = { + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorIndelCalls___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorIndelCalls___next__)}, {0, 0, 0, 0} }; -static struct PyGetSetDef __pyx_getsets_9csamtools_SNPCall[] = { - {(char *)"tid", __pyx_getprop_9csamtools_7SNPCall_tid, 0, __Pyx_DOCSTR(__pyx_k_214), 0}, - {(char *)"pos", __pyx_getprop_9csamtools_7SNPCall_pos, 0, __Pyx_DOCSTR(__pyx_k_222), 0}, - {(char *)"reference_base", __pyx_getprop_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_223), 0}, - {(char *)"genotype", __pyx_getprop_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_224), 0}, - {(char *)"consensus_quality", __pyx_getprop_9csamtools_7SNPCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_225), 0}, - {(char *)"snp_quality", __pyx_getprop_9csamtools_7SNPCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_226), 0}, - {(char *)"mapping_quality", __pyx_getprop_9csamtools_7SNPCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_227), 0}, - {(char *)"coverage", __pyx_getprop_9csamtools_7SNPCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_228), 0}, - {0, 0, 0, 0, 0} -}; - -static PyNumberMethods __pyx_tp_as_number_SNPCall = { +static PyNumberMethods __pyx_tp_as_number_IteratorIndelCalls = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ @@ -30787,7 +35273,7 @@ static PyNumberMethods __pyx_tp_as_number_SNPCall = { #endif }; -static PySequenceMethods __pyx_tp_as_sequence_SNPCall = { +static PySequenceMethods __pyx_tp_as_sequence_IteratorIndelCalls = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ @@ -30800,13 +35286,13 @@ static PySequenceMethods __pyx_tp_as_sequence_SNPCall = { 0, /*sq_inplace_repeat*/ }; -static PyMappingMethods __pyx_tp_as_mapping_SNPCall = { +static PyMappingMethods __pyx_tp_as_mapping_IteratorIndelCalls = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; -static PyBufferProcs __pyx_tp_as_buffer_SNPCall = { +static PyBufferProcs __pyx_tp_as_buffer_IteratorIndelCalls = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif @@ -30827,12 +35313,12 @@ static PyBufferProcs __pyx_tp_as_buffer_SNPCall = { #endif }; -static PyTypeObject __pyx_type_9csamtools_SNPCall = { +PyTypeObject __pyx_type_9csamtools_IteratorIndelCalls = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("csamtools.SNPCall"), /*tp_name*/ - sizeof(struct __pyx_obj_9csamtools_SNPCall), /*tp_basicsize*/ + __Pyx_NAMESTR("csamtools.IteratorIndelCalls"), /*tp_name*/ + sizeof(struct __pyx_obj_9csamtools_IteratorIndelCalls), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_9csamtools_SNPCall, /*tp_dealloc*/ + __pyx_tp_dealloc_9csamtools_IndelCallerBase, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -30842,26 +35328,26 @@ static PyTypeObject __pyx_type_9csamtools_SNPCall = { 0, /*reserved*/ #endif 0, /*tp_repr*/ - &__pyx_tp_as_number_SNPCall, /*tp_as_number*/ - &__pyx_tp_as_sequence_SNPCall, /*tp_as_sequence*/ - &__pyx_tp_as_mapping_SNPCall, /*tp_as_mapping*/ + &__pyx_tp_as_number_IteratorIndelCalls, /*tp_as_number*/ + &__pyx_tp_as_sequence_IteratorIndelCalls, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_IteratorIndelCalls, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ - __pyx_pf_9csamtools_7SNPCall___str__, /*tp_str*/ + 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ - &__pyx_tp_as_buffer_SNPCall, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ - __Pyx_DOCSTR("the results of a SNP call."), /*tp_doc*/ - 0, /*tp_traverse*/ - 0, /*tp_clear*/ + &__pyx_tp_as_buffer_IteratorIndelCalls, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + __Pyx_DOCSTR("*(IteratorColumn iterator)*\n\n call indels within a region.\n\n *iterator* is a pileup iterator. 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It is slow, if instantiated frequently and in random\n order as the sequence will have to be reloaded.\n\n "), /*tp_doc*/ + __pyx_tp_traverse_9csamtools_IndelCallerBase, /*tp_traverse*/ + __pyx_tp_clear_9csamtools_IndelCallerBase, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - 0, /*tp_iter*/ - 0, /*tp_iternext*/ - __pyx_methods_9csamtools_SNPCall, /*tp_methods*/ + __pyx_pf_9csamtools_18IteratorIndelCalls___iter__, /*tp_iter*/ + __pyx_pf_9csamtools_18IteratorIndelCalls___next__, /*tp_iternext*/ + __pyx_methods_9csamtools_IteratorIndelCalls, /*tp_methods*/ 0, /*tp_members*/ - __pyx_getsets_9csamtools_SNPCall, /*tp_getset*/ + 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ @@ -30869,7 +35355,7 @@ static PyTypeObject __pyx_type_9csamtools_SNPCall = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_9csamtools_SNPCall, /*tp_new*/ + __pyx_tp_new_9csamtools_IteratorIndelCalls, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -30899,7 +35385,7 @@ static void __pyx_tp_dealloc_9csamtools_IndexedReads(PyObject *o) { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(o); + __pyx_pf_9csamtools_12IndexedReads___dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); @@ -30934,8 +35420,8 @@ static int __pyx_tp_clear_9csamtools_IndexedReads(PyObject *o) { } static PyMethodDef __pyx_methods_9csamtools_IndexedReads[] = { - {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_1build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_1build)}, - {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_2find, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_2find)}, + {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_build)}, + {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_find, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_find)}, {0, 0, 0, 0} }; @@ -31037,7 +35523,7 @@ static PyBufferProcs __pyx_tp_as_buffer_IndexedReads = { #endif }; -static PyTypeObject __pyx_type_9csamtools_IndexedReads = { +PyTypeObject __pyx_type_9csamtools_IndexedReads = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("csamtools.IndexedReads"), /*tp_name*/ sizeof(struct __pyx_obj_9csamtools_IndexedReads), /*tp_basicsize*/ @@ -31061,7 +35547,7 @@ static PyTypeObject __pyx_type_9csamtools_IndexedReads = { 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_IndexedReads, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("IndexedReads(Samfile samfile, int reopen=True)\nindex a bamfile by read.\n\n The index is kept in memory.\n\n By default, the file is re-openend to avoid conflicts if\n multiple operators work on the same file. 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{&__pyx_kp_s_96, __pyx_k_96, sizeof(__pyx_k_96), 0, 0, 1, 0}, {&__pyx_kp_s_97, __pyx_k_97, sizeof(__pyx_k_97), 0, 0, 1, 0}, - {&__pyx_kp_s_98, __pyx_k_98, sizeof(__pyx_k_98), 0, 0, 1, 0}, - {&__pyx_kp_s_99, __pyx_k_99, sizeof(__pyx_k_99), 0, 0, 1, 0}, {&__pyx_n_s__A, __pyx_k__A, sizeof(__pyx_k__A), 0, 0, 1, 1}, {&__pyx_n_s__AS, __pyx_k__AS, sizeof(__pyx_k__AS), 0, 0, 1, 1}, {&__pyx_n_s__AlignedRead, __pyx_k__AlignedRead, sizeof(__pyx_k__AlignedRead), 0, 0, 1, 1}, - {&__pyx_n_s__AttributeError, __pyx_k__AttributeError, sizeof(__pyx_k__AttributeError), 0, 0, 1, 1}, {&__pyx_n_s__C, __pyx_k__C, sizeof(__pyx_k__C), 0, 0, 1, 1}, {&__pyx_n_s__CL, __pyx_k__CL, sizeof(__pyx_k__CL), 0, 0, 1, 1}, {&__pyx_n_s__CN, __pyx_k__CN, sizeof(__pyx_k__CN), 0, 0, 1, 1}, @@ -31236,16 +35769,21 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__I, __pyx_k__I, sizeof(__pyx_k__I), 0, 0, 1, 1}, {&__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__IndelCaller, __pyx_k__IndelCaller, sizeof(__pyx_k__IndelCaller), 0, 0, 1, 1}, {&__pyx_n_s__IndexedReads, __pyx_k__IndexedReads, sizeof(__pyx_k__IndexedReads), 0, 0, 1, 1}, {&__pyx_n_s__IntType, __pyx_k__IntType, sizeof(__pyx_k__IntType), 0, 0, 1, 1}, {&__pyx_n_s__IteratorColumn, __pyx_k__IteratorColumn, sizeof(__pyx_k__IteratorColumn), 0, 0, 1, 1}, + {&__pyx_n_s__IteratorIndelCalls, __pyx_k__IteratorIndelCalls, sizeof(__pyx_k__IteratorIndelCalls), 0, 0, 1, 1}, {&__pyx_n_s__IteratorRow, __pyx_k__IteratorRow, sizeof(__pyx_k__IteratorRow), 0, 0, 1, 1}, + {&__pyx_n_s__IteratorRowAll, __pyx_k__IteratorRowAll, sizeof(__pyx_k__IteratorRowAll), 0, 0, 1, 1}, + {&__pyx_n_s__IteratorRowAllRefs, __pyx_k__IteratorRowAllRefs, sizeof(__pyx_k__IteratorRowAllRefs), 0, 0, 1, 1}, + {&__pyx_n_s__IteratorRowRegion, __pyx_k__IteratorRowRegion, sizeof(__pyx_k__IteratorRowRegion), 0, 0, 1, 1}, + {&__pyx_n_s__IteratorSNPCalls, __pyx_k__IteratorSNPCalls, sizeof(__pyx_k__IteratorSNPCalls), 0, 0, 1, 1}, {&__pyx_n_s__KeyError, __pyx_k__KeyError, sizeof(__pyx_k__KeyError), 0, 0, 1, 1}, {&__pyx_n_s__LB, __pyx_k__LB, sizeof(__pyx_k__LB), 0, 0, 1, 1}, {&__pyx_n_s__LN, __pyx_k__LN, sizeof(__pyx_k__LN), 0, 0, 1, 1}, {&__pyx_n_s__M5, __pyx_k__M5, sizeof(__pyx_k__M5), 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_CREAT, __pyx_k__O_CREAT, sizeof(__pyx_k__O_CREAT), 0, 0, 1, 1}, {&__pyx_n_s__O_WRONLY, __pyx_k__O_WRONLY, sizeof(__pyx_k__O_WRONLY), 0, 0, 1, 1}, {&__pyx_n_s__Outs, __pyx_k__Outs, sizeof(__pyx_k__Outs), 0, 0, 1, 1}, @@ -31262,6 +35800,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__S, __pyx_k__S, sizeof(__pyx_k__S), 0, 0, 1, 1}, {&__pyx_n_s__SM, __pyx_k__SM, sizeof(__pyx_k__SM), 0, 0, 1, 1}, {&__pyx_n_s__SN, __pyx_k__SN, sizeof(__pyx_k__SN), 0, 0, 1, 1}, + {&__pyx_n_s__SNPCaller, __pyx_k__SNPCaller, sizeof(__pyx_k__SNPCaller), 0, 0, 1, 1}, {&__pyx_n_s__SO, __pyx_k__SO, sizeof(__pyx_k__SO), 0, 0, 1, 1}, {&__pyx_n_s__SP, __pyx_k__SP, sizeof(__pyx_k__SP), 0, 0, 1, 1}, {&__pyx_n_s__SQ, __pyx_k__SQ, sizeof(__pyx_k__SQ), 0, 0, 1, 1}, @@ -31285,11 +35824,13 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s____getattribute__, __pyx_k____getattribute__, sizeof(__pyx_k____getattribute__), 0, 0, 1, 1}, {&__pyx_n_s____init__, __pyx_k____init__, sizeof(__pyx_k____init__), 0, 0, 1, 1}, {&__pyx_n_s____main__, __pyx_k____main__, sizeof(__pyx_k____main__), 0, 0, 1, 1}, + {&__pyx_n_s____next__, __pyx_k____next__, sizeof(__pyx_k____next__), 0, 0, 1, 1}, {&__pyx_n_s____str__, __pyx_k____str__, sizeof(__pyx_k____str__), 0, 0, 1, 1}, {&__pyx_n_s____test__, __pyx_k____test__, sizeof(__pyx_k____test__), 0, 0, 1, 1}, {&__pyx_n_s___alignment, __pyx_k___alignment, sizeof(__pyx_k___alignment), 0, 0, 1, 1}, {&__pyx_n_s___buildHeader, __pyx_k___buildHeader, sizeof(__pyx_k___buildHeader), 0, 0, 1, 1}, {&__pyx_n_s___buildLine, __pyx_k___buildLine, sizeof(__pyx_k___buildLine), 0, 0, 1, 1}, + {&__pyx_n_s___call, __pyx_k___call, sizeof(__pyx_k___call), 0, 0, 1, 1}, {&__pyx_n_s___consensus_quality, __pyx_k___consensus_quality, sizeof(__pyx_k___consensus_quality), 0, 0, 1, 1}, {&__pyx_n_s___coverage, __pyx_k___coverage, sizeof(__pyx_k___coverage), 0, 0, 1, 1}, {&__pyx_n_s___delegate, __pyx_k___delegate, sizeof(__pyx_k___delegate), 0, 0, 1, 1}, @@ -31307,23 +35848,26 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s___parseRegion, __pyx_k___parseRegion, sizeof(__pyx_k___parseRegion), 0, 0, 1, 1}, {&__pyx_n_s___pos, __pyx_k___pos, sizeof(__pyx_k___pos), 0, 0, 1, 1}, {&__pyx_n_s___qpos, __pyx_k___qpos, sizeof(__pyx_k___qpos), 0, 0, 1, 1}, + {&__pyx_n_s___r, __pyx_k___r, sizeof(__pyx_k___r), 0, 0, 1, 1}, {&__pyx_n_s___reference_base, __pyx_k___reference_base, sizeof(__pyx_k___reference_base), 0, 0, 1, 1}, {&__pyx_n_s___samtools_dispatch, __pyx_k___samtools_dispatch, sizeof(__pyx_k___samtools_dispatch), 0, 0, 1, 1}, {&__pyx_n_s___snp_quality, __pyx_k___snp_quality, sizeof(__pyx_k___snp_quality), 0, 0, 1, 1}, {&__pyx_n_s___tid, __pyx_k___tid, sizeof(__pyx_k___tid), 0, 0, 1, 1}, - {&__pyx_n_s__add_sq_text, __pyx_k__add_sq_text, sizeof(__pyx_k__add_sq_text), 0, 0, 1, 1}, + {&__pyx_n_s__addReference, __pyx_k__addReference, sizeof(__pyx_k__addReference), 0, 0, 1, 1}, {&__pyx_n_s__alignment, __pyx_k__alignment, sizeof(__pyx_k__alignment), 0, 0, 1, 1}, {&__pyx_n_s__all, __pyx_k__all, sizeof(__pyx_k__all), 0, 0, 1, 1}, - {&__pyx_n_s__append, __pyx_k__append, sizeof(__pyx_k__append), 0, 0, 1, 1}, {&__pyx_n_s__args, __pyx_k__args, sizeof(__pyx_k__args), 0, 0, 1, 1}, {&__pyx_n_s__b, __pyx_k__b, sizeof(__pyx_k__b), 0, 0, 1, 1}, {&__pyx_n_s__bam, __pyx_k__bam, sizeof(__pyx_k__bam), 0, 0, 1, 1}, {&__pyx_n_s__beg, __pyx_k__beg, sizeof(__pyx_k__beg), 0, 0, 1, 1}, {&__pyx_n_s__bin, __pyx_k__bin, sizeof(__pyx_k__bin), 0, 0, 1, 1}, {&__pyx_n_s__bqual, __pyx_k__bqual, sizeof(__pyx_k__bqual), 0, 0, 1, 1}, + {&__pyx_n_s__build, __pyx_k__build, sizeof(__pyx_k__build), 0, 0, 1, 1}, {&__pyx_n_s__c, __pyx_k__c, sizeof(__pyx_k__c), 0, 0, 1, 1}, {&__pyx_n_s__calcsize, __pyx_k__calcsize, sizeof(__pyx_k__calcsize), 0, 0, 1, 1}, + {&__pyx_n_s__call, __pyx_k__call, sizeof(__pyx_k__call), 0, 0, 1, 1}, {&__pyx_n_s__callback, __pyx_k__callback, sizeof(__pyx_k__callback), 0, 0, 1, 1}, + {&__pyx_n_s__cap_mapQ, __pyx_k__cap_mapQ, sizeof(__pyx_k__cap_mapQ), 0, 0, 1, 1}, {&__pyx_n_s__catch_stderr, __pyx_k__catch_stderr, sizeof(__pyx_k__catch_stderr), 0, 0, 1, 1}, {&__pyx_n_s__catch_stdout, __pyx_k__catch_stdout, sizeof(__pyx_k__catch_stdout), 0, 0, 1, 1}, {&__pyx_n_s__chr, __pyx_k__chr, sizeof(__pyx_k__chr), 0, 0, 1, 1}, @@ -31331,11 +35875,15 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__close, __pyx_k__close, sizeof(__pyx_k__close), 0, 0, 1, 1}, {&__pyx_n_s__cmp, __pyx_k__cmp, sizeof(__pyx_k__cmp), 0, 0, 1, 1}, {&__pyx_n_s__cnext, __pyx_k__cnext, sizeof(__pyx_k__cnext), 0, 0, 1, 1}, + {&__pyx_n_s__cnt1, __pyx_k__cnt1, sizeof(__pyx_k__cnt1), 0, 0, 1, 1}, + {&__pyx_n_s__cnt2, __pyx_k__cnt2, sizeof(__pyx_k__cnt2), 0, 0, 1, 1}, + {&__pyx_n_s__cnt_anti, __pyx_k__cnt_anti, sizeof(__pyx_k__cnt_anti), 0, 0, 1, 1}, {&__pyx_n_s__collections, __pyx_k__collections, sizeof(__pyx_k__collections), 0, 0, 1, 1}, + {&__pyx_n_s__compare, __pyx_k__compare, sizeof(__pyx_k__compare), 0, 0, 1, 1}, {&__pyx_n_s__consensus_quality, __pyx_k__consensus_quality, sizeof(__pyx_k__consensus_quality), 0, 0, 1, 1}, {&__pyx_n_s__core, __pyx_k__core, sizeof(__pyx_k__core), 0, 0, 1, 1}, + {&__pyx_n_s__count, __pyx_k__count, sizeof(__pyx_k__count), 0, 0, 1, 1}, {&__pyx_n_s__coverage, __pyx_k__coverage, sizeof(__pyx_k__coverage), 0, 0, 1, 1}, - {&__pyx_n_s__csamtools, __pyx_k__csamtools, sizeof(__pyx_k__csamtools), 0, 0, 1, 1}, {&__pyx_n_s__ctypes, __pyx_k__ctypes, sizeof(__pyx_k__ctypes), 0, 0, 1, 1}, {&__pyx_n_s__current_pos, __pyx_k__current_pos, sizeof(__pyx_k__current_pos), 0, 0, 1, 1}, {&__pyx_n_s__d, __pyx_k__d, sizeof(__pyx_k__d), 0, 0, 1, 1}, @@ -31346,25 +35894,35 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__dup, __pyx_k__dup, sizeof(__pyx_k__dup), 0, 0, 1, 1}, {&__pyx_n_s__dup2, __pyx_k__dup2, sizeof(__pyx_k__dup2), 0, 0, 1, 1}, {&__pyx_n_s__end, __pyx_k__end, sizeof(__pyx_k__end), 0, 0, 1, 1}, + {&__pyx_n_s__errmod, __pyx_k__errmod, sizeof(__pyx_k__errmod), 0, 0, 1, 1}, {&__pyx_n_s__exc_type, __pyx_k__exc_type, sizeof(__pyx_k__exc_type), 0, 0, 1, 1}, {&__pyx_n_s__exc_value, __pyx_k__exc_value, sizeof(__pyx_k__exc_value), 0, 0, 1, 1}, {&__pyx_n_s__exists, __pyx_k__exists, sizeof(__pyx_k__exists), 0, 0, 1, 1}, {&__pyx_n_s__f, __pyx_k__f, sizeof(__pyx_k__f), 0, 0, 1, 1}, + {&__pyx_n_s__fancy_str, __pyx_k__fancy_str, sizeof(__pyx_k__fancy_str), 0, 0, 1, 1}, {&__pyx_n_s__fastafile, __pyx_k__fastafile, sizeof(__pyx_k__fastafile), 0, 0, 1, 1}, {&__pyx_n_s__fd, __pyx_k__fd, sizeof(__pyx_k__fd), 0, 0, 1, 1}, + {&__pyx_n_s__fetch, __pyx_k__fetch, sizeof(__pyx_k__fetch), 0, 0, 1, 1}, {&__pyx_n_s__fields, __pyx_k__fields, sizeof(__pyx_k__fields), 0, 0, 1, 1}, {&__pyx_n_s__filename, __pyx_k__filename, sizeof(__pyx_k__filename), 0, 0, 1, 1}, {&__pyx_n_s__fileno, __pyx_k__fileno, sizeof(__pyx_k__fileno), 0, 0, 1, 1}, + {&__pyx_n_s__first_allele, __pyx_k__first_allele, sizeof(__pyx_k__first_allele), 0, 0, 1, 1}, {&__pyx_n_s__flag, __pyx_k__flag, sizeof(__pyx_k__flag), 0, 0, 1, 1}, {&__pyx_n_s__flush, __pyx_k__flush, sizeof(__pyx_k__flush), 0, 0, 1, 1}, {&__pyx_n_s__fp, __pyx_k__fp, sizeof(__pyx_k__fp), 0, 0, 1, 1}, {&__pyx_n_s__genotype, __pyx_k__genotype, sizeof(__pyx_k__genotype), 0, 0, 1, 1}, + {&__pyx_n_s__getSequence, __pyx_k__getSequence, sizeof(__pyx_k__getSequence), 0, 0, 1, 1}, + {&__pyx_n_s__getrname, __pyx_k__getrname, sizeof(__pyx_k__getrname), 0, 0, 1, 1}, {&__pyx_n_s__gettid, __pyx_k__gettid, sizeof(__pyx_k__gettid), 0, 0, 1, 1}, + {&__pyx_n_s__hasReference, __pyx_k__hasReference, sizeof(__pyx_k__hasReference), 0, 0, 1, 1}, {&__pyx_n_s__hash, __pyx_k__hash, sizeof(__pyx_k__hash), 0, 0, 1, 1}, {&__pyx_n_s__header, __pyx_k__header, sizeof(__pyx_k__header), 0, 0, 1, 1}, + {&__pyx_n_s__het_rate, __pyx_k__het_rate, sizeof(__pyx_k__het_rate), 0, 0, 1, 1}, {&__pyx_n_s__i, __pyx_k__i, sizeof(__pyx_k__i), 0, 0, 1, 1}, {&__pyx_n_s__id, __pyx_k__id, sizeof(__pyx_k__id), 0, 0, 1, 1}, {&__pyx_n_s__indel, __pyx_k__indel, sizeof(__pyx_k__indel), 0, 0, 1, 1}, + {&__pyx_n_s__indel1, __pyx_k__indel1, sizeof(__pyx_k__indel1), 0, 0, 1, 1}, + {&__pyx_n_s__indel2, __pyx_k__indel2, sizeof(__pyx_k__indel2), 0, 0, 1, 1}, {&__pyx_n_s__index, __pyx_k__index, sizeof(__pyx_k__index), 0, 0, 1, 1}, {&__pyx_n_s__is_del, __pyx_k__is_del, sizeof(__pyx_k__is_del), 0, 0, 1, 1}, {&__pyx_n_s__is_head, __pyx_k__is_head, sizeof(__pyx_k__is_head), 0, 0, 1, 1}, @@ -31372,9 +35930,9 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__isbam, __pyx_k__isbam, sizeof(__pyx_k__isbam), 0, 0, 1, 1}, {&__pyx_n_s__isize, __pyx_k__isize, sizeof(__pyx_k__isize), 0, 0, 1, 1}, {&__pyx_n_s__isremote, __pyx_k__isremote, sizeof(__pyx_k__isremote), 0, 0, 1, 1}, - {&__pyx_n_s__isstream, __pyx_k__isstream, sizeof(__pyx_k__isstream), 0, 0, 1, 1}, {&__pyx_n_s__isupper, __pyx_k__isupper, sizeof(__pyx_k__isupper), 0, 0, 1, 1}, {&__pyx_n_s__iter, __pyx_k__iter, sizeof(__pyx_k__iter), 0, 0, 1, 1}, + {&__pyx_n_s__iterator_column, __pyx_k__iterator_column, sizeof(__pyx_k__iterator_column), 0, 0, 1, 1}, {&__pyx_n_s__iterdata, __pyx_k__iterdata, sizeof(__pyx_k__iterdata), 0, 0, 1, 1}, {&__pyx_n_s__itertools, __pyx_k__itertools, sizeof(__pyx_k__itertools), 0, 0, 1, 1}, {&__pyx_n_s__join, __pyx_k__join, sizeof(__pyx_k__join), 0, 0, 1, 1}, @@ -31391,6 +35949,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__mate, __pyx_k__mate, sizeof(__pyx_k__mate), 0, 0, 1, 1}, {&__pyx_n_s__max_depth, __pyx_k__max_depth, sizeof(__pyx_k__max_depth), 0, 0, 1, 1}, {&__pyx_n_s__method, __pyx_k__method, sizeof(__pyx_k__method), 0, 0, 1, 1}, + {&__pyx_n_s__min_baseQ, __pyx_k__min_baseQ, sizeof(__pyx_k__min_baseQ), 0, 0, 1, 1}, {&__pyx_n_s__mkstemp, __pyx_k__mkstemp, sizeof(__pyx_k__mkstemp), 0, 0, 1, 1}, {&__pyx_n_s__mode, __pyx_k__mode, sizeof(__pyx_k__mode), 0, 0, 1, 1}, {&__pyx_n_s__mpos, __pyx_k__mpos, sizeof(__pyx_k__mpos), 0, 0, 1, 1}, @@ -31398,6 +35957,8 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__mtid, __pyx_k__mtid, sizeof(__pyx_k__mtid), 0, 0, 1, 1}, {&__pyx_n_s__n, __pyx_k__n, sizeof(__pyx_k__n), 0, 0, 1, 1}, {&__pyx_n_s__n_cigar, __pyx_k__n_cigar, sizeof(__pyx_k__n_cigar), 0, 0, 1, 1}, + {&__pyx_n_s__n_hap, __pyx_k__n_hap, sizeof(__pyx_k__n_hap), 0, 0, 1, 1}, + {&__pyx_n_s__n_haplotypes, __pyx_k__n_haplotypes, sizeof(__pyx_k__n_haplotypes), 0, 0, 1, 1}, {&__pyx_n_s__n_plp, __pyx_k__n_plp, sizeof(__pyx_k__n_plp), 0, 0, 1, 1}, {&__pyx_n_s__n_pu, __pyx_k__n_pu, sizeof(__pyx_k__n_pu), 0, 0, 1, 1}, {&__pyx_n_s__n_targets, __pyx_k__n_targets, sizeof(__pyx_k__n_targets), 0, 0, 1, 1}, @@ -31407,10 +35968,14 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__object, __pyx_k__object, sizeof(__pyx_k__object), 0, 0, 1, 1}, {&__pyx_n_s__offset, __pyx_k__offset, sizeof(__pyx_k__offset), 0, 0, 1, 1}, {&__pyx_n_s__open, __pyx_k__open, sizeof(__pyx_k__open), 0, 0, 1, 1}, + {&__pyx_n_s__opt, __pyx_k__opt, sizeof(__pyx_k__opt), 0, 0, 1, 1}, + {&__pyx_n_s__options, __pyx_k__options, sizeof(__pyx_k__options), 0, 0, 1, 1}, {&__pyx_n_s__os, __pyx_k__os, sizeof(__pyx_k__os), 0, 0, 1, 1}, + {&__pyx_n_s__overlap, __pyx_k__overlap, sizeof(__pyx_k__overlap), 0, 0, 1, 1}, {&__pyx_n_s__owns_samfile, __pyx_k__owns_samfile, sizeof(__pyx_k__owns_samfile), 0, 0, 1, 1}, {&__pyx_n_s__pack_into, __pyx_k__pack_into, sizeof(__pyx_k__pack_into), 0, 0, 1, 1}, {&__pyx_n_s__path, __pyx_k__path, sizeof(__pyx_k__path), 0, 0, 1, 1}, + {&__pyx_n_s__pileup, __pyx_k__pileup, sizeof(__pyx_k__pileup), 0, 0, 1, 1}, {&__pyx_n_s__pileup_iter, __pyx_k__pileup_iter, sizeof(__pyx_k__pileup_iter), 0, 0, 1, 1}, {&__pyx_n_s__pileups, __pyx_k__pileups, sizeof(__pyx_k__pileups), 0, 0, 1, 1}, {&__pyx_n_s__platform, __pyx_k__platform, sizeof(__pyx_k__platform), 0, 0, 1, 1}, @@ -31418,17 +35983,25 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__port, __pyx_k__port, sizeof(__pyx_k__port), 0, 0, 1, 1}, {&__pyx_n_s__pos, __pyx_k__pos, sizeof(__pyx_k__pos), 0, 0, 1, 1}, {&__pyx_n_s__positions, __pyx_k__positions, sizeof(__pyx_k__positions), 0, 0, 1, 1}, + {&__pyx_n_s__q_cns, __pyx_k__q_cns, sizeof(__pyx_k__q_cns), 0, 0, 1, 1}, + {&__pyx_n_s__q_indel, __pyx_k__q_indel, sizeof(__pyx_k__q_indel), 0, 0, 1, 1}, + {&__pyx_n_s__q_r, __pyx_k__q_r, sizeof(__pyx_k__q_r), 0, 0, 1, 1}, + {&__pyx_n_s__q_ref, __pyx_k__q_ref, sizeof(__pyx_k__q_ref), 0, 0, 1, 1}, {&__pyx_n_s__qname, __pyx_k__qname, sizeof(__pyx_k__qname), 0, 0, 1, 1}, {&__pyx_n_s__qpos, __pyx_k__qpos, sizeof(__pyx_k__qpos), 0, 0, 1, 1}, {&__pyx_n_s__qseq, __pyx_k__qseq, sizeof(__pyx_k__qseq), 0, 0, 1, 1}, {&__pyx_n_s__qual, __pyx_k__qual, sizeof(__pyx_k__qual), 0, 0, 1, 1}, {&__pyx_n_s__r, __pyx_k__r, sizeof(__pyx_k__r), 0, 0, 1, 1}, - {&__pyx_n_s__rU, __pyx_k__rU, sizeof(__pyx_k__rU), 0, 0, 1, 1}, + {&__pyx_n_s__r_indel, __pyx_k__r_indel, sizeof(__pyx_k__r_indel), 0, 0, 1, 1}, + {&__pyx_n_s__range, __pyx_k__range, sizeof(__pyx_k__range), 0, 0, 1, 1}, {&__pyx_n_s__raw, __pyx_k__raw, sizeof(__pyx_k__raw), 0, 0, 1, 1}, {&__pyx_n_s__rb, __pyx_k__rb, sizeof(__pyx_k__rb), 0, 0, 1, 1}, {&__pyx_n_s__re, __pyx_k__re, sizeof(__pyx_k__re), 0, 0, 1, 1}, {&__pyx_n_s__readAndRelease, __pyx_k__readAndRelease, sizeof(__pyx_k__readAndRelease), 0, 0, 1, 1}, {&__pyx_n_s__readlines, __pyx_k__readlines, sizeof(__pyx_k__readlines), 0, 0, 1, 1}, + {&__pyx_n_s__reads_diff, __pyx_k__reads_diff, sizeof(__pyx_k__reads_diff), 0, 0, 1, 1}, + {&__pyx_n_s__reads_first, __pyx_k__reads_first, sizeof(__pyx_k__reads_first), 0, 0, 1, 1}, + {&__pyx_n_s__reads_second, __pyx_k__reads_second, sizeof(__pyx_k__reads_second), 0, 0, 1, 1}, {&__pyx_n_s__record, __pyx_k__record, sizeof(__pyx_k__record), 0, 0, 1, 1}, {&__pyx_n_s__reference, __pyx_k__reference, sizeof(__pyx_k__reference), 0, 0, 1, 1}, {&__pyx_n_s__reference_base, __pyx_k__reference_base, sizeof(__pyx_k__reference_base), 0, 0, 1, 1}, @@ -31438,6 +36011,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__release, __pyx_k__release, sizeof(__pyx_k__release), 0, 0, 1, 1}, {&__pyx_n_s__remove, __pyx_k__remove, sizeof(__pyx_k__remove), 0, 0, 1, 1}, {&__pyx_n_s__reopen, __pyx_k__reopen, sizeof(__pyx_k__reopen), 0, 0, 1, 1}, + {&__pyx_n_s__reset, __pyx_k__reset, sizeof(__pyx_k__reset), 0, 0, 1, 1}, {&__pyx_n_s__restore, __pyx_k__restore, sizeof(__pyx_k__restore), 0, 0, 1, 1}, {&__pyx_n_s__retval, __pyx_k__retval, sizeof(__pyx_k__retval), 0, 0, 1, 1}, {&__pyx_n_s__rg2lib, __pyx_k__rg2lib, sizeof(__pyx_k__rg2lib), 0, 0, 1, 1}, @@ -31447,6 +36021,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__s, __pyx_k__s, sizeof(__pyx_k__s), 0, 0, 1, 1}, {&__pyx_n_s__samfile, __pyx_k__samfile, sizeof(__pyx_k__samfile), 0, 0, 1, 1}, {&__pyx_n_s__samtools, __pyx_k__samtools, sizeof(__pyx_k__samtools), 0, 0, 1, 1}, + {&__pyx_n_s__second_allele, __pyx_k__second_allele, sizeof(__pyx_k__second_allele), 0, 0, 1, 1}, {&__pyx_n_s__seek, __pyx_k__seek, sizeof(__pyx_k__seek), 0, 0, 1, 1}, {&__pyx_n_s__self, __pyx_k__self, sizeof(__pyx_k__self), 0, 0, 1, 1}, {&__pyx_n_s__seq, __pyx_k__seq, sizeof(__pyx_k__seq), 0, 0, 1, 1}, @@ -31458,7 +36033,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__snp_quality, __pyx_k__snp_quality, sizeof(__pyx_k__snp_quality), 0, 0, 1, 1}, {&__pyx_n_s__split, __pyx_k__split, sizeof(__pyx_k__split), 0, 0, 1, 1}, {&__pyx_n_s__start, __pyx_k__start, sizeof(__pyx_k__start), 0, 0, 1, 1}, - {&__pyx_n_s__start_offset, __pyx_k__start_offset, sizeof(__pyx_k__start_offset), 0, 0, 1, 1}, {&__pyx_n_s__startswith, __pyx_k__startswith, sizeof(__pyx_k__startswith), 0, 0, 1, 1}, {&__pyx_n_s__stderr, __pyx_k__stderr, sizeof(__pyx_k__stderr), 0, 0, 1, 1}, {&__pyx_n_s__stderr_f, __pyx_k__stderr_f, sizeof(__pyx_k__stderr_f), 0, 0, 1, 1}, @@ -31474,9 +36048,11 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__tags, __pyx_k__tags, sizeof(__pyx_k__tags), 0, 0, 1, 1}, {&__pyx_n_s__target_len, __pyx_k__target_len, sizeof(__pyx_k__target_len), 0, 0, 1, 1}, {&__pyx_n_s__target_name, __pyx_k__target_name, sizeof(__pyx_k__target_name), 0, 0, 1, 1}, + {&__pyx_n_s__tell, __pyx_k__tell, sizeof(__pyx_k__tell), 0, 0, 1, 1}, {&__pyx_n_s__tempfile, __pyx_k__tempfile, sizeof(__pyx_k__tempfile), 0, 0, 1, 1}, {&__pyx_n_s__template, __pyx_k__template, sizeof(__pyx_k__template), 0, 0, 1, 1}, {&__pyx_n_s__text, __pyx_k__text, sizeof(__pyx_k__text), 0, 0, 1, 1}, + {&__pyx_n_s__theta, __pyx_k__theta, sizeof(__pyx_k__theta), 0, 0, 1, 1}, {&__pyx_n_s__tid, __pyx_k__tid, sizeof(__pyx_k__tid), 0, 0, 1, 1}, {&__pyx_n_s__traceback, __pyx_k__traceback, sizeof(__pyx_k__traceback), 0, 0, 1, 1}, {&__pyx_n_s__types, __pyx_k__types, sizeof(__pyx_k__types), 0, 0, 1, 1}, @@ -31497,2025 +36073,1641 @@ static int __Pyx_InitCachedBuiltins(void) { __pyx_builtin_map = __Pyx_GetName(__pyx_b, __pyx_n_s__map); if (!__pyx_builtin_map) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __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 = 271; __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 = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_OverflowError = __Pyx_GetName(__pyx_b, __pyx_n_s__OverflowError); if (!__pyx_builtin_OverflowError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_NotImplementedError = __Pyx_GetName(__pyx_b, __pyx_n_s__NotImplementedError); if (!__pyx_builtin_NotImplementedError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 721; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_OSError = __Pyx_GetName(__pyx_b, __pyx_n_s__OSError); if (!__pyx_builtin_OSError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_AttributeError = __Pyx_GetName(__pyx_b, __pyx_n_s__AttributeError); if (!__pyx_builtin_AttributeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_KeyError = __Pyx_GetName(__pyx_b, __pyx_n_s__KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_StopIteration = __Pyx_GetName(__pyx_b, 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int __pyx_t_5; + #if CYTHON_REFNANNY + void* __pyx_refnanny = NULL; + __Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny"); + if (!__Pyx_RefNanny) { + PyErr_Clear(); + __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny"); + if (!__Pyx_RefNanny) + Py_FatalError("failed to import 'refnanny' module"); + } + __pyx_refnanny = __Pyx_RefNanny->SetupContext("PyMODINIT_FUNC PyInit_csamtools(void)", __LINE__, __FILE__); + #endif + __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #ifdef __pyx_binding_PyCFunctionType_USED + if (__pyx_binding_PyCFunctionType_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + /*--- Library function declarations ---*/ + /*--- Threads initialization code ---*/ + #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS + #ifdef WITH_THREAD /* Python build with threading support? */ + PyEval_InitThreads(); + #endif + #endif + /*--- Module creation code ---*/ + #if PY_MAJOR_VERSION < 3 + __pyx_m = Py_InitModule4(__Pyx_NAMESTR("csamtools"), __pyx_methods, 0, 0, PYTHON_API_VERSION); + #else + __pyx_m = PyModule_Create(&__pyx_moduledef); + #endif + if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + #if PY_MAJOR_VERSION < 3 + Py_INCREF(__pyx_m); + #endif + __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); + if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + /*--- Initialize various global constants etc. ---*/ + if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__pyx_module_is_main_csamtools) { + if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + } + /*--- Builtin init code ---*/ + if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*--- Global init code ---*/ + /*--- Function export code ---*/ + /*--- Type init code ---*/ + __pyx_ptype_9csamtools_file = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "file", sizeof(PyFileObject), 0); if (unlikely(!__pyx_ptype_9csamtools_file)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1867; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + { + PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1867; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { + __pyx_wrapperbase_9csamtools_11AlignedRead___str__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_11AlignedRead___str__.doc = __pyx_doc_9csamtools_11AlignedRead___str__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_11AlignedRead___str__; + } + } + if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1867; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_AlignedRead = &__pyx_type_9csamtools_AlignedRead; + __pyx_vtabptr_9csamtools_Samfile = &__pyx_vtable_9csamtools_Samfile; + #if PY_MAJOR_VERSION >= 3 + __pyx_vtable_9csamtools_Samfile._buildHeader = (bam_header_t *(*)(struct __pyx_obj_9csamtools_Samfile *, PyObject *))__pyx_f_9csamtools_7Samfile__buildHeader; + __pyx_vtable_9csamtools_Samfile.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_getCurrent; + __pyx_vtable_9csamtools_Samfile.cnext = (int (*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_cnext; + __pyx_vtable_9csamtools_Samfile.write = (int (*)(struct __pyx_obj_9csamtools_Samfile *, struct __pyx_obj_9csamtools_AlignedRead *, int __pyx_skip_dispatch))__pyx_f_9csamtools_7Samfile_write; + __pyx_vtable_9csamtools_Samfile._getrname = (char *(*)(struct __pyx_obj_9csamtools_Samfile *, int))__pyx_f_9csamtools_7Samfile__getrname; + #else + *(void(**)(void))&__pyx_vtable_9csamtools_Samfile._buildHeader = (void(*)(void))__pyx_f_9csamtools_7Samfile__buildHeader; + *(void(**)(void))&__pyx_vtable_9csamtools_Samfile.getCurrent = (void(*)(void))__pyx_f_9csamtools_7Samfile_getCurrent; + *(void(**)(void))&__pyx_vtable_9csamtools_Samfile.cnext = (void(*)(void))__pyx_f_9csamtools_7Samfile_cnext; + *(void(**)(void))&__pyx_vtable_9csamtools_Samfile.write = (void(*)(void))__pyx_f_9csamtools_7Samfile_write; + *(void(**)(void))&__pyx_vtable_9csamtools_Samfile._getrname = (void(*)(void))__pyx_f_9csamtools_7Samfile__getrname; + #endif + if (PyType_Ready(&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + { + PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { + __pyx_wrapperbase_9csamtools_7Samfile___next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_7Samfile___next__.doc = __pyx_doc_9csamtools_7Samfile___next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_7Samfile___next__; + } + } + if (__Pyx_SetVtable(__pyx_type_9csamtools_Samfile.tp_dict, __pyx_vtabptr_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_Samfile = &__pyx_type_9csamtools_Samfile; + if (PyType_Ready(&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "PileupProxy", (PyObject *)&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_PileupProxy = &__pyx_type_9csamtools_PileupProxy; + if (PyType_Ready(&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2654; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2654; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_PileupRead = &__pyx_type_9csamtools_PileupRead; + __pyx_vtabptr_9csamtools_Fastafile = &__pyx_vtable_9csamtools_Fastafile; + #if PY_MAJOR_VERSION >= 3 + __pyx_vtable_9csamtools_Fastafile._fetch = (char *(*)(struct __pyx_obj_9csamtools_Fastafile *, char *, int, int, int *))__pyx_f_9csamtools_9Fastafile__fetch; + #else + *(void(**)(void))&__pyx_vtable_9csamtools_Fastafile._fetch = (void(*)(void))__pyx_f_9csamtools_9Fastafile__fetch; + #endif + if (PyType_Ready(&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetVtable(__pyx_type_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_Fastafile = &__pyx_type_9csamtools_Fastafile; + if (PyType_Ready(&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_IteratorRow = &__pyx_type_9csamtools_IteratorRow; + __pyx_vtabptr_9csamtools_IteratorRowRegion = &__pyx_vtable_9csamtools_IteratorRowRegion; + #if PY_MAJOR_VERSION >= 3 + __pyx_vtable_9csamtools_IteratorRowRegion.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_getCurrent; + __pyx_vtable_9csamtools_IteratorRowRegion.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_cnext; + #else + *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowRegion.getCurrent = (void(*)(void))__pyx_f_9csamtools_17IteratorRowRegion_getCurrent; + *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowRegion.cnext = (void(*)(void))__pyx_f_9csamtools_17IteratorRowRegion_cnext; + #endif + __pyx_type_9csamtools_IteratorRowRegion.tp_base = __pyx_ptype_9csamtools_IteratorRow; + if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + { + PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { + __pyx_wrapperbase_9csamtools_17IteratorRowRegion___next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_17IteratorRowRegion___next__.doc = __pyx_doc_9csamtools_17IteratorRowRegion___next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_17IteratorRowRegion___next__; + } + } + if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "IteratorRowRegion", (PyObject *)&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_IteratorRowRegion = &__pyx_type_9csamtools_IteratorRowRegion; + __pyx_vtabptr_9csamtools_IteratorRowAll = &__pyx_vtable_9csamtools_IteratorRowAll; + #if PY_MAJOR_VERSION >= 3 + __pyx_vtable_9csamtools_IteratorRowAll.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_getCurrent; + __pyx_vtable_9csamtools_IteratorRowAll.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_cnext; + #else + *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowAll.getCurrent = (void(*)(void))__pyx_f_9csamtools_14IteratorRowAll_getCurrent; + *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowAll.cnext = (void(*)(void))__pyx_f_9csamtools_14IteratorRowAll_cnext; + #endif + __pyx_type_9csamtools_IteratorRowAll.tp_base = __pyx_ptype_9csamtools_IteratorRow; + if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + { + PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { + __pyx_wrapperbase_9csamtools_14IteratorRowAll___next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_14IteratorRowAll___next__.doc = __pyx_doc_9csamtools_14IteratorRowAll___next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_14IteratorRowAll___next__; + } + } + if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAll", (PyObject *)&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_IteratorRowAll = &__pyx_type_9csamtools_IteratorRowAll; + __pyx_type_9csamtools_IteratorRowAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorRow; + if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + { + PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { + __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs___next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs___next__.doc = __pyx_doc_9csamtools_18IteratorRowAllRefs___next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs___next__; + } + } + if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_IteratorRowAllRefs = &__pyx_type_9csamtools_IteratorRowAllRefs; + __pyx_vtabptr_9csamtools_IteratorRowSelection = &__pyx_vtable_9csamtools_IteratorRowSelection; + #if PY_MAJOR_VERSION >= 3 + __pyx_vtable_9csamtools_IteratorRowSelection.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_getCurrent; + __pyx_vtable_9csamtools_IteratorRowSelection.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_cnext; + #else + *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowSelection.getCurrent = (void(*)(void))__pyx_f_9csamtools_20IteratorRowSelection_getCurrent; + *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowSelection.cnext = (void(*)(void))__pyx_f_9csamtools_20IteratorRowSelection_cnext; + #endif + __pyx_type_9csamtools_IteratorRowSelection.tp_base = __pyx_ptype_9csamtools_IteratorRow; + if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + { + PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { + __pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__.doc = __pyx_doc_9csamtools_20IteratorRowSelection___next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__; + } + } + if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "IteratorRowSelection", (PyObject *)&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_IteratorRowSelection = &__pyx_type_9csamtools_IteratorRowSelection; + __pyx_vtabptr_9csamtools_IteratorColumn = &__pyx_vtable_9csamtools_IteratorColumn; + #if PY_MAJOR_VERSION >= 3 + __pyx_vtable_9csamtools_IteratorColumn.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_cnext; + __pyx_vtable_9csamtools_IteratorColumn.getSequence = (char *(*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_getSequence; + __pyx_vtable_9csamtools_IteratorColumn.setMask = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_setMask; + __pyx_vtable_9csamtools_IteratorColumn.setupIteratorData = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args))__pyx_f_9csamtools_14IteratorColumn_setupIteratorData; + __pyx_vtable_9csamtools_IteratorColumn.reset = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_reset; + #else + *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.cnext = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_cnext; + *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.getSequence = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_getSequence; + *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.setMask = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_setMask; + *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.setupIteratorData = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_setupIteratorData; + *(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.reset = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_reset; + #endif + if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1542; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1542; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1542; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_IteratorColumn = &__pyx_type_9csamtools_IteratorColumn; + __pyx_vtabptr_9csamtools_IteratorColumnRegion = &__pyx_vtable_9csamtools_IteratorColumnRegion; + __pyx_vtable_9csamtools_IteratorColumnRegion.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn; + __pyx_type_9csamtools_IteratorColumnRegion.tp_base = __pyx_ptype_9csamtools_IteratorColumn; + if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + { + PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { + __pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__.doc = __pyx_doc_9csamtools_20IteratorColumnRegion___next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__; + } + } + if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_IteratorColumnRegion = &__pyx_type_9csamtools_IteratorColumnRegion; + __pyx_vtabptr_9csamtools_IteratorColumnAllRefs = &__pyx_vtable_9csamtools_IteratorColumnAllRefs; + __pyx_vtable_9csamtools_IteratorColumnAllRefs.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn; + __pyx_type_9csamtools_IteratorColumnAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorColumn; + if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + { + PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { + __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs___next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs___next__.doc = __pyx_doc_9csamtools_21IteratorColumnAllRefs___next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs___next__; + } + } + if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnAllRefs.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_IteratorColumnAllRefs = &__pyx_type_9csamtools_IteratorColumnAllRefs; + if (PyType_Ready(&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2816; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "SNPCall", (PyObject *)&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2816; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_SNPCall = &__pyx_type_9csamtools_SNPCall; + __pyx_vtabptr_9csamtools_SNPCallerBase = &__pyx_vtable_9csamtools_SNPCallerBase; + #if PY_MAJOR_VERSION >= 3 + __pyx_vtable_9csamtools_SNPCallerBase.__dump = (PyObject *(*)(struct __pyx_obj_9csamtools_SNPCallerBase *, glf1_t *, uint32_t, int))__pyx_f_9csamtools_13SNPCallerBase___dump; + #else + *(void(**)(void))&__pyx_vtable_9csamtools_SNPCallerBase.__dump = (void(*)(void))__pyx_f_9csamtools_13SNPCallerBase___dump; + #endif + if (PyType_Ready(&__pyx_type_9csamtools_SNPCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2873; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetVtable(__pyx_type_9csamtools_SNPCallerBase.tp_dict, __pyx_vtabptr_9csamtools_SNPCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2873; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "SNPCallerBase", (PyObject *)&__pyx_type_9csamtools_SNPCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2873; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_SNPCallerBase = &__pyx_type_9csamtools_SNPCallerBase; + __pyx_vtabptr_9csamtools_IteratorSNPCalls = &__pyx_vtable_9csamtools_IteratorSNPCalls; + __pyx_vtable_9csamtools_IteratorSNPCalls.__pyx_base = *__pyx_vtabptr_9csamtools_SNPCallerBase; + __pyx_type_9csamtools_IteratorSNPCalls.tp_base = __pyx_ptype_9csamtools_SNPCallerBase; + if (PyType_Ready(&__pyx_type_9csamtools_IteratorSNPCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + { + PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorSNPCalls, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { + __pyx_wrapperbase_9csamtools_16IteratorSNPCalls___next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_16IteratorSNPCalls___next__.doc = __pyx_doc_9csamtools_16IteratorSNPCalls___next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_16IteratorSNPCalls___next__; + } + } + if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorSNPCalls.tp_dict, __pyx_vtabptr_9csamtools_IteratorSNPCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "IteratorSNPCalls", (PyObject *)&__pyx_type_9csamtools_IteratorSNPCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools_IteratorSNPCalls = &__pyx_type_9csamtools_IteratorSNPCalls; + __pyx_vtabptr_9csamtools_SNPCaller = &__pyx_vtable_9csamtools_SNPCaller; + __pyx_vtable_9csamtools_SNPCaller.__pyx_base = *__pyx_vtabptr_9csamtools_SNPCallerBase; + __pyx_type_9csamtools_SNPCaller.tp_base = __pyx_ptype_9csamtools_SNPCallerBase; + if (PyType_Ready(&__pyx_type_9csamtools_SNPCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3021; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if 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__pyx_t_3 = 0; - - /* "csamtools.pyx":1 - * # cython: embedsignature=True # <<<<<<<<<<<<<< - * # cython: profile=True - * # adds doc-strings for sphinx - */ - __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_3)); + if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_kp_u_220), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; - /* "cpython/type.pxd":2 + /* "/ifs/apps/apps/python-2.7.1/lib/python2.7/site-packages/Cython-0.13-py2.7-linux-x86_64.egg/Cython/Includes/cpython/type.pxd":2 * * cdef extern from "Python.h": # <<<<<<<<<<<<<< * # The C structure of the objects used to describe built-in types. @@ -33526,6 +37718,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_4); if (__pyx_m) { __Pyx_AddTraceback("init csamtools"); Py_DECREF(__pyx_m); __pyx_m = 0; @@ -33612,10 +37805,10 @@ static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const cha __pyx_empty_bytes /*PyObject *lnotab*/ ); -bad: +bad: Py_XDECREF(py_srcfile); Py_XDECREF(py_funcname); - + return py_code; } @@ -33709,143 +37902,6 @@ invalid_keyword: return 0; } -static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - PyThreadState *tstate = PyThreadState_GET(); - - tmp_type = tstate->curexc_type; - tmp_value = tstate->curexc_value; - tmp_tb = tstate->curexc_traceback; - tstate->curexc_type = type; - tstate->curexc_value = value; - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} - -static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { - PyThreadState *tstate = PyThreadState_GET(); - *type = tstate->curexc_type; - *value = tstate->curexc_value; - *tb = tstate->curexc_traceback; - - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -} - - -#if PY_MAJOR_VERSION < 3 -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) { - Py_XINCREF(type); - Py_XINCREF(value); - Py_XINCREF(tb); - /* First, check the traceback argument, replacing None with NULL. */ - if (tb == Py_None) { - Py_DECREF(tb); - tb = 0; - } - else if (tb != NULL && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto raise_error; - } - /* Next, replace a missing value with None */ - if (value == NULL) { - value = Py_None; - Py_INCREF(value); - } - #if PY_VERSION_HEX < 0x02050000 - if (!PyClass_Check(type)) - #else - if (!PyType_Check(type)) - #endif - { - /* Raising an instance. The value should be a dummy. */ - if (value != Py_None) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto raise_error; - } - /* Normalize to raise , */ - Py_DECREF(value); - value = type; - #if PY_VERSION_HEX < 0x02050000 - if (PyInstance_Check(type)) { - type = (PyObject*) ((PyInstanceObject*)type)->in_class; - Py_INCREF(type); - } - else { - type = 0; - PyErr_SetString(PyExc_TypeError, - "raise: exception must be an old-style class or instance"); - goto raise_error; - } - #else - type = (PyObject*) Py_TYPE(type); - Py_INCREF(type); - if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto raise_error; - } - #endif - } - - __Pyx_ErrRestore(type, value, tb); - return; -raise_error: - Py_XDECREF(value); - Py_XDECREF(type); - Py_XDECREF(tb); - return; -} - -#else /* Python 3+ */ - -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) { - if (tb == Py_None) { - tb = 0; - } else if (tb && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto bad; - } - if (value == Py_None) - value = 0; - - if (PyExceptionInstance_Check(type)) { - if (value) { - PyErr_SetString(PyExc_TypeError, - "instance exception may not have a separate value"); - goto bad; - } - value = type; - type = (PyObject*) Py_TYPE(value); - } else if (!PyExceptionClass_Check(type)) { - PyErr_SetString(PyExc_TypeError, - "raise: exception class must be a subclass of BaseException"); - goto bad; - } - - PyErr_SetObject(type, value); - - if (tb) { - PyThreadState *tstate = PyThreadState_GET(); - PyObject* tmp_tb = tstate->curexc_traceback; - if (tb != tmp_tb) { - Py_INCREF(tb); - tstate->curexc_traceback = tb; - Py_XDECREF(tmp_tb); - } - } - -bad: - return; -} -#endif - static void __Pyx_RaiseDoubleKeywordsError( const char* func_name, PyObject* kw_name) @@ -33854,9 +37910,39 @@ static void __Pyx_RaiseDoubleKeywordsError( #if PY_MAJOR_VERSION >= 3 "%s() got multiple values for keyword argument '%U'", func_name, kw_name); #else - "%s() got multiple values for keyword argument '%s'", func_name, - PyString_AS_STRING(kw_name)); + "%s() got multiple values for keyword argument '%s'", func_name, + PyString_AS_STRING(kw_name)); + #endif +} + +static void __Pyx_RaiseArgtupleInvalid( + const char* func_name, + int exact, + Py_ssize_t num_min, + Py_ssize_t num_max, + Py_ssize_t num_found) +{ + Py_ssize_t num_expected; + const char *number, *more_or_less; + + if (num_found < num_min) { + num_expected = num_min; + more_or_less = "at least"; + } else { + num_expected = num_max; + more_or_less = "at most"; + } + if (exact) { + more_or_less = "exactly"; + } + number = (num_expected == 1) ? "" : "s"; + PyErr_Format(PyExc_TypeError, + #if PY_VERSION_HEX < 0x02050000 + "%s() takes %s %d positional argument%s (%d given)", + #else + "%s() takes %s %zd positional argument%s (%zd given)", #endif + func_name, more_or_less, num_expected, number, num_found); } static int __Pyx_ParseOptionalKeywords( @@ -33938,36 +38024,33 @@ bad: return -1; } -static void __Pyx_RaiseArgtupleInvalid( - const char* func_name, - int exact, - Py_ssize_t num_min, - Py_ssize_t num_max, - Py_ssize_t num_found) -{ - Py_ssize_t num_expected; - const char *number, *more_or_less; +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); - if (num_found < num_min) { - num_expected = num_min; - more_or_less = "at least"; - } else { - num_expected = num_max; - more_or_less = "at most"; - } - if (exact) { - more_or_less = "exactly"; - } - number = (num_expected == 1) ? "" : "s"; - PyErr_Format(PyExc_TypeError, - #if PY_VERSION_HEX < 0x02050000 - "%s() takes %s %d positional argument%s (%d given)", - #else - "%s() takes %s %zd positional argument%s (%zd given)", - #endif - func_name, more_or_less, num_expected, number, num_found); + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +} + +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->curexc_type; + *value = tstate->curexc_value; + *tb = tstate->curexc_traceback; + + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; } + static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact) { @@ -34035,6 +38118,10 @@ bad: +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable"); } @@ -34110,92 +38197,31 @@ bad: return module; } -static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) { - PyObject *metaclass; - /* Default metaclass */ -#if PY_MAJOR_VERSION < 3 - if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) { - PyObject *base = PyTuple_GET_ITEM(bases, 0); - metaclass = PyObject_GetAttrString(base, "__class__"); - if (!metaclass) { - PyErr_Clear(); - metaclass = (PyObject*) Py_TYPE(base); - } - } else { - metaclass = (PyObject *) &PyClass_Type; - } -#else - if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) { - PyObject *base = PyTuple_GET_ITEM(bases, 0); - metaclass = (PyObject*) Py_TYPE(base); - } else { - metaclass = (PyObject *) &PyType_Type; - } -#endif - Py_INCREF(metaclass); - return metaclass; -} - -static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, - PyObject *modname) { - PyObject *result; - PyObject *metaclass; - - if (PyDict_SetItemString(dict, "__module__", modname) < 0) - return NULL; +static PyObject *__Pyx_CreateClass( + PyObject *bases, PyObject *dict, PyObject *name, const char *modname) +{ + PyObject *py_modname; + PyObject *result = 0; - /* Python2 __metaclass__ */ - metaclass = PyDict_GetItemString(dict, "__metaclass__"); - if (metaclass) { - Py_INCREF(metaclass); - } else { - metaclass = __Pyx_FindPy2Metaclass(bases); - } - result = PyObject_CallFunctionObjArgs(metaclass, name, bases, dict, NULL); - Py_DECREF(metaclass); + #if PY_MAJOR_VERSION < 3 + py_modname = PyString_FromString(modname); + #else + py_modname = PyUnicode_FromString(modname); + #endif + if (!py_modname) + goto bad; + if (PyDict_SetItemString(dict, "__module__", py_modname) < 0) + goto bad; + #if PY_MAJOR_VERSION < 3 + result = PyClass_New(bases, dict, name); + #else + result = PyObject_CallFunctionObjArgs((PyObject *)&PyType_Type, name, bases, dict, NULL); + #endif +bad: + Py_XDECREF(py_modname); return result; } - -static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module) { - __pyx_binding_PyCFunctionType_object *op = PyObject_GC_New(__pyx_binding_PyCFunctionType_object, __pyx_binding_PyCFunctionType); - if (op == NULL) - return NULL; - op->func.m_ml = ml; - Py_XINCREF(self); - op->func.m_self = self; - Py_XINCREF(module); - op->func.m_module = module; - PyObject_GC_Track(op); - return (PyObject *)op; -} - -static void __pyx_binding_PyCFunctionType_dealloc(__pyx_binding_PyCFunctionType_object *m) { - PyObject_GC_UnTrack(m); - Py_XDECREF(m->func.m_self); - Py_XDECREF(m->func.m_module); - PyObject_GC_Del(m); -} - -static PyObject *__pyx_binding_PyCFunctionType_descr_get(PyObject *func, PyObject *obj, PyObject *type) { - if (obj == Py_None) - obj = NULL; - return PyMethod_New(func, obj, type); -} - -static int __pyx_binding_PyCFunctionType_init(void) { - __pyx_binding_PyCFunctionType_type = PyCFunction_Type; - __pyx_binding_PyCFunctionType_type.tp_name = __Pyx_NAMESTR("cython_binding_builtin_function_or_method"); - __pyx_binding_PyCFunctionType_type.tp_dealloc = (destructor)__pyx_binding_PyCFunctionType_dealloc; - __pyx_binding_PyCFunctionType_type.tp_descr_get = __pyx_binding_PyCFunctionType_descr_get; - if (PyType_Ready(&__pyx_binding_PyCFunctionType_type) < 0) { - return -1; - } - __pyx_binding_PyCFunctionType = &__pyx_binding_PyCFunctionType_type; - return 0; - -} - static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) { const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0; const int is_unsigned = const_zero < neg_one; @@ -34221,6 +38247,116 @@ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) { } } +#if PY_MAJOR_VERSION < 3 +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) { + Py_XINCREF(type); + Py_XINCREF(value); + Py_XINCREF(tb); + /* First, check the traceback argument, replacing None with NULL. */ + if (tb == Py_None) { + Py_DECREF(tb); + tb = 0; + } + else if (tb != NULL && !PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } + /* Next, replace a missing value with None */ + if (value == NULL) { + value = Py_None; + Py_INCREF(value); + } + #if PY_VERSION_HEX < 0x02050000 + if (!PyClass_Check(type)) + #else + if (!PyType_Check(type)) + #endif + { + /* Raising an instance. The value should be a dummy. */ + if (value != Py_None) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto raise_error; + } + /* Normalize to raise , */ + Py_DECREF(value); + value = type; + #if PY_VERSION_HEX < 0x02050000 + if (PyInstance_Check(type)) { + type = (PyObject*) ((PyInstanceObject*)type)->in_class; + Py_INCREF(type); + } + else { + type = 0; + PyErr_SetString(PyExc_TypeError, + "raise: exception must be an old-style class or instance"); + goto raise_error; + } + #else + type = (PyObject*) Py_TYPE(type); + Py_INCREF(type); + if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto raise_error; + } + #endif + } + + __Pyx_ErrRestore(type, value, tb); + return; +raise_error: + Py_XDECREF(value); + Py_XDECREF(type); + Py_XDECREF(tb); + return; +} + +#else /* Python 3+ */ + +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) { + if (tb == Py_None) { + tb = 0; + } else if (tb && !PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto bad; + } + if (value == Py_None) + value = 0; + + if (PyExceptionInstance_Check(type)) { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto bad; + } + value = type; + type = (PyObject*) Py_TYPE(value); + } else if (!PyExceptionClass_Check(type)) { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto bad; + } + + PyErr_SetObject(type, value); + + if (tb) { + PyThreadState *tstate = PyThreadState_GET(); + PyObject* tmp_tb = tstate->curexc_traceback; + if (tb != tmp_tb) { + Py_INCREF(tb); + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_tb); + } + } + +bad: + return; +} +#endif + static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) { const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0; const int is_unsigned = const_zero < neg_one; @@ -34452,6 +38588,143 @@ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint8_t(uint8_t val) { } } +#if PY_MAJOR_VERSION < 3 +static PyObject *__Pyx_GetStdout(void) { + PyObject *f = PySys_GetObject((char *)"stdout"); + if (!f) { + PyErr_SetString(PyExc_RuntimeError, "lost sys.stdout"); + } + return f; +} + +static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) { + PyObject* v; + int i; + + if (!f) { + if (!(f = __Pyx_GetStdout())) + return -1; + } + for (i=0; i < PyTuple_GET_SIZE(arg_tuple); i++) { + if (PyFile_SoftSpace(f, 1)) { + if (PyFile_WriteString(" ", f) < 0) + return -1; + } + v = PyTuple_GET_ITEM(arg_tuple, i); + if (PyFile_WriteObject(v, f, Py_PRINT_RAW) < 0) + return -1; + if (PyString_Check(v)) { + char *s = PyString_AsString(v); + Py_ssize_t len = PyString_Size(v); + if (len > 0 && + isspace(Py_CHARMASK(s[len-1])) && + s[len-1] != ' ') + PyFile_SoftSpace(f, 0); + } + } + if (newline) { + if (PyFile_WriteString("\n", f) < 0) + return -1; + PyFile_SoftSpace(f, 0); + } + return 0; +} + +#else /* Python 3 has a print function */ + +static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) { + PyObject* kwargs = 0; + PyObject* result = 0; + PyObject* end_string; + if (unlikely(!__pyx_print)) { + __pyx_print = __Pyx_GetAttrString(__pyx_b, "print"); + if (!__pyx_print) + return -1; + } + if (stream) { + kwargs = PyDict_New(); + if (unlikely(!kwargs)) + return -1; + if (unlikely(PyDict_SetItemString(kwargs, "file", stream) < 0)) + goto bad; + if (!newline) { + end_string = PyUnicode_FromStringAndSize(" ", 1); + if (unlikely(!end_string)) + goto bad; + if (PyDict_SetItemString(kwargs, "end", end_string) < 0) { + Py_DECREF(end_string); + goto bad; + } + Py_DECREF(end_string); + } + } else if (!newline) { + if (unlikely(!__pyx_print_kwargs)) { + __pyx_print_kwargs = PyDict_New(); + if (unlikely(!__pyx_print_kwargs)) + return -1; + end_string = PyUnicode_FromStringAndSize(" ", 1); + if (unlikely(!end_string)) + return -1; + if (PyDict_SetItemString(__pyx_print_kwargs, "end", end_string) < 0) { + Py_DECREF(end_string); + return -1; + } + Py_DECREF(end_string); + } + kwargs = __pyx_print_kwargs; + } + result = PyObject_Call(__pyx_print, arg_tuple, kwargs); + if (unlikely(kwargs) && (kwargs != __pyx_print_kwargs)) + Py_DECREF(kwargs); + if (!result) + return -1; + Py_DECREF(result); + return 0; +bad: + if (kwargs != __pyx_print_kwargs) + Py_XDECREF(kwargs); + return -1; +} + +#endif + +#if PY_MAJOR_VERSION < 3 + +static int __Pyx_PrintOne(PyObject* f, PyObject *o) { + if (!f) { + if (!(f = __Pyx_GetStdout())) + return -1; + } + if (PyFile_SoftSpace(f, 0)) { + if (PyFile_WriteString(" ", f) < 0) + return -1; + } + if (PyFile_WriteObject(o, f, Py_PRINT_RAW) < 0) + return -1; + if (PyFile_WriteString("\n", f) < 0) + return -1; + return 0; + /* the line below is just to avoid compiler + * compiler warnings about unused functions */ + return __Pyx_Print(f, NULL, 0); +} + +#else /* Python 3 has a print function */ + +static int __Pyx_PrintOne(PyObject* stream, PyObject *o) { + int res; + PyObject* arg_tuple = PyTuple_New(1); + if (unlikely(!arg_tuple)) + return -1; + Py_INCREF(o); + PyTuple_SET_ITEM(arg_tuple, 0, o); + res = __Pyx_Print(stream, arg_tuple, 1); + Py_DECREF(arg_tuple); + return res; +} + +#endif + static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint64_t(uint64_t val) { const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0; const int is_unsigned = const_zero < neg_one; @@ -34923,13 +39196,13 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class if (!result) goto bad; if (!PyType_Check(result)) { - PyErr_Format(PyExc_TypeError, + PyErr_Format(PyExc_TypeError, "%s.%s is not a type object", module_name, class_name); goto bad; } if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) { - PyOS_snprintf(warning, sizeof(warning), + PyOS_snprintf(warning, sizeof(warning), "%s.%s size changed, may indicate binary incompatibility", module_name, class_name); #if PY_VERSION_HEX < 0x02050000 @@ -34939,7 +39212,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class #endif } else if (((PyTypeObject *)result)->tp_basicsize != size) { - PyErr_Format(PyExc_ValueError, + PyErr_Format(PyExc_ValueError, "%s.%s has the wrong size, try recompiling", module_name, class_name); goto bad;