/* Generated by Cython 0.15.1 on Mon Jan 14 23:52:53 2013 */ #define PY_SSIZE_T_CLEAN #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. #else #include /* For offsetof */ #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) #endif #if !defined(WIN32) && !defined(MS_WINDOWS) #ifndef __stdcall #define __stdcall #endif #ifndef __cdecl #define __cdecl #endif #ifndef __fastcall #define __fastcall #endif #endif #ifndef DL_IMPORT #define DL_IMPORT(t) t #endif #ifndef DL_EXPORT #define DL_EXPORT(t) t #endif #ifndef PY_LONG_LONG #define PY_LONG_LONG LONG_LONG #endif #if PY_VERSION_HEX < 0x02040000 #define METH_COEXIST 0 #define PyDict_CheckExact(op) (Py_TYPE(op) == &PyDict_Type) #define PyDict_Contains(d,o) PySequence_Contains(d,o) #endif #if PY_VERSION_HEX < 0x02050000 typedef int Py_ssize_t; #define PY_SSIZE_T_MAX INT_MAX #define PY_SSIZE_T_MIN INT_MIN #define PY_FORMAT_SIZE_T "" #define PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) #define PyNumber_Index(o) PyNumber_Int(o) #define PyIndex_Check(o) PyNumber_Check(o) #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) #endif #if PY_VERSION_HEX < 0x02060000 #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt) #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type) #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size) #define PyVarObject_HEAD_INIT(type, size) \ PyObject_HEAD_INIT(type) size, #define PyType_Modified(t) typedef struct { void *buf; 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PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) #ifdef __GNUC__ /* Test for GCC > 2.95 */ #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 ... */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ > 2 ... */ #else /* __GNUC__ */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ */ static PyObject *__pyx_m; static PyObject *__pyx_b; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static int __pyx_lineno; static int __pyx_clineno = 0; static const char * __pyx_cfilenm= __FILE__; static const char *__pyx_filename; static const char *__pyx_f[] = { "csamtools.pyx", "bool.pxd", "complex.pxd", }; static PyObject *__Pyx_Generator_Next(PyObject *self); static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value); static PyObject *__Pyx_Generator_Close(PyObject *self); static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args, CYTHON_UNUSED PyObject *kwds); typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *); /*--- Type declarations ---*/ struct __pyx_Generator_object; struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr; struct __pyx_obj_9csamtools_IteratorRow; struct __pyx_obj_9csamtools_IteratorRowAllRefs; struct __pyx_obj_9csamtools_IteratorRowAll; struct __pyx_obj_9csamtools_PileupProxy; struct __pyx_obj_9csamtools_AlignedRead; struct __pyx_obj_9csamtools_Fastafile; struct __pyx_obj_9csamtools_IteratorRowSelection; struct __pyx_obj_9csamtools_IteratorColumn; struct __pyx_obj_9csamtools_IteratorColumnAllRefs; struct __pyx_obj_9csamtools_IteratorRowRegion; struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr; struct __pyx_obj_9csamtools_Samfile; struct __pyx_obj_9csamtools_SNPCall; struct __pyx_obj_9csamtools_IndexedReads; struct __pyx_obj_9csamtools_IteratorColumnRegion; struct __pyx_obj_9csamtools_PileupRead; struct __pyx_t_9csamtools___iterdata; typedef struct __pyx_t_9csamtools___iterdata __pyx_t_9csamtools___iterdata; struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData; struct __pyx_t_9csamtools_MateData; typedef struct __pyx_t_9csamtools_MateData __pyx_t_9csamtools_MateData; /* "csamtools.pxd":394 * # Utility types * * ctypedef struct __iterdata: # <<<<<<<<<<<<<< * samfile_t * samfile * bam_iter_t iter */ struct __pyx_t_9csamtools___iterdata { samfile_t *samfile; bam_iter_t iter; faidx_t *fastafile; int tid; char *seq; int seq_len; }; /* "csamtools.pxd":523 * cdef char * getSequence( self ) * cdef setMask( self, mask ) * cdef setupIteratorData( self, # <<<<<<<<<<<<<< * int tid, * int start, */ struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData { int __pyx_n; int reopen; }; /* "csamtools.pyx":518 * counter[0] += 1; * * ctypedef struct MateData: # <<<<<<<<<<<<<< * char * name * bam1_t * mate */ struct __pyx_t_9csamtools_MateData { char *name; bam1_t *mate; uint32_t flag; }; /* "csamtools.pyx":140 * cdef char* CODE2CIGAR= "MIDNSHP=X" * if IS_PYTHON3: * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<< * else: * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) */ struct __pyx_Generator_object { PyObject_HEAD __pyx_generator_body_t body; int is_running; int resume_label; PyObject *exc_type; PyObject *exc_value; PyObject *exc_traceback; }; struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr { struct __pyx_Generator_object __pyx_base; PyObject *__pyx_v_x; PyObject *__pyx_v_y; PyObject *__pyx_t_0; PyObject *__pyx_t_1; PyObject *(*__pyx_t_2)(PyObject *); }; /* "csamtools.pxd":464 * cdef uint32_t _is_tail * * cdef class IteratorRow: # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_9csamtools_IteratorRow { PyObject_HEAD }; /* "csamtools.pxd":487 * cdef int cnext(self) * * cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<< * cdef Samfile samfile * cdef int tid */ struct __pyx_obj_9csamtools_IteratorRowAllRefs { struct __pyx_obj_9csamtools_IteratorRow __pyx_base; struct __pyx_obj_9csamtools_Samfile *samfile; int tid; struct __pyx_obj_9csamtools_IteratorRowRegion *rowiter; }; /* "csamtools.pxd":480 * cdef int cnext(self) * * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<< * cdef bam1_t * b * cdef samfile_t * fp */ 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.pxd":449 * cdef char * _getrname( self, int tid ) * * cdef class PileupProxy: # <<<<<<<<<<<<<< * cdef bam_pileup1_t ** plp * cdef int tid */ struct __pyx_obj_9csamtools_PileupProxy { PyObject_HEAD bam_pileup1_t **plp; int tid; int pos; int n_pu; }; /* "csamtools.pxd":415 * cdef char * _fetch( self, char * reference, int start, int end, int * length ) * * cdef class AlignedRead: # <<<<<<<<<<<<<< * * # object that this AlignedRead represents */ struct __pyx_obj_9csamtools_AlignedRead { PyObject_HEAD bam1_t *_delegate; }; /* "csamtools.pxd":408 * # Note: need to declare all C fields and methods here * # * cdef class Fastafile: # <<<<<<<<<<<<<< * cdef char * _filename * # pointer to fastafile */ struct __pyx_obj_9csamtools_Fastafile { PyObject_HEAD struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtab; char *_filename; faidx_t *fastafile; }; /* "csamtools.pxd":492 * cdef IteratorRowRegion rowiter * * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<< * cdef bam1_t * b * cdef int current_pos */ struct __pyx_obj_9csamtools_IteratorRowSelection { struct __pyx_obj_9csamtools_IteratorRow __pyx_base; struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtab; bam1_t *b; int current_pos; samfile_t *fp; PyObject *positions; int owns_samfile; }; /* "csamtools.pxd":504 * cdef int cnext(self) * * cdef class IteratorColumn: # <<<<<<<<<<<<<< * * # result of the last plbuf_push */ struct __pyx_obj_9csamtools_IteratorColumn { 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; }; /* "csamtools.pxd":536 * cdef int truncate * * cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_9csamtools_IteratorColumnAllRefs { struct __pyx_obj_9csamtools_IteratorColumn __pyx_base; }; /* "csamtools.pxd":467 * pass * * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<< * cdef bam_iter_t iter # iterator state object * cdef bam1_t * b */ struct __pyx_obj_9csamtools_IteratorRowRegion { struct __pyx_obj_9csamtools_IteratorRow __pyx_base; struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtab; bam_iter_t iter; bam1_t *b; int retval; struct __pyx_obj_9csamtools_Samfile *samfile; samfile_t *fp; int owns_samfile; }; /* "csamtools.pyx":142 * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) * else: * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<< * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" ) * */ struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr { struct __pyx_Generator_object __pyx_base; PyObject *__pyx_v_x; PyObject *__pyx_v_y; PyObject *__pyx_t_0; PyObject *__pyx_t_1; PyObject *(*__pyx_t_2)(PyObject *); }; /* "csamtools.pxd":420 * cdef bam1_t * _delegate * * cdef class Samfile: # <<<<<<<<<<<<<< * cdef char * _filename * # pointer to samfile */ struct __pyx_obj_9csamtools_Samfile { PyObject_HEAD struct __pyx_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; }; /* "csamtools.pyx":3222 * return retval, out_stderr, out_stdout * * 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; }; /* "csamtools.pxd":539 * pass * * cdef class IndexedReads: # <<<<<<<<<<<<<< * cdef Samfile samfile * cdef samfile_t * fp */ struct __pyx_obj_9csamtools_IndexedReads { PyObject_HEAD struct __pyx_obj_9csamtools_Samfile *samfile; samfile_t *fp; PyObject *index; int owns_samfile; }; /* "csamtools.pxd":531 * cdef reset( self, tid, start, end ) * * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<< * cdef int start * cdef int end */ struct __pyx_obj_9csamtools_IteratorColumnRegion { struct __pyx_obj_9csamtools_IteratorColumn __pyx_base; int start; int end; int truncate; }; /* "csamtools.pxd":455 * cdef int n_pu * * cdef class PileupRead: # <<<<<<<<<<<<<< * cdef AlignedRead _alignment * cdef int32_t _qpos */ struct __pyx_obj_9csamtools_PileupRead { PyObject_HEAD struct __pyx_obj_9csamtools_AlignedRead *_alignment; int32_t _qpos; int _indel; int _level; uint32_t _is_del; uint32_t _is_head; uint32_t _is_tail; }; /* "csamtools.pyx":1766 * return ret * * cdef class IteratorColumn: # <<<<<<<<<<<<<< * '''abstract base class for iterators over columns. * */ struct __pyx_vtabstruct_9csamtools_IteratorColumn { int (*cnext)(struct __pyx_obj_9csamtools_IteratorColumn *); char *(*getSequence)(struct __pyx_obj_9csamtools_IteratorColumn *); PyObject *(*setMask)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *); PyObject *(*setupIteratorData)(struct __pyx_obj_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args); PyObject *(*reset)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *); }; static struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtabptr_9csamtools_IteratorColumn; /* "csamtools.pyx":1931 * self.iterdata.seq = NULL * * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<< * '''iterates over a region only. * ''' */ struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion { struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_base; }; static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *__pyx_vtabptr_9csamtools_IteratorColumnRegion; /* "csamtools.pyx":1461 * * * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<< * """*(Samfile samfile, int tid, int beg, int end, int reopen = True )* * */ struct __pyx_vtabstruct_9csamtools_IteratorRowRegion { bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_IteratorRowRegion *); int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowRegion *); }; static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtabptr_9csamtools_IteratorRowRegion; /* "csamtools.pyx":1641 * raise StopIteration * * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<< * """*(Samfile samfile)* * */ struct __pyx_vtabstruct_9csamtools_IteratorRowSelection { bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_IteratorRowSelection *); int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowSelection *); }; static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtabptr_9csamtools_IteratorRowSelection; /* "csamtools.pyx":1968 * self.n_plp ) * * cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<< * """iterates over all columns by chaining iterators over each reference * """ */ struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs { struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_base; }; static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *__pyx_vtabptr_9csamtools_IteratorColumnAllRefs; /* "csamtools.pyx":545 * * * cdef class Samfile: # <<<<<<<<<<<<<< * '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None, * add_sq_text = False, check_header = True, check_sq = True )* */ struct __pyx_vtabstruct_9csamtools_Samfile { bam_header_t *(*_buildHeader)(struct __pyx_obj_9csamtools_Samfile *, PyObject *); bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_Samfile *); int (*cnext)(struct __pyx_obj_9csamtools_Samfile *); int (*write)(struct __pyx_obj_9csamtools_Samfile *, struct __pyx_obj_9csamtools_AlignedRead *, int __pyx_skip_dispatch); char *(*_getrname)(struct __pyx_obj_9csamtools_Samfile *, int); }; static struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtabptr_9csamtools_Samfile; /* "csamtools.pyx":375 * ## Public methods * ###################################################################### * cdef class Fastafile: # <<<<<<<<<<<<<< * '''*(filename)* * */ struct __pyx_vtabstruct_9csamtools_Fastafile { char *(*_fetch)(struct __pyx_obj_9csamtools_Fastafile *, char *, int, int, int *); }; static struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtabptr_9csamtools_Fastafile; /* "csamtools.pyx":1540 * if self.owns_samfile: samclose( self.fp ) * * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<< * """*(Samfile samfile, int reopen = True)* * */ struct __pyx_vtabstruct_9csamtools_IteratorRowAll { bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_IteratorRowAll *); int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowAll *); }; static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtools_IteratorRowAll; 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static PyTypeObject *__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr = 0; static PyObject *__pyx_v_9csamtools__FILENAME_ENCODING = 0; static char *__pyx_v_9csamtools_CODE2CIGAR; static char *__pyx_v_9csamtools_bam_nt16_rev_table; static int __pyx_v_9csamtools_max_pos; static PyObject *__pyx_f_9csamtools_from_string_and_size(char *, size_t); /*proto*/ static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *); /*proto*/ static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *); /*proto*/ static CYTHON_INLINE PyObject *__pyx_f_9csamtools__force_cmdline_bytes(PyObject *); /*proto*/ static PyObject *__pyx_f_9csamtools__charptr_to_str(char *); /*proto*/ static PyObject *__pyx_f_9csamtools__force_str(PyObject *); /*proto*/ static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *); /*proto*/ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **, int, int, int); /*proto*/ static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *); /*proto*/ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *); /*proto*/ static int __pyx_f_9csamtools_fetch_callback(bam1_t *, void *); /*proto*/ static int __pyx_f_9csamtools_pileup_callback(uint32_t, uint32_t, int, bam_pileup1_t *, void *); /*proto*/ static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *, void *); /*proto*/ static int __pyx_f_9csamtools_count_callback(bam1_t *, void *); /*proto*/ static int __pyx_f_9csamtools_mate_callback(bam1_t *, void *); /*proto*/ static int __pyx_f_9csamtools___advance_all(void *, bam1_t *); /*proto*/ static int __pyx_f_9csamtools___advance_snpcalls(void *, bam1_t *); /*proto*/ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *); /*proto*/ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *); /*proto*/ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *, uint32_t, uint32_t); /*proto*/ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *, uint32_t, uint32_t); /*proto*/ #define __Pyx_MODULE_NAME "csamtools" int __pyx_module_is_main_csamtools = 0; /* Implementation of 'csamtools' */ static PyObject *__pyx_builtin_object; static PyObject *__pyx_builtin_TypeError; static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_ord; static PyObject *__pyx_builtin_map; 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_zip; static PyObject *__pyx_builtin_sorted; static PyObject *__pyx_builtin_KeyError; static PyObject *__pyx_builtin_StopIteration; static PyObject *__pyx_builtin_min; static PyObject *__pyx_builtin_max; static PyObject *__pyx_builtin_chr; static PyObject *__pyx_builtin_open; static PyObject *__pyx_builtin_UnicodeDecodeError; static char __pyx_k_1[] = "Argument must be string or unicode."; static char __pyx_k_3[] = "Argument must be string, bytes or unicode."; static char __pyx_k_5[] = "\t"; static char __pyx_k_6[] = "\n"; static char __pyx_k_7[] = "calling len() on closed file"; static char __pyx_k_9[] = "could not open file `%s`"; static char __pyx_k_10[] = "I/O operation on closed file"; static char __pyx_k_13[] = "no sequence/region supplied."; static char __pyx_k_15[] = "invalid region: start (%i) > end (%i)"; static char __pyx_k_16[] = ""; static char __pyx_k_17[] = "start out of range (%i)"; static char __pyx_k_18[] = "end out of range (%i)"; static char __pyx_k_19[] = "%s:%i-%i"; static char __pyx_k_24[] = "invalid file opening mode `%s`"; static char __pyx_k_26[] = "-"; static char __pyx_k_27[] = "http:"; static char __pyx_k_28[] = "ftp:"; static char __pyx_k_29[] = "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing"; static char __pyx_k_30[] = "unequal names and lengths of reference sequences"; static char __pyx_k_31[] = "@SQ\tSN:%s\tLN:%s\n"; static char __pyx_k_32[] = "file `%s` not found"; static char __pyx_k_33[] = "could not open file (mode='%s') - is it SAM/BAM format?"; static char __pyx_k_34[] = "file does not have valid header (mode='%s') - is it BAM format?"; static char __pyx_k_35[] = "file does not have valid header (mode='%s') - is it SAM format?"; static char __pyx_k_36[] = "file header is empty (mode='%s') - is it SAM/BAM format?"; static char __pyx_k_37[] = ".bai"; static char __pyx_k_38[] = "error while opening index `%s` "; static char __pyx_k_41[] = "tid %i out of range 0<=tid<%i"; static char __pyx_k_43[] = "[:-]"; static char __pyx_k_45[] = "invalid reference `%s`"; static char __pyx_k_46[] = "invalid coordinates: start (%i) > end (%i)"; static char __pyx_k_48[] = "seek only available in bam files"; static char __pyx_k_50[] = "seek no available in streams"; static char __pyx_k_56[] = "fetch called on bamfile without index"; static char __pyx_k_58[] = "callback functionality requires a region/reference"; static char __pyx_k_60[] = "no index available for fetch"; static char __pyx_k_62[] = "fetching by region is not available for sam files"; static char __pyx_k_64[] = "callback not implemented yet"; static char __pyx_k_66[] = "fetch called for samfile without header"; static char __pyx_k_69[] = "read %s: is unpaired"; static char __pyx_k_70[] = "mate %s: is unmapped"; static char __pyx_k_71[] = "mate not found"; static char __pyx_k_76[] = "counting functionality requires a region/reference"; static char __pyx_k_79[] = "count for a region is not available for sam files"; static char __pyx_k_82[] = "no index available for pileup"; static char __pyx_k_85[] = "pileup of samfiles not implemented yet"; static char __pyx_k_92[] = "Samfile.mapped only available in bam files"; static char __pyx_k_95[] = "Samfile.unmapped only available in bam files"; static char __pyx_k__A[] = "A"; static char __pyx_k__B[] = "B"; static char __pyx_k__C[] = "C"; static char __pyx_k__D[] = "D"; static char __pyx_k__F[] = "F"; static char __pyx_k__H[] = "H"; static char __pyx_k__I[] = "I"; static char __pyx_k__S[] = "S"; static char __pyx_k__Z[] = "Z"; static char __pyx_k__b[] = "b"; static char __pyx_k__c[] = "c"; static char __pyx_k__d[] = "d"; static char __pyx_k__f[] = "f"; static char __pyx_k__h[] = "h"; static char __pyx_k__i[] = "i"; static char __pyx_k__n[] = "n"; static char __pyx_k__r[] = "r"; static char __pyx_k__s[] = "s"; static char __pyx_k__w[] = "w"; static char __pyx_k_100[] = "@"; static char __pyx_k_102[] = "header line without '@': '%s'"; static char __pyx_k_104[] = "header line with invalid type '%s': '%s'"; static char __pyx_k_105[] = ":"; static char __pyx_k_107[] = "unknown field code '%s' in record '%s'"; static char __pyx_k_108[] = "multiple '%s' lines are not permitted"; static char __pyx_k_109[] = "@%s"; static char __pyx_k_110[] = "%s:%s"; static char __pyx_k_111[] = "invalid type for record %s: %s, expected %s"; static char __pyx_k_113[] = "incomplete sequence information in '%s'"; static char __pyx_k_116[] = "can not iterate over samfile without header"; static char __pyx_k_119[] = "no index available for iteration"; static char __pyx_k_125[] = "can only use this iterator on bam files"; static char __pyx_k_126[] = "reference sequence for '%s' (tid=%i) not found"; static char __pyx_k_127[] = "unknown stepper option `%s` in IteratorColumn"; static char __pyx_k_129[] = "error during iteration"; static char __pyx_k_132[] = "Invalid clipping in CIGAR string"; static char __pyx_k_135[] = "%c%i"; static char __pyx_k_136[] = "quality and sequence mismatch: %i != %i"; static char __pyx_k_137[] = "%c"; static char __pyx_k_138[] = "<"; static char __pyx_k_140[] = "integer %i out of range of BAM/SAM specification"; static char __pyx_k_141[] = "2sccI%i%s"; static char __pyx_k_145[] = "2sc%is"; static char __pyx_k_147[] = "create_string_buffer"; static char __pyx_k_148[] = "tag '%s' not present"; static char __pyx_k_149[] = "unknown auxilliary type '%s'"; static char __pyx_k_150[] = "Contig index"; static char __pyx_k_151[] = "Mapped position on contig"; static char __pyx_k_152[] = "Contig index for mate pair"; static char __pyx_k_153[] = "Position of mate pair"; static char __pyx_k_154[] = "Insert size"; static char __pyx_k_155[] = "Binary flag"; static char __pyx_k_156[] = "Count of cigar entries"; static char __pyx_k_157[] = "Cigar entries"; static char __pyx_k_158[] = "Mapping quality"; static char __pyx_k_159[] = "Bam index bin number"; static char __pyx_k_160[] = "Length of query name"; static char __pyx_k_161[] = "Query name"; static char __pyx_k_162[] = "Length of query sequence"; static char __pyx_k_163[] = "Query sequence"; static char __pyx_k_164[] = "Quality scores"; static char __pyx_k_165[] = "Length of auxilary data"; static char __pyx_k_166[] = "Maximum data length"; static char __pyx_k_167[] = "Current data length"; static char __pyx_k_168[] = "%-30s %-10s= %s"; static char __pyx_k_169[] = "("; static char __pyx_k_170[] = ")"; static char __pyx_k_171[] = "This class cannot be instantiated from Python"; static char __pyx_k_173[] = "PileupProxy accessed after iterator finished"; static char __pyx_k_177[] = "No such file or directory: '%s'"; static char __pyx_k_178[] = "-o"; static char __pyx_k_179[] = "option -o is forbidden in samtools view"; static char __pyx_k_185[] = "can only IndexReads on bam files"; static char __pyx_k_186[] = "read %s not found"; static char __pyx_k_187[] = "number of :term:`filename` associated with this object."; static char __pyx_k_188[] = "the query name (None if not present)"; static char __pyx_k_189[] = "the :term:`cigar` alignment (None if not present). The alignment\n is returned as a list of operations. The operations are:\n\n +-----+--------------+-----+\n |M |BAM_CMATCH |0 |\n +-----+--------------+-----+\n |I |BAM_CINS |1 |\n +-----+--------------+-----+\n |D |BAM_CDEL |2 |\n +-----+--------------+-----+\n |N |BAM_CREF_SKIP |3 |\n +-----+--------------+-----+\n |S |BAM_CSOFT_CLIP|4 |\n +-----+--------------+-----+\n |H |BAM_CHARD_CLIP|5 |\n +-----+--------------+-----+\n |P |BAM_CPAD |6 |\n +-----+--------------+-----+\n |= |BAM_CEQUAL |7 |\n +-----+--------------+-----+\n |X |BAM_CDIFF |8 |\n +-----+--------------+-----+\n\n "; static char __pyx_k_190[] = "the :term:`cigar` alignment as a string.\n \n Returns the empty string if not present.\n "; static char __pyx_k_191[] = "read sequence bases, including :term:`soft clipped` bases (None if not present).\n\n In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient."; static char __pyx_k_192[] = "read sequence base qualities, including :term:`soft clipped` bases (None if not present).\n\n In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient."; static char __pyx_k_193[] = "aligned portion of the read and excludes any flanking bases that were :term:`soft clipped` (None if not present).\n\n In Python 3, this property is of type bytes. Assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient.\n\n SAM/BAM files may included extra flanking bases sequences that were\n not part of the alignment. These bases may be the result of the\n Smith-Waterman or other algorithms, which may not require alignments\n that begin at the first residue or end at the last. In addition,\n extra sequencing adapters, multiplex identifiers, and low-quality bases that\n were not considered for alignment may have been retained."; static char __pyx_k_194[] = "aligned query sequence quality values (None if not present). This property is read-only.\n\n In Python 3, this property is of type bytes."; static char __pyx_k_195[] = "start index of the aligned query portion of the sequence (0-based, inclusive)"; static char __pyx_k_196[] = "end index of the aligned query portion of the sequence (0-based, exclusive)"; static char __pyx_k_197[] = "Length of the aligned query sequence"; static char __pyx_k_198[] = "the tags in the AUX field.\n\n This property permits convenience access to\n the tags. Changes it the returned list will\n not update the tags automatically. Instead,\n the following is required for adding a\n new tag::\n\n read.tags = read.tags + [(\"RG\",0)]\n\n\n This method will happily write the same tag\n multiple times.\n "; static char __pyx_k_199[] = "properties flag"; static char __pyx_k_200[] = "\n :term:`target` ID\n\n DEPRECATED from pysam-0.4 - use tid in the future.\n The rname field caused a lot of confusion as it returns\n the :term:`target` ID instead of the reference sequence\n name.\n\n .. note::\n\n This field contains the index of the reference sequence\n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n\n "; static char __pyx_k_201[] = "\n :term:`target` ID\n\n .. note::\n\n This field contains the index of the reference sequence\n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n\n "; static char __pyx_k_202[] = "0-based leftmost coordinate"; static char __pyx_k_203[] = "properties bin"; static char __pyx_k_204[] = "length of the read (read only). Returns 0 if not given."; static char __pyx_k_205[] = "aligned reference position of the read on the reference genome. \n \n aend points to one past the last aligned residue.\n Returns None if not available."; static char __pyx_k_206[] = "aligned length of the read on the reference genome. Returns None if\n not available."; static char __pyx_k_207[] = "mapping quality"; static char __pyx_k_208[] = "the :term:`reference` id of the mate\n deprecated, use RNEXT instead.\n "; static char __pyx_k_209[] = "the :term:`reference` id of the mate "; static char __pyx_k_210[] = "the position of the mate\n deprecated, use PNEXT instead."; static char __pyx_k_211[] = "the position of the mate"; static char __pyx_k_212[] = "the insert size\n deprecated: use tlen instead"; static char __pyx_k_213[] = "the insert size"; static char __pyx_k_214[] = "true if read is paired in sequencing"; static char __pyx_k_215[] = "true if read is mapped in a proper pair"; static char __pyx_k_216[] = "true if read itself is unmapped"; static char __pyx_k_217[] = "true if the mate is unmapped"; static char __pyx_k_218[] = "true if read is mapped to reverse strand"; static char __pyx_k_219[] = "true is read is mapped to reverse strand"; static char __pyx_k_220[] = "true if this is read1"; static char __pyx_k_221[] = "true if this is read2"; static char __pyx_k_222[] = "true if not primary alignment"; static char __pyx_k_223[] = "true if QC failure"; static char __pyx_k_224[] = "true if optical or PCR duplicate"; static char __pyx_k_225[] = "a list of reference positions that this read aligns to."; static char __pyx_k_226[] = "a list of aligned read and reference positions.\n\n Unaligned position are marked by None.\n "; static char __pyx_k_227[] = "number of :term:`reference` sequences in the file."; static char __pyx_k_228[] = "tuple with the names of :term:`reference` sequences."; static char __pyx_k_229[] = "tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as\n :attr:`pysam.Samfile.references`\n "; static char __pyx_k_230[] = "total number of mapped reads in file.\n "; static char __pyx_k_231[] = "total number of unmapped reads in file.\n "; static char __pyx_k_232[] = "full contents of the :term:`sam file` header as a string."; static char __pyx_k_233[] = "header information within the :term:`sam file`. The records and fields are returned as\n a two-level dictionary.\n "; static char __pyx_k_234[] = "the chromosome ID as is defined in the header"; static char __pyx_k_235[] = "number of reads mapping to this column."; static char __pyx_k_236[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column"; static char __pyx_k_237[] = "a :class:`pysam.AlignedRead` object of the aligned read"; static char __pyx_k_238[] = "position of the read base at the pileup site, 0-based"; static char __pyx_k_239[] = "indel length; 0 for no indel, positive for ins and negative for del"; static char __pyx_k_240[] = "1 iff the base on the padded read is a deletion"; static char __pyx_k_241[] = "current sequence length."; static char __pyx_k_242[] = "nucleotide position of SNP."; static char __pyx_k_243[] = "reference base at pos. ``N`` if no reference sequence supplied."; static char __pyx_k_244[] = "the genotype called."; static char __pyx_k_245[] = "the genotype quality (Phred-scaled)."; static char __pyx_k_246[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence."; static char __pyx_k_247[] = "the root mean square (rms) of the mapping quality of all reads involved in the call."; static char __pyx_k_248[] = "coverage or read depth - the number of reads involved in the call."; static char __pyx_k_249[] = "getfilesystemencoding"; static char __pyx_k_250[] = "MIDNSHP=X"; static char __pyx_k_251[] = "([MIDNSHP=X])(\\d+)"; static char __pyx_k_253[] = "=ACMGRSVTWYHKDBN"; static char __pyx_k_254[] = "A pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column\n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n "; static char __pyx_k_255[] = "\n stderr is captured.\n "; static char __pyx_k_256[] = "does nothing. stderr can't be redirected on windows"; static char __pyx_k_262[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html"; static char __pyx_k__AS[] = "AS"; static char __pyx_k__CL[] = "CL"; static char __pyx_k__CN[] = "CN"; static char __pyx_k__CO[] = "CO"; static char __pyx_k__DS[] = "DS"; static char __pyx_k__DT[] = "DT"; static char __pyx_k__FO[] = "FO"; static char __pyx_k__GO[] = "GO"; static char __pyx_k__HD[] = "HD"; static char __pyx_k__ID[] = "ID"; static char __pyx_k__KS[] = "KS"; static char __pyx_k__LB[] = "LB"; static char __pyx_k__LN[] = "LN"; static char __pyx_k__M5[] = "M5"; static char __pyx_k__PG[] = "PG"; static char __pyx_k__PI[] = "PI"; static char __pyx_k__PL[] = "PL"; static char __pyx_k__PN[] = "PN"; static char __pyx_k__PP[] = "PP"; static char __pyx_k__PU[] = "PU"; static char __pyx_k__RG[] = "RG"; static char __pyx_k__SM[] = "SM"; static char __pyx_k__SN[] = "SN"; static char __pyx_k__SO[] = "SO"; static char __pyx_k__SP[] = "SP"; static char __pyx_k__SQ[] = "SQ"; static char __pyx_k__UR[] = "UR"; static char __pyx_k__VN[] = "VN"; static char __pyx_k__fd[] = "fd"; static char __pyx_k__id[] = "id"; static char __pyx_k__os[] = "os"; static char __pyx_k__rU[] = "rU"; static char __pyx_k__rb[] = "rb"; static char __pyx_k__re[] = "re"; static char __pyx_k__wb[] = "wb"; static char __pyx_k__wh[] = "wh"; static char __pyx_k__all[] = "all"; static char __pyx_k__beg[] = "beg"; static char __pyx_k__bin[] = "bin"; static char __pyx_k__chr[] = "chr"; static char __pyx_k__dup[] = "dup"; static char __pyx_k__end[] = "end"; static char __pyx_k__map[] = "map"; static char __pyx_k__max[] = "max"; static char __pyx_k__min[] = "min"; static char __pyx_k__ord[] = "ord"; static char __pyx_k__pos[] = "pos"; static char __pyx_k__raw[] = "raw"; static char __pyx_k__seq[] = "seq"; static char __pyx_k__sys[] = "sys"; static char __pyx_k__tid[] = "tid"; static char __pyx_k__wbu[] = "wbu"; static char __pyx_k__zip[] = "zip"; static char __pyx_k__2scB[] = "2scB"; static char __pyx_k__2scH[] = "2scH"; static char __pyx_k__2scI[] = "2scI"; static char __pyx_k__2scb[] = "2scb"; static char __pyx_k__2scc[] = "2scc"; static char __pyx_k__2scf[] = "2scf"; static char __pyx_k__2sch[] = "2sch"; static char __pyx_k__2sci[] = "2sci"; static char __pyx_k__Outs[] = "Outs"; static char __pyx_k__args[] = "args"; static char __pyx_k__dup2[] = "dup2"; static char __pyx_k__flag[] = "flag"; static char __pyx_k__join[] = "join"; static char __pyx_k__mapq[] = "mapq"; static char __pyx_k__mask[] = "mask"; static char __pyx_k__mode[] = "mode"; static char __pyx_k__mpos[] = "mpos"; static char __pyx_k__mrnm[] = "mrnm"; static char __pyx_k__mtid[] = "mtid"; static char __pyx_k__open[] = "open"; static char __pyx_k__path[] = "path"; static char __pyx_k__port[] = "port"; static char __pyx_k__qpos[] = "qpos"; static char __pyx_k__qseq[] = "qseq"; static char __pyx_k__qual[] = "qual"; static char __pyx_k__read[] = "read"; static char __pyx_k__rlen[] = "rlen"; static char __pyx_k__seek[] = "seek"; static char __pyx_k__self[] = "self"; static char __pyx_k__tags[] = "tags"; static char __pyx_k__text[] = "text"; static char __pyx_k__view[] = "view"; static char __pyx_k__warn[] = "warn"; static char __pyx_k___open[] = "_open"; static char __pyx_k__ascii[] = "ascii"; static char __pyx_k__bqual[] = "bqual"; static char __pyx_k__cigar[] = "cigar"; static char __pyx_k__close[] = "close"; static char __pyx_k__flush[] = "flush"; static char __pyx_k__indel[] = "indel"; static char __pyx_k__index[] = "index"; static char __pyx_k__isize[] = "isize"; static char __pyx_k__items[] = "items"; static char __pyx_k__l_aux[] = "l_aux"; static char __pyx_k__level[] = "level"; static char __pyx_k__qname[] = "qname"; static char __pyx_k__rname[] = "rname"; static char __pyx_k__setfd[] = "setfd"; static char __pyx_k__split[] = "split"; static char __pyx_k__start[] = "start"; static char __pyx_k__strip[] = "strip"; static char __pyx_k__types[] = "types"; static char __pyx_k__where[] = "where"; static char __pyx_k__write[] = "write"; static char __pyx_k__ctypes[] = "ctypes"; static char __pyx_k__decode[] = "decode"; static char __pyx_k__encode[] = "encode"; static char __pyx_k__exists[] = "exists"; static char __pyx_k__extend[] = "extend"; static char __pyx_k__fields[] = "fields"; static char __pyx_k__fileno[] = "fileno"; static char __pyx_k__gettid[] = "gettid"; static char __pyx_k__header[] = "header"; static char __pyx_k__is_del[] = "is_del"; static char __pyx_k__l_qseq[] = "l_qseq"; static char __pyx_k__m_data[] = "m_data"; static char __pyx_k__method[] = "method"; static char __pyx_k__object[] = "object"; static char __pyx_k__offset[] = "offset"; static char __pyx_k__record[] = "record"; static char __pyx_k__region[] = "region"; static char __pyx_k__remove[] = "remove"; static char __pyx_k__reopen[] = "reopen"; static char __pyx_k__sorted[] = "sorted"; static char __pyx_k__stderr[] = "stderr"; static char __pyx_k__stdout[] = "stdout"; static char __pyx_k__struct[] = "struct"; static char __pyx_k__system[] = "system"; static char __pyx_k__IOError[] = "IOError"; static char __pyx_k__OSError[] = "OSError"; static char __pyx_k__O_CREAT[] = "O_CREAT"; static char __pyx_k__Samfile[] = "Samfile"; static char __pyx_k__Windows[] = "Windows"; static char __pyx_k____all__[] = "__all__"; static char __pyx_k____del__[] = "__del__"; static char __pyx_k____str__[] = "__str__"; static char __pyx_k___isOpen[] = "_isOpen"; static char __pyx_k__compile[] = "compile"; static char __pyx_k__findall[] = "findall"; static char __pyx_k__is_head[] = "is_head"; static char __pyx_k__is_tail[] = "is_tail"; static char __pyx_k__islower[] = "islower"; static char __pyx_k__isupper[] = "isupper"; static char __pyx_k__l_qname[] = "l_qname"; static char __pyx_k__lengths[] = "lengths"; static char __pyx_k__mkstemp[] = "mkstemp"; static char __pyx_k__n_cigar[] = "n_cigar"; static char __pyx_k__pileups[] = "pileups"; static char __pyx_k__release[] = "release"; static char __pyx_k__restore[] = "restore"; static char __pyx_k__samfile[] = "samfile"; static char __pyx_k__setfile[] = "setfile"; static char __pyx_k__stepper[] = "stepper"; static char __pyx_k__streams[] = "streams"; static char __pyx_k__KeyError[] = "KeyError"; static char __pyx_k__O_WRONLY[] = "O_WRONLY"; static char __pyx_k____dict__[] = "__dict__"; static char __pyx_k____exit__[] = "__exit__"; static char __pyx_k____init__[] = "__init__"; static char __pyx_k____main__[] = "__main__"; static char __pyx_k____test__[] = "__test__"; static char __pyx_k__calcsize[] = "calcsize"; static char __pyx_k__callback[] = "callback"; static char __pyx_k__check_sq[] = "check_sq"; static char __pyx_k__coverage[] = "coverage"; static char __pyx_k__data_len[] = "data_len"; static char __pyx_k__exc_type[] = "exc_type"; static char __pyx_k__filename[] = "filename"; static char __pyx_k__genotype[] = "genotype"; static char __pyx_k__nextiter[] = "nextiter"; static char __pyx_k__platform[] = "platform"; static char __pyx_k__samtools[] = "samtools"; static char __pyx_k__tempfile[] = "tempfile"; static char __pyx_k__template[] = "template"; static char __pyx_k__truncate[] = "truncate"; static char __pyx_k__warnings[] = "warnings"; static char __pyx_k__Fastafile[] = "Fastafile"; static char __pyx_k__TypeError[] = "TypeError"; static char __pyx_k____enter__[] = "__enter__"; static char __pyx_k___hasIndex[] = "_hasIndex"; static char __pyx_k__alignment[] = "alignment"; static char __pyx_k__csamtools[] = "csamtools"; static char __pyx_k__enumerate[] = "enumerate"; static char __pyx_k__exc_value[] = "exc_value"; static char __pyx_k__fastafile[] = "fastafile"; static char __pyx_k__itertools[] = "itertools"; static char __pyx_k__max_depth[] = "max_depth"; static char __pyx_k__pack_into[] = "pack_into"; static char __pyx_k__positions[] = "positions"; static char __pyx_k__readlines[] = "readlines"; static char __pyx_k__reference[] = "reference"; static char __pyx_k__setdevice[] = "setdevice"; static char __pyx_k__traceback[] = "traceback"; static char __pyx_k__until_eof[] = "until_eof"; static char __pyx_k__CIGAR2CODE[] = "CIGAR2CODE"; static char __pyx_k__IS_PYTHON3[] = "IS_PYTHON3"; static char __pyx_k__PileupRead[] = "PileupRead"; static char __pyx_k__ValueError[] = "ValueError"; static char __pyx_k___buildLine[] = "_buildLine"; static char __pyx_k__references[] = "references"; static char __pyx_k__startswith[] = "startswith"; static char __pyx_k__AlignedRead[] = "AlignedRead"; static char __pyx_k__CIGAR_REGEX[] = "CIGAR_REGEX"; static char __pyx_k__IteratorRow[] = "IteratorRow"; static char __pyx_k__PileupProxy[] = "PileupProxy"; static char __pyx_k__StderrStore[] = "StderrStore"; static char __pyx_k__add_sq_text[] = "add_sq_text"; static char __pyx_k__collections[] = "collections"; static char __pyx_k__defaultdict[] = "defaultdict"; static char __pyx_k__nreferences[] = "nreferences"; static char __pyx_k__snp_quality[] = "snp_quality"; static char __pyx_k__IndexedReads[] = "IndexedReads"; static char __pyx_k__PileupColumn[] = "PileupColumn"; static char __pyx_k___parseRegion[] = "_parseRegion"; static char __pyx_k__catch_stdout[] = "catch_stdout"; static char __pyx_k__check_header[] = "check_header"; static char __pyx_k__version_info[] = "version_info"; static char __pyx_k__OverflowError[] = "OverflowError"; static char __pyx_k__StopIteration[] = "StopIteration"; static char __pyx_k__VALID_HEADERS[] = "VALID_HEADERS"; static char __pyx_k__AttributeError[] = "AttributeError"; static char __pyx_k__IteratorColumn[] = "IteratorColumn"; static char __pyx_k__readAndRelease[] = "readAndRelease"; static char __pyx_k__reference_base[] = "reference_base"; static char __pyx_k__referencenames[] = "referencenames"; static char __pyx_k__mapping_quality[] = "mapping_quality"; static char __pyx_k____getattribute__[] = "__getattribute__"; static char __pyx_k__referencelengths[] = "referencelengths"; static char __pyx_k__consensus_quality[] = "consensus_quality"; static char __pyx_k__StderrStoreWindows[] = "StderrStoreWindows"; static char __pyx_k__UnicodeDecodeError[] = "UnicodeDecodeError"; static char __pyx_k__VALID_HEADER_ORDER[] = "VALID_HEADER_ORDER"; static char __pyx_k__VALID_HEADER_TYPES[] = "VALID_HEADER_TYPES"; static char __pyx_k___samtools_dispatch[] = "_samtools_dispatch"; static char __pyx_k__getdefaultencoding[] = "getdefaultencoding"; static char __pyx_k__NotImplementedError[] = "NotImplementedError"; static char __pyx_k__VALID_HEADER_FIELDS[] = "VALID_HEADER_FIELDS"; static PyObject *__pyx_kp_u_1; static PyObject *__pyx_kp_s_10; static PyObject *__pyx_kp_s_100; static PyObject *__pyx_kp_s_102; static PyObject *__pyx_kp_s_104; static PyObject *__pyx_kp_s_105; static PyObject *__pyx_kp_s_107; static PyObject *__pyx_kp_s_108; static PyObject *__pyx_kp_s_109; static PyObject *__pyx_kp_s_110; static PyObject *__pyx_kp_s_111; 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static PyObject *__pyx_n_s____init__; static PyObject *__pyx_n_s____main__; static PyObject *__pyx_n_s____str__; static PyObject *__pyx_n_s____test__; static PyObject *__pyx_n_s___buildLine; static PyObject *__pyx_n_s___hasIndex; static PyObject *__pyx_n_s___isOpen; static PyObject *__pyx_n_s___open; static PyObject *__pyx_n_s___parseRegion; static PyObject *__pyx_n_s___samtools_dispatch; static PyObject *__pyx_n_s__add_sq_text; static PyObject *__pyx_n_s__alignment; static PyObject *__pyx_n_s__all; static PyObject *__pyx_n_s__args; static PyObject *__pyx_n_s__ascii; static PyObject *__pyx_n_s__b; static PyObject *__pyx_n_s__beg; static PyObject *__pyx_n_s__bin; static PyObject *__pyx_n_s__bqual; static PyObject *__pyx_n_s__c; static PyObject *__pyx_n_s__calcsize; static PyObject *__pyx_n_s__callback; static PyObject *__pyx_n_s__catch_stdout; static PyObject *__pyx_n_s__check_header; static PyObject *__pyx_n_s__check_sq; static PyObject *__pyx_n_s__chr; static PyObject *__pyx_n_s__cigar; static PyObject *__pyx_n_s__close; static PyObject *__pyx_n_s__collections; static PyObject *__pyx_n_s__compile; static PyObject *__pyx_n_s__consensus_quality; static PyObject *__pyx_n_s__coverage; static PyObject *__pyx_n_s__csamtools; static PyObject *__pyx_n_s__ctypes; static PyObject *__pyx_n_s__d; static PyObject *__pyx_n_s__data_len; static PyObject *__pyx_n_s__decode; static PyObject *__pyx_n_s__defaultdict; static PyObject *__pyx_n_s__dup; static PyObject *__pyx_n_s__dup2; static PyObject *__pyx_n_s__encode; static PyObject *__pyx_n_s__end; static PyObject *__pyx_n_s__enumerate; static PyObject *__pyx_n_s__exc_type; static PyObject *__pyx_n_s__exc_value; static PyObject *__pyx_n_s__exists; static PyObject *__pyx_n_s__extend; static PyObject *__pyx_n_s__f; static PyObject *__pyx_n_s__fastafile; static PyObject *__pyx_n_s__fd; static PyObject *__pyx_n_s__fields; static PyObject *__pyx_n_s__filename; static PyObject *__pyx_n_s__fileno; static PyObject *__pyx_n_s__findall; static PyObject *__pyx_n_s__flag; 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static PyObject *__pyx_n_s__mask; static PyObject *__pyx_n_s__max; static PyObject *__pyx_n_s__max_depth; static PyObject *__pyx_n_s__method; static PyObject *__pyx_n_s__min; static PyObject *__pyx_n_s__mkstemp; static PyObject *__pyx_n_s__mode; static PyObject *__pyx_n_s__mpos; static PyObject *__pyx_n_s__mrnm; static PyObject *__pyx_n_s__mtid; static PyObject *__pyx_n_s__n; static PyObject *__pyx_n_s__n_cigar; static PyObject *__pyx_n_s__nextiter; static PyObject *__pyx_n_s__nreferences; static PyObject *__pyx_n_s__object; static PyObject *__pyx_n_s__offset; static PyObject *__pyx_n_s__open; static PyObject *__pyx_n_s__ord; static PyObject *__pyx_n_s__os; static PyObject *__pyx_n_s__pack_into; static PyObject *__pyx_n_s__path; static PyObject *__pyx_n_s__pileups; static PyObject *__pyx_n_s__platform; static PyObject *__pyx_n_s__port; static PyObject *__pyx_n_s__pos; static PyObject *__pyx_n_s__positions; static PyObject *__pyx_n_s__qname; static PyObject *__pyx_n_s__qpos; static PyObject *__pyx_n_s__qseq; static PyObject *__pyx_n_s__qual; static PyObject *__pyx_n_b__r; static PyObject *__pyx_n_s__r; static PyObject *__pyx_n_s__rU; static PyObject *__pyx_n_s__raw; static PyObject *__pyx_n_b__rb; static PyObject *__pyx_n_s__rb; static PyObject *__pyx_n_s__re; static PyObject *__pyx_n_s__read; static PyObject *__pyx_n_s__readAndRelease; static PyObject *__pyx_n_s__readlines; static PyObject *__pyx_n_s__record; static PyObject *__pyx_n_s__reference; static PyObject *__pyx_n_s__reference_base; static PyObject *__pyx_n_s__referencelengths; static PyObject *__pyx_n_s__referencenames; static PyObject *__pyx_n_s__references; static PyObject *__pyx_n_s__region; static PyObject *__pyx_n_s__release; static PyObject *__pyx_n_s__remove; static PyObject *__pyx_n_s__reopen; static PyObject *__pyx_n_s__restore; static PyObject *__pyx_n_s__rlen; static PyObject *__pyx_n_s__rname; static PyObject *__pyx_n_s__s; static PyObject *__pyx_n_s__samfile; static PyObject *__pyx_n_s__samtools; static PyObject *__pyx_n_s__seek; 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if (__pyx_t_1) { /* "csamtools.pyx":751 * if self.isbam: * if self.samfile.header == NULL: * raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode ) # <<<<<<<<<<<<<< * else: * # in sam files it is optional (samfile full of unmapped reads) */ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_34), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_8)); __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_7)); PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8)); __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; 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return -1; } } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mpos(PyObject *o, void *x) { return __pyx_pf_9csamtools_11AlignedRead_4mpos___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v, void *x) { if (v) { return __pyx_pf_9csamtools_11AlignedRead_4mpos_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pnext(PyObject *o, void *x) { return __pyx_pf_9csamtools_11AlignedRead_5pnext___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v, void *x) { if (v) { return __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_isize(PyObject *o, void *x) { return __pyx_pf_9csamtools_11AlignedRead_5isize___get__(o); } static int 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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_1__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_1__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_1__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_1__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_1__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_1__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_1__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_1__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_1__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_1__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 PyObject *__pyx_getprop_9csamtools_11AlignedRead_aligned_pairs(PyObject *o, void *x) { return __pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(o); } static PyMethodDef __pyx_methods_9csamtools_AlignedRead[] = { {__Pyx_NAMESTR("compare"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_3compare, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_3compare)}, {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_5overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_5overlap)}, {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_6opt, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_6opt)}, {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_7fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_7fancy_str)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_9csamtools_AlignedRead[] = { {(char *)"qname", __pyx_getprop_9csamtools_11AlignedRead_qname, __pyx_setprop_9csamtools_11AlignedRead_qname, __Pyx_DOCSTR(__pyx_k_188), 0}, {(char *)"cigar", __pyx_getprop_9csamtools_11AlignedRead_cigar, __pyx_setprop_9csamtools_11AlignedRead_cigar, __Pyx_DOCSTR(__pyx_k_189), 0}, {(char *)"cigarstring", __pyx_getprop_9csamtools_11AlignedRead_cigarstring, __pyx_setprop_9csamtools_11AlignedRead_cigarstring, __Pyx_DOCSTR(__pyx_k_190), 0}, {(char *)"seq", __pyx_getprop_9csamtools_11AlignedRead_seq, __pyx_setprop_9csamtools_11AlignedRead_seq, __Pyx_DOCSTR(__pyx_k_191), 0}, {(char *)"qual", __pyx_getprop_9csamtools_11AlignedRead_qual, __pyx_setprop_9csamtools_11AlignedRead_qual, __Pyx_DOCSTR(__pyx_k_192), 0}, {(char *)"query", __pyx_getprop_9csamtools_11AlignedRead_query, 0, __Pyx_DOCSTR(__pyx_k_193), 0}, {(char *)"qqual", __pyx_getprop_9csamtools_11AlignedRead_qqual, 0, __Pyx_DOCSTR(__pyx_k_194), 0}, {(char *)"qstart", __pyx_getprop_9csamtools_11AlignedRead_qstart, 0, __Pyx_DOCSTR(__pyx_k_195), 0}, {(char *)"qend", __pyx_getprop_9csamtools_11AlignedRead_qend, 0, __Pyx_DOCSTR(__pyx_k_196), 0}, {(char *)"qlen", __pyx_getprop_9csamtools_11AlignedRead_qlen, 0, __Pyx_DOCSTR(__pyx_k_197), 0}, {(char *)"tags", __pyx_getprop_9csamtools_11AlignedRead_tags, __pyx_setprop_9csamtools_11AlignedRead_tags, __Pyx_DOCSTR(__pyx_k_198), 0}, {(char *)"flag", __pyx_getprop_9csamtools_11AlignedRead_flag, __pyx_setprop_9csamtools_11AlignedRead_flag, __Pyx_DOCSTR(__pyx_k_199), 0}, {(char *)"rname", __pyx_getprop_9csamtools_11AlignedRead_rname, __pyx_setprop_9csamtools_11AlignedRead_rname, __Pyx_DOCSTR(__pyx_k_200), 0}, {(char *)"tid", __pyx_getprop_9csamtools_11AlignedRead_tid, __pyx_setprop_9csamtools_11AlignedRead_tid, __Pyx_DOCSTR(__pyx_k_201), 0}, {(char *)"pos", __pyx_getprop_9csamtools_11AlignedRead_pos, __pyx_setprop_9csamtools_11AlignedRead_pos, __Pyx_DOCSTR(__pyx_k_202), 0}, {(char *)"bin", __pyx_getprop_9csamtools_11AlignedRead_bin, __pyx_setprop_9csamtools_11AlignedRead_bin, __Pyx_DOCSTR(__pyx_k_203), 0}, {(char *)"rlen", __pyx_getprop_9csamtools_11AlignedRead_rlen, 0, __Pyx_DOCSTR(__pyx_k_204), 0}, {(char *)"aend", __pyx_getprop_9csamtools_11AlignedRead_aend, 0, __Pyx_DOCSTR(__pyx_k_205), 0}, {(char *)"alen", __pyx_getprop_9csamtools_11AlignedRead_alen, 0, __Pyx_DOCSTR(__pyx_k_206), 0}, {(char *)"mapq", __pyx_getprop_9csamtools_11AlignedRead_mapq, __pyx_setprop_9csamtools_11AlignedRead_mapq, __Pyx_DOCSTR(__pyx_k_207), 0}, {(char *)"mrnm", __pyx_getprop_9csamtools_11AlignedRead_mrnm, __pyx_setprop_9csamtools_11AlignedRead_mrnm, __Pyx_DOCSTR(__pyx_k_208), 0}, {(char *)"rnext", __pyx_getprop_9csamtools_11AlignedRead_rnext, __pyx_setprop_9csamtools_11AlignedRead_rnext, __Pyx_DOCSTR(__pyx_k_209), 0}, {(char *)"mpos", __pyx_getprop_9csamtools_11AlignedRead_mpos, __pyx_setprop_9csamtools_11AlignedRead_mpos, __Pyx_DOCSTR(__pyx_k_210), 0}, {(char *)"pnext", __pyx_getprop_9csamtools_11AlignedRead_pnext, __pyx_setprop_9csamtools_11AlignedRead_pnext, __Pyx_DOCSTR(__pyx_k_211), 0}, {(char *)"isize", __pyx_getprop_9csamtools_11AlignedRead_isize, __pyx_setprop_9csamtools_11AlignedRead_isize, __Pyx_DOCSTR(__pyx_k_212), 0}, {(char *)"tlen", __pyx_getprop_9csamtools_11AlignedRead_tlen, __pyx_setprop_9csamtools_11AlignedRead_tlen, __Pyx_DOCSTR(__pyx_k_213), 0}, {(char *)"is_paired", __pyx_getprop_9csamtools_11AlignedRead_is_paired, __pyx_setprop_9csamtools_11AlignedRead_is_paired, __Pyx_DOCSTR(__pyx_k_214), 0}, {(char *)"is_proper_pair", __pyx_getprop_9csamtools_11AlignedRead_is_proper_pair, __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair, __Pyx_DOCSTR(__pyx_k_215), 0}, {(char *)"is_unmapped", __pyx_getprop_9csamtools_11AlignedRead_is_unmapped, __pyx_setprop_9csamtools_11AlignedRead_is_unmapped, __Pyx_DOCSTR(__pyx_k_216), 0}, {(char *)"mate_is_unmapped", __pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped, __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped, __Pyx_DOCSTR(__pyx_k_217), 0}, {(char *)"is_reverse", __pyx_getprop_9csamtools_11AlignedRead_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_is_reverse, __Pyx_DOCSTR(__pyx_k_218), 0}, {(char *)"mate_is_reverse", __pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse, __Pyx_DOCSTR(__pyx_k_219), 0}, {(char *)"is_read1", __pyx_getprop_9csamtools_11AlignedRead_is_read1, __pyx_setprop_9csamtools_11AlignedRead_is_read1, __Pyx_DOCSTR(__pyx_k_220), 0}, {(char *)"is_read2", __pyx_getprop_9csamtools_11AlignedRead_is_read2, __pyx_setprop_9csamtools_11AlignedRead_is_read2, __Pyx_DOCSTR(__pyx_k_221), 0}, {(char *)"is_secondary", __pyx_getprop_9csamtools_11AlignedRead_is_secondary, __pyx_setprop_9csamtools_11AlignedRead_is_secondary, __Pyx_DOCSTR(__pyx_k_222), 0}, {(char *)"is_qcfail", __pyx_getprop_9csamtools_11AlignedRead_is_qcfail, __pyx_setprop_9csamtools_11AlignedRead_is_qcfail, __Pyx_DOCSTR(__pyx_k_223), 0}, {(char *)"is_duplicate", __pyx_getprop_9csamtools_11AlignedRead_is_duplicate, __pyx_setprop_9csamtools_11AlignedRead_is_duplicate, __Pyx_DOCSTR(__pyx_k_224), 0}, {(char *)"positions", __pyx_getprop_9csamtools_11AlignedRead_positions, 0, __Pyx_DOCSTR(__pyx_k_225), 0}, {(char *)"aligned_pairs", __pyx_getprop_9csamtools_11AlignedRead_aligned_pairs, 0, __Pyx_DOCSTR(__pyx_k_226), 0}, {0, 0, 0, 0, 0} }; 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 }; static 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_4__hash__, /*tp_hash*/ 0, /*tp_call*/ __pyx_pf_9csamtools_11AlignedRead_2__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_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*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\n In Python 3, the fields containing sequence and quality\n (seq, query, qual and qqual) data are of type bytes. Other\n string data, such as the qname field and strings in the\n tags tuple, is represented as unicode strings. On assignment,\n both bytes and unicode objects are allowed, but unicode strings\n must contain only ASCII characters.\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_15__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } (*Py_TYPE(o)->tp_free)(o); } static PyObject *__pyx_getprop_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_mapped(PyObject *o, void *x) { return __pyx_pf_9csamtools_7Samfile_6mapped___get__(o); } static PyObject *__pyx_getprop_9csamtools_7Samfile_unmapped(PyObject *o, void *x) { return __pyx_pf_9csamtools_7Samfile_8unmapped___get__(o); } static PyObject *__pyx_getprop_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_1_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_1_isOpen)}, {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_2_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_2_hasIndex)}, {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_3_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_3_open)}, {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_4gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_4gettid)}, {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_5getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_5getrname)}, {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_6_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_6_parseRegion)}, {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_7reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_7reset)}, {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_8seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_8seek)}, {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_9tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_9tell)}, {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_10fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_10fetch)}, {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_11mate, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_11mate)}, {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_12count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_12count)}, {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_13pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_13pileup)}, {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_14close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_14close)}, {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_16write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_16write)}, {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_17__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_17__enter__)}, {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_18__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_18__exit__)}, {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_19_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_19_buildLine)}, {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_21__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_21__next__)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_9csamtools_Samfile[] = { {(char *)"filename", __pyx_getprop_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_187), 0}, {(char *)"nreferences", __pyx_getprop_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_227), 0}, {(char *)"references", __pyx_getprop_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_228), 0}, {(char *)"lengths", __pyx_getprop_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_229), 0}, {(char *)"mapped", __pyx_getprop_9csamtools_7Samfile_mapped, 0, __Pyx_DOCSTR(__pyx_k_230), 0}, {(char *)"unmapped", __pyx_getprop_9csamtools_7Samfile_unmapped, 0, __Pyx_DOCSTR(__pyx_k_231), 0}, {(char *)"text", __pyx_getprop_9csamtools_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_232), 0}, {(char *)"header", __pyx_getprop_9csamtools_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_233), 0}, {0, 0, 0, 0, 0} }; 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 }; static 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_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None,\n add_sq_text = False, check_header = True, check_sq = True )*\n\n A :term:`SAM`/:term:`BAM` formatted file. The file is automatically opened.\n\n *mode* should be ``r`` for reading or ``w`` for writing. The default is text mode (:term:`SAM`). For binary\n (:term:`BAM`) I/O you should append ``b`` for compressed or ``u`` for uncompressed :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 'rb', 'r', thus both the following\n should work::\n\n f1 = pysam.Samfile('ex1.bam' )\n f2 = pysam.Samfile('ex1.sam' )\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. The header is constructed first from all the defined fields,\n followed by user tags in alphabetical order.\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 By default, 'SQ' and 'LN' tags will be added to the header text. This option can be\n changed by unsetting the flag *add_sq_text*. \n\n By default, if file a file is opened in mode 'r', it is checked for a valid header\n (*check_header* = True) and a definition of chromosome names (*check_sq* = True). \n \n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pf_9csamtools_7Samfile_20__iter__, /*tp_iter*/ __pyx_pf_9csamtools_7Samfile_21__next__, /*tp_iternext*/ __pyx_methods_9csamtools_Samfile, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_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_1__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_234), 0}, {(char *)"n", __pyx_getprop_9csamtools_11PileupProxy_n, __pyx_setprop_9csamtools_11PileupProxy_n, __Pyx_DOCSTR(__pyx_k_235), 0}, {(char *)"pos", __pyx_getprop_9csamtools_11PileupProxy_pos, 0, 0, 0}, {(char *)"pileups", __pyx_getprop_9csamtools_11PileupProxy_pileups, 0, __Pyx_DOCSTR(__pyx_k_236), 0}, {0, 0, 0, 0, 0} }; 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 }; static 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_1__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_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*/ 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_237), 0}, {(char *)"qpos", __pyx_getprop_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_238), 0}, {(char *)"indel", __pyx_getprop_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_239), 0}, {(char *)"is_del", __pyx_getprop_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_240), 0}, {(char *)"is_head", __pyx_getprop_9csamtools_10PileupRead_is_head, 0, 0, 0}, {(char *)"is_tail", __pyx_getprop_9csamtools_10PileupRead_is_tail, 0, 0, 0}, {(char *)"level", __pyx_getprop_9csamtools_10PileupRead_level, 0, 0, 0}, {0, 0, 0, 0, 0} }; 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 }; static 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_1__str__, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_PileupRead, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("PileupRead()\nA read aligned to a column.\n "), /*tp_doc*/ __pyx_tp_traverse_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 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 }; static 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_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*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_3__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_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_17IteratorRowRegion_2__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 }; static 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_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*/ 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_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_3__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_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorRowAll_2__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 }; static 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_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*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_1__iter__, /*tp_iter*/ __pyx_pf_9csamtools_14IteratorRowAll_2__next__, /*tp_iternext*/ __pyx_methods_9csamtools_IteratorRowAll, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_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_1nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_1nextiter)}, {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__)}, {0, 0, 0, 0} }; 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 }; static 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_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*/ 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*/ 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_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__)}, {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 }; static 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_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*/ 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_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_4__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_2addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_2addReference)}, {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_3hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_3hasReference)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_9csamtools_IteratorColumn[] = { {(char *)"seq_len", __pyx_getprop_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_241), 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_IteratorColumn = { 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_IteratorColumn = { 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_IteratorColumn = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_9csamtools_IteratorColumn = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("csamtools.IteratorColumn"), /*tp_name*/ sizeof(struct __pyx_obj_9csamtools_IteratorColumn), /*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_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*/ 0, /*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 controls how the iterator advances.\n Possible options for the stepper are\n\n all\n use all reads for pileup.\n samtools\n same filter and read processing as in :term:`csamtools` pileup\n\n The default is to use \"all\" if no stepper is given.\n\n fastafile\n A :class:`FastaFile` object\n mask\n Skip all reads with bits set in mask.\n max_depth\n maximum read depth. The default is 8000.\n "), /*tp_doc*/ __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/ __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pf_9csamtools_14IteratorColumn_1__iter__, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_9csamtools_IteratorColumn, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_9csamtools_IteratorColumn, /*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_IteratorColumn, /*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_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); 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) { 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__)}, {0, 0, 0, 0} }; 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 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 PyMappingMethods __pyx_tp_as_mapping_IteratorColumnRegion = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; 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 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_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*/ 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_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_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_IteratorColumnAllRefs[] = { {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_IteratorColumnAllRefs = { 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_IteratorColumnAllRefs = { 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_IteratorColumnAllRefs = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("csamtools.IteratorColumnAllRefs"), /*tp_name*/ sizeof(struct __pyx_obj_9csamtools_IteratorColumnAllRefs), /*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_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*/ 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*/ 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_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_IteratorColumnAllRefs, /*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_IndexedReads(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_9csamtools_IndexedReads *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_9csamtools_IndexedReads *)o); p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); p->index = Py_None; Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_9csamtools_IndexedReads(PyObject *o) { struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o; { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } Py_XDECREF(((PyObject *)p->samfile)); Py_XDECREF(p->index); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_9csamtools_IndexedReads(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o; if (p->samfile) { e = (*v)(((PyObject*)p->samfile), a); if (e) return e; } if (p->index) { e = (*v)(p->index, a); if (e) return e; } return 0; } static int __pyx_tp_clear_9csamtools_IndexedReads(PyObject *o) { struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o; PyObject* tmp; tmp = ((PyObject*)p->samfile); p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->index); p->index = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_9csamtools_IndexedReads[] = { {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_1build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_1build)}, {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_2find, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_2find)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_IndexedReads = { 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_IndexedReads = { 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_IndexedReads = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_IndexedReads = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_9csamtools_IndexedReads = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("csamtools.IndexedReads"), /*tp_name*/ sizeof(struct __pyx_obj_9csamtools_IndexedReads), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_9csamtools_IndexedReads, /*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_IndexedReads, /*tp_as_number*/ &__pyx_tp_as_sequence_IndexedReads, /*tp_as_sequence*/ &__pyx_tp_as_mapping_IndexedReads, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 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*/ __Pyx_DOCSTR("IndexedReads(Samfile samfile, int reopen=True)\nindex a bamfile by read.\n\n The index is kept in memory.\n\n By default, the file is re-openend to avoid conflicts if\n multiple operators work on the same file. Set *reopen* = False\n to not re-open *samfile*.\n "), /*tp_doc*/ __pyx_tp_traverse_9csamtools_IndexedReads, /*tp_traverse*/ __pyx_tp_clear_9csamtools_IndexedReads, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_9csamtools_IndexedReads, /*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*/ __pyx_pf_9csamtools_12IndexedReads___init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_9csamtools_IndexedReads, /*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_SNPCall(PyTypeObject *t, PyObject *a, PyObject *k) { PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; return o; } static void __pyx_tp_dealloc_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[] = { {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_9csamtools_SNPCall[] = { {(char *)"tid", __pyx_getprop_9csamtools_7SNPCall_tid, 0, __Pyx_DOCSTR(__pyx_k_234), 0}, {(char *)"pos", __pyx_getprop_9csamtools_7SNPCall_pos, 0, __Pyx_DOCSTR(__pyx_k_242), 0}, {(char *)"reference_base", __pyx_getprop_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_243), 0}, {(char *)"genotype", __pyx_getprop_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_244), 0}, {(char *)"consensus_quality", __pyx_getprop_9csamtools_7SNPCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_245), 0}, {(char *)"snp_quality", __pyx_getprop_9csamtools_7SNPCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_246), 0}, {(char *)"mapping_quality", 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#endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_9csamtools_SNPCall = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("csamtools.SNPCall"), /*tp_name*/ sizeof(struct __pyx_obj_9csamtools_SNPCall), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_9csamtools_SNPCall, /*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_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*/ __pyx_pf_9csamtools_7SNPCall___str__, /*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*/ 0, /*tp_richcompare*/ 0, 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#endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_Generator_type = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("csamtools.__pyx_Generator"), /*tp_name*/ sizeof(struct __pyx_Generator_object), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_9csamtools___pyx_Generator, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number___pyx_Generator, /*tp_as_number*/ &__pyx_tp_as_sequence___pyx_Generator, /*tp_as_sequence*/ &__pyx_tp_as_mapping___pyx_Generator, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer___pyx_Generator, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ 0, 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if (PyType_Ready(&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;} { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { __pyx_wrapperbase_9csamtools_7Samfile_21__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; __pyx_wrapperbase_9csamtools_7Samfile_21__next__.doc = __pyx_doc_9csamtools_7Samfile_21__next__; ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_7Samfile_21__next__; } } if (__Pyx_SetVtable(__pyx_type_9csamtools_Samfile.tp_dict, __pyx_vtabptr_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools_Samfile = &__pyx_type_9csamtools_Samfile; if (PyType_Ready(&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3002; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "PileupProxy", (PyObject *)&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3002; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools_PileupProxy = &__pyx_type_9csamtools_PileupProxy; if (PyType_Ready(&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3054; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3054; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools_PileupRead = &__pyx_type_9csamtools_PileupRead; if (PyType_Ready(&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools_IteratorRow = &__pyx_type_9csamtools_IteratorRow; __pyx_vtabptr_9csamtools_IteratorRowRegion = &__pyx_vtable_9csamtools_IteratorRowRegion; __pyx_vtable_9csamtools_IteratorRowRegion.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_getCurrent; __pyx_vtable_9csamtools_IteratorRowRegion.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_cnext; __pyx_type_9csamtools_IteratorRowRegion.tp_base = __pyx_ptype_9csamtools_IteratorRow; if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { __pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; __pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__.doc = __pyx_doc_9csamtools_17IteratorRowRegion_2__next__; ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__; } } if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "IteratorRowRegion", (PyObject *)&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools_IteratorRowRegion = &__pyx_type_9csamtools_IteratorRowRegion; __pyx_vtabptr_9csamtools_IteratorRowAll = &__pyx_vtable_9csamtools_IteratorRowAll; __pyx_vtable_9csamtools_IteratorRowAll.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_getCurrent; __pyx_vtable_9csamtools_IteratorRowAll.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_cnext; __pyx_type_9csamtools_IteratorRowAll.tp_base = __pyx_ptype_9csamtools_IteratorRow; if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;} { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { __pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; __pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__.doc = __pyx_doc_9csamtools_14IteratorRowAll_2__next__; ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__; } } if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAll", (PyObject *)&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools_IteratorRowAll = &__pyx_type_9csamtools_IteratorRowAll; __pyx_type_9csamtools_IteratorRowAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorRow; if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;} { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__.doc = __pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__; ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__; } } if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools_IteratorRowAllRefs = &__pyx_type_9csamtools_IteratorRowAllRefs; __pyx_vtabptr_9csamtools_IteratorRowSelection = &__pyx_vtable_9csamtools_IteratorRowSelection; __pyx_vtable_9csamtools_IteratorRowSelection.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_getCurrent; __pyx_vtable_9csamtools_IteratorRowSelection.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_cnext; __pyx_type_9csamtools_IteratorRowSelection.tp_base = __pyx_ptype_9csamtools_IteratorRow; if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { __pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; __pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__.doc = __pyx_doc_9csamtools_20IteratorRowSelection_2__next__; ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__; } } if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "IteratorRowSelection", (PyObject *)&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools_IteratorRowSelection = &__pyx_type_9csamtools_IteratorRowSelection; __pyx_vtabptr_9csamtools_IteratorColumn = &__pyx_vtable_9csamtools_IteratorColumn; __pyx_vtable_9csamtools_IteratorColumn.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_cnext; __pyx_vtable_9csamtools_IteratorColumn.getSequence = (char *(*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_getSequence; __pyx_vtable_9csamtools_IteratorColumn.setMask = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_setMask; __pyx_vtable_9csamtools_IteratorColumn.setupIteratorData = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args))__pyx_f_9csamtools_14IteratorColumn_setupIteratorData; __pyx_vtable_9csamtools_IteratorColumn.reset = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_reset; if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools_IteratorColumn = &__pyx_type_9csamtools_IteratorColumn; __pyx_vtabptr_9csamtools_IteratorColumnRegion = &__pyx_vtable_9csamtools_IteratorColumnRegion; __pyx_vtable_9csamtools_IteratorColumnRegion.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn; __pyx_type_9csamtools_IteratorColumnRegion.tp_base = __pyx_ptype_9csamtools_IteratorColumn; if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;} { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__.doc = __pyx_doc_9csamtools_20IteratorColumnRegion_1__next__; ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__; } } if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools_IteratorColumnRegion = &__pyx_type_9csamtools_IteratorColumnRegion; __pyx_vtabptr_9csamtools_IteratorColumnAllRefs = &__pyx_vtable_9csamtools_IteratorColumnAllRefs; __pyx_vtable_9csamtools_IteratorColumnAllRefs.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn; __pyx_type_9csamtools_IteratorColumnAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorColumn; if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;} { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__.doc = __pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__; ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__; } } if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnAllRefs.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools_IteratorColumnAllRefs = &__pyx_type_9csamtools_IteratorColumnAllRefs; if (PyType_Ready(&__pyx_type_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3776; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "IndexedReads", (PyObject *)&__pyx_type_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3776; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools_IndexedReads = &__pyx_type_9csamtools_IndexedReads; if (PyType_Ready(&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "SNPCall", (PyObject *)&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools_SNPCall = &__pyx_type_9csamtools_SNPCall; 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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 int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { if (unlikely(!type)) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (likely(PyObject_TypeCheck(obj, type))) return 1; PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", Py_TYPE(obj)->tp_name, type->tp_name); return 0; } static CYTHON_INLINE int __Pyx_CheckKeywordStrings( PyObject *kwdict, const char* function_name, int kw_allowed) { PyObject* key = 0; Py_ssize_t pos = 0; while (PyDict_Next(kwdict, &pos, &key, 0)) { #if PY_MAJOR_VERSION < 3 if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) #else if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) #endif goto invalid_keyword_type; } if ((!kw_allowed) && unlikely(key)) goto invalid_keyword; return 1; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); return 0; invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif return 0; } static void __Pyx_RaiseDoubleKeywordsError( const char* func_name, PyObject* kw_name) { PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION >= 3 "%s() got multiple values for keyword argument '%U'", func_name, kw_name); #else "%s() got multiple values for keyword argument '%s'", func_name, PyString_AS_STRING(kw_name)); #endif } static int __Pyx_ParseOptionalKeywords( PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name) { PyObject *key = 0, *value = 0; Py_ssize_t pos = 0; PyObject*** name; PyObject*** first_kw_arg = argnames + num_pos_args; while (PyDict_Next(kwds, &pos, &key, &value)) { name = first_kw_arg; while (*name && (**name != key)) name++; if (*name) { values[name-argnames] = value; } else { #if PY_MAJOR_VERSION < 3 if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) { #else if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) { #endif goto invalid_keyword_type; } else { for (name = first_kw_arg; *name; name++) { #if PY_MAJOR_VERSION >= 3 if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && PyUnicode_Compare(**name, key) == 0) break; #else if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) && _PyString_Eq(**name, key)) break; #endif } if (*name) { values[name-argnames] = value; } else { /* unexpected keyword found */ for (name=argnames; name != first_kw_arg; name++) { if (**name == key) goto arg_passed_twice; #if PY_MAJOR_VERSION >= 3 if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice; #else if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) && _PyString_Eq(**name, key)) goto arg_passed_twice; #endif } if (kwds2) { if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; } else { goto invalid_keyword; } } } } } return 0; arg_passed_twice: __Pyx_RaiseDoubleKeywordsError(function_name, **name); goto bad; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); goto bad; invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif 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 *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"; } PyErr_Format(PyExc_TypeError, "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)", func_name, more_or_less, num_expected, (num_expected == 1) ? "" : "s", num_found); } static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact) { if (!type) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (none_allowed && obj == Py_None) return 1; else if (exact) { if (Py_TYPE(obj) == type) return 1; } else { if (PyObject_TypeCheck(obj, type)) return 1; } PyErr_Format(PyExc_TypeError, "Argument '%s' has incorrect type (expected %s, got %s)", name, type->tp_name, Py_TYPE(obj)->tp_name); return 0; } static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { PyObject *local_type, *local_value, *local_tb; PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); local_type = tstate->curexc_type; local_value = tstate->curexc_value; local_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; PyErr_NormalizeException(&local_type, &local_value, &local_tb); if (unlikely(tstate->curexc_type)) goto bad; #if PY_MAJOR_VERSION >= 3 if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) goto bad; #endif *type = local_type; *value = local_value; *tb = local_tb; Py_INCREF(local_type); Py_INCREF(local_value); Py_INCREF(local_tb); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = local_type; tstate->exc_value = local_value; tstate->exc_traceback = local_tb; /* Make sure tstate is in a consistent state when we XDECREF these objects (XDECREF may run arbitrary code). */ Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); return 0; bad: *type = 0; *value = 0; *tb = 0; Py_XDECREF(local_type); Py_XDECREF(local_value); Py_XDECREF(local_tb); return -1; } static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack", index, (index == 1) ? "" : "s"); } static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { PyErr_Format(PyExc_ValueError, "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected); } static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { if (unlikely(retval)) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); return -1; } else if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { PyErr_Clear(); return 0; } else { return -1; } } return 0; } static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable"); } static CYTHON_INLINE long __Pyx_div_long(long a, long b) { long q = a / b; long r = a - q*b; q -= ((r != 0) & ((r ^ b) < 0)); return q; } static CYTHON_INLINE long __Pyx_mod_long(long a, long b) { long r = a % b; r += ((r != 0) & ((r ^ b) < 0)) * b; return r; } static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); } static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { PyThreadState *tstate = PyThreadState_GET(); *type = tstate->exc_type; *value = tstate->exc_value; *tb = tstate->exc_traceback; Py_XINCREF(*type); Py_XINCREF(*value); Py_XINCREF(*tb); } static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = type; tstate->exc_value = value; tstate->exc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); } static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) { PyObject *py_import = 0; PyObject *empty_list = 0; PyObject *module = 0; PyObject *global_dict = 0; PyObject *empty_dict = 0; PyObject *list; py_import = __Pyx_GetAttrString(__pyx_b, "__import__"); if (!py_import) goto bad; if (from_list) list = from_list; else { empty_list = PyList_New(0); if (!empty_list) goto bad; list = empty_list; } global_dict = PyModule_GetDict(__pyx_m); if (!global_dict) goto bad; empty_dict = PyDict_New(); if (!empty_dict) goto bad; #if PY_VERSION_HEX >= 0x02050000 { PyObject *py_level = PyInt_FromLong(level); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); } #else if (level>0) { PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4."); goto bad; } module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, NULL); #endif bad: Py_XDECREF(empty_list); Py_XDECREF(py_import); Py_XDECREF(empty_dict); 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, (char *)"__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; /* 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); 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 int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { if (s1 == s2) { /* as done by PyObject_RichCompareBool(); also catches the (interned) empty string */ return (equals == Py_EQ); } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) { return (equals == Py_NE); } else if (PyBytes_GET_SIZE(s1) == 1) { if (equals == Py_EQ) return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]); else return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]); } else { int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1)); return (equals == Py_EQ) ? (result == 0) : (result != 0); } } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { return (equals == Py_NE); } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { return (equals == Py_NE); } else { int result; PyObject* py_result = PyObject_RichCompare(s1, s2, equals); if (!py_result) return -1; result = __Pyx_PyObject_IsTrue(py_result); Py_DECREF(py_result); return result; } } static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { if (s1 == s2) { /* as done by PyObject_RichCompareBool(); also catches the (interned) empty string */ return (equals == Py_EQ); } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) { if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) { return (equals == Py_NE); } else if (PyUnicode_GET_SIZE(s1) == 1) { if (equals == Py_EQ) return (PyUnicode_AS_UNICODE(s1)[0] == PyUnicode_AS_UNICODE(s2)[0]); else return (PyUnicode_AS_UNICODE(s1)[0] != PyUnicode_AS_UNICODE(s2)[0]); } else { int result = PyUnicode_Compare(s1, s2); if ((result == -1) && unlikely(PyErr_Occurred())) return -1; return (equals == Py_EQ) ? (result == 0) : (result != 0); } } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) { return (equals == Py_NE); } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) { return (equals == Py_NE); } else { int result; PyObject* py_result = PyObject_RichCompare(s1, s2, equals); if (!py_result) return -1; result = __Pyx_PyObject_IsTrue(py_result); Py_DECREF(py_result); return result; } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int8_t(int8_t val) { const int8_t neg_one = (int8_t)-1, const_zero = (int8_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(int8_t) == sizeof(char)) || (sizeof(int8_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(int8_t) == sizeof(int)) || (sizeof(int8_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(int8_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(int8_t), little, !is_unsigned); } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint8_t(uint8_t val) { const uint8_t neg_one = (uint8_t)-1, const_zero = (uint8_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(uint8_t) == sizeof(char)) || (sizeof(uint8_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(uint8_t) == sizeof(int)) || (sizeof(uint8_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(uint8_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(uint8_t), little, !is_unsigned); } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int16_t(int16_t val) { const int16_t neg_one = (int16_t)-1, const_zero = (int16_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(int16_t) == sizeof(char)) || (sizeof(int16_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(int16_t) == sizeof(int)) || (sizeof(int16_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(int16_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(int16_t), little, !is_unsigned); } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint16_t(uint16_t val) { const uint16_t neg_one = (uint16_t)-1, const_zero = (uint16_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(uint16_t) == sizeof(char)) || (sizeof(uint16_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(uint16_t) == sizeof(int)) || (sizeof(uint16_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(uint16_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(uint16_t), little, !is_unsigned); } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int32_t(int32_t val) { const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(int32_t) == sizeof(char)) || (sizeof(int32_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(int32_t) == sizeof(int)) || (sizeof(int32_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(int32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(int32_t), little, !is_unsigned); } } 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; if ((sizeof(uint32_t) == sizeof(char)) || (sizeof(uint32_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(uint32_t) == sizeof(int)) || (sizeof(uint32_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(uint32_t), little, !is_unsigned); } } static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) { const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0; const int is_unsigned = const_zero < neg_one; if (sizeof(uint32_t) == sizeof(char)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedChar(x); else return (uint32_t)__Pyx_PyInt_AsSignedChar(x); } else if (sizeof(uint32_t) == sizeof(short)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedShort(x); else return (uint32_t)__Pyx_PyInt_AsSignedShort(x); } else if (sizeof(uint32_t) == sizeof(int)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedInt(x); else return (uint32_t)__Pyx_PyInt_AsSignedInt(x); } else if (sizeof(uint32_t) == sizeof(long)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedLong(x); else return (uint32_t)__Pyx_PyInt_AsSignedLong(x); } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedLongLong(x); else return (uint32_t)__Pyx_PyInt_AsSignedLongLong(x); } else { uint32_t val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } return (uint32_t)-1; } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t val) { const int64_t neg_one = (int64_t)-1, const_zero = (int64_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(int64_t) == sizeof(char)) || (sizeof(int64_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(int64_t) == sizeof(int)) || (sizeof(int64_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(int64_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(int64_t), little, !is_unsigned); } } static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject* x) { const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0; const int is_unsigned = const_zero < neg_one; if (sizeof(uint64_t) == sizeof(char)) { if (is_unsigned) return (uint64_t)__Pyx_PyInt_AsUnsignedChar(x); else return (uint64_t)__Pyx_PyInt_AsSignedChar(x); } else if (sizeof(uint64_t) == sizeof(short)) { if (is_unsigned) return (uint64_t)__Pyx_PyInt_AsUnsignedShort(x); else return (uint64_t)__Pyx_PyInt_AsSignedShort(x); } else if (sizeof(uint64_t) == sizeof(int)) { if (is_unsigned) return (uint64_t)__Pyx_PyInt_AsUnsignedInt(x); else return (uint64_t)__Pyx_PyInt_AsSignedInt(x); } else if (sizeof(uint64_t) == sizeof(long)) { if (is_unsigned) return (uint64_t)__Pyx_PyInt_AsUnsignedLong(x); else return (uint64_t)__Pyx_PyInt_AsSignedLong(x); } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return (uint64_t)__Pyx_PyInt_AsUnsignedLongLong(x); else return (uint64_t)__Pyx_PyInt_AsSignedLongLong(x); } else { uint64_t val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } return (uint64_t)-1; } } static CYTHON_INLINE uint8_t __Pyx_PyInt_from_py_uint8_t(PyObject* x) { const uint8_t neg_one = (uint8_t)-1, const_zero = (uint8_t)0; const int is_unsigned = const_zero < neg_one; if (sizeof(uint8_t) == sizeof(char)) { if (is_unsigned) return (uint8_t)__Pyx_PyInt_AsUnsignedChar(x); else return (uint8_t)__Pyx_PyInt_AsSignedChar(x); } else if (sizeof(uint8_t) == sizeof(short)) { if (is_unsigned) return (uint8_t)__Pyx_PyInt_AsUnsignedShort(x); else return (uint8_t)__Pyx_PyInt_AsSignedShort(x); } else if (sizeof(uint8_t) == sizeof(int)) { if (is_unsigned) return (uint8_t)__Pyx_PyInt_AsUnsignedInt(x); else return (uint8_t)__Pyx_PyInt_AsSignedInt(x); } else if (sizeof(uint8_t) == sizeof(long)) { if (is_unsigned) return (uint8_t)__Pyx_PyInt_AsUnsignedLong(x); else return (uint8_t)__Pyx_PyInt_AsSignedLong(x); } else if (sizeof(uint8_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return (uint8_t)__Pyx_PyInt_AsUnsignedLongLong(x); else return (uint8_t)__Pyx_PyInt_AsSignedLongLong(x); } else { uint8_t val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } return (uint8_t)-1; } } static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) { const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0; const int is_unsigned = const_zero < neg_one; if (sizeof(int32_t) == sizeof(char)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedChar(x); else return (int32_t)__Pyx_PyInt_AsSignedChar(x); } else if (sizeof(int32_t) == sizeof(short)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedShort(x); else return (int32_t)__Pyx_PyInt_AsSignedShort(x); } else if (sizeof(int32_t) == sizeof(int)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedInt(x); else return (int32_t)__Pyx_PyInt_AsSignedInt(x); } else if (sizeof(int32_t) == sizeof(long)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedLong(x); else return (int32_t)__Pyx_PyInt_AsSignedLong(x); } else if (sizeof(int32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedLongLong(x); else return (int32_t)__Pyx_PyInt_AsSignedLongLong(x); } else { int32_t val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } return (int32_t)-1; } } 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; if ((sizeof(uint64_t) == sizeof(char)) || (sizeof(uint64_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(uint64_t) == sizeof(int)) || (sizeof(uint64_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(uint64_t), little, !is_unsigned); } } static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned char" : "value too large to convert to unsigned char"); } return (unsigned char)-1; } return (unsigned char)val; } return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { const unsigned short neg_one = (unsigned short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned short" : "value too large to convert to unsigned short"); } return (unsigned short)-1; } return (unsigned short)val; } return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { const unsigned int neg_one = (unsigned int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned int" : "value too large to convert to unsigned int"); } return (unsigned int)-1; } return (unsigned int)val; } return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { const char neg_one = (char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to char" : "value too large to convert to char"); } return (char)-1; } return (char)val; } return (char)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { const short neg_one = (short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to short" : "value too large to convert to short"); } return (short)-1; } return (short)val; } return (short)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { const signed char neg_one = (signed char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed char" : "value too large to convert to signed char"); } return (signed char)-1; } return (signed char)val; } return (signed char)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { const signed short neg_one = (signed short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed short" : "value too large to convert to signed short"); } return (signed short)-1; } return (signed short)val; } return (signed short)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { const signed int neg_one = (signed int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed int" : "value too large to convert to signed int"); } return (signed int)-1; } return (signed int)val; } return (signed int)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) { const unsigned long neg_one = (unsigned long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)PyLong_AsUnsignedLong(x); } else { return (unsigned long)PyLong_AsLong(x); } } else { unsigned long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned long)-1; val = __Pyx_PyInt_AsUnsignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) { const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x); } } else { unsigned PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned PY_LONG_LONG)-1; val = __Pyx_PyInt_AsUnsignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) { const long neg_one = (long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)PyLong_AsUnsignedLong(x); } else { return (long)PyLong_AsLong(x); } } else { long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (long)-1; val = __Pyx_PyInt_AsLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (PY_LONG_LONG)PyLong_AsLongLong(x); } } else { PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; val = __Pyx_PyInt_AsLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) { const signed long neg_one = (signed long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)PyLong_AsUnsignedLong(x); } else { return (signed long)PyLong_AsLong(x); } } else { signed long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed long)-1; val = __Pyx_PyInt_AsSignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (signed PY_LONG_LONG)PyLong_AsLongLong(x); } } else { signed PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed PY_LONG_LONG)-1; val = __Pyx_PyInt_AsSignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = *type; tstate->exc_value = *value; tstate->exc_traceback = *tb; *type = tmp_type; *value = tmp_value; *tb = tmp_tb; } static CYTHON_INLINE void __Pyx_Generator_ExceptionClear(struct __pyx_Generator_object *self) { Py_XDECREF(self->exc_type); Py_XDECREF(self->exc_value); Py_XDECREF(self->exc_traceback); self->exc_type = NULL; self->exc_value = NULL; self->exc_traceback = NULL; } static CYTHON_INLINE PyObject *__Pyx_Generator_SendEx(struct __pyx_Generator_object *self, PyObject *value) { PyObject *retval; if (self->is_running) { PyErr_SetString(PyExc_ValueError, "generator already executing"); return NULL; } if (self->resume_label == 0) { if (value && value != Py_None) { PyErr_SetString(PyExc_TypeError, "can't send non-None value to a " "just-started generator"); return NULL; } } if (self->resume_label == -1) { PyErr_SetNone(PyExc_StopIteration); return NULL; } if (value) __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); else __Pyx_Generator_ExceptionClear(self); self->is_running = 1; retval = self->body((PyObject *) self, value); self->is_running = 0; if (retval) __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); else __Pyx_Generator_ExceptionClear(self); return retval; } static PyObject *__Pyx_Generator_Next(PyObject *self) { return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, Py_None); } static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) { return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, value); } static PyObject *__Pyx_Generator_Close(PyObject *self) { struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self; PyObject *retval; #if PY_VERSION_HEX < 0x02050000 PyErr_SetNone(PyExc_StopIteration); #else PyErr_SetNone(PyExc_GeneratorExit); #endif retval = __Pyx_Generator_SendEx(generator, NULL); if (retval) { Py_DECREF(retval); PyErr_SetString(PyExc_RuntimeError, "generator ignored GeneratorExit"); return NULL; } #if PY_VERSION_HEX < 0x02050000 if (PyErr_ExceptionMatches(PyExc_StopIteration)) #else if (PyErr_ExceptionMatches(PyExc_StopIteration) || PyErr_ExceptionMatches(PyExc_GeneratorExit)) #endif { PyErr_Clear(); /* ignore these errors */ Py_INCREF(Py_None); return Py_None; } return NULL; } static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args, CYTHON_UNUSED PyObject *kwds) { struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self; PyObject *typ; PyObject *tb = NULL; PyObject *val = NULL; if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb)) return NULL; __Pyx_Raise(typ, val, tb, NULL); return __Pyx_Generator_SendEx(generator, NULL); } static void __Pyx_WriteUnraisable(const char *name, int clineno, int lineno, const char *filename) { PyObject *old_exc, *old_val, *old_tb; PyObject *ctx; __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); #if PY_MAJOR_VERSION < 3 ctx = PyString_FromString(name); #else ctx = PyUnicode_FromString(name); #endif __Pyx_ErrRestore(old_exc, old_val, old_tb); if (!ctx) { PyErr_WriteUnraisable(Py_None); } else { PyErr_WriteUnraisable(ctx); Py_DECREF(ctx); } } static int __Pyx_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { char message[200]; PyOS_snprintf(message, sizeof(message), "compiletime version %s of module '%.100s' " "does not match runtime version %s", ctversion, __Pyx_MODULE_NAME, rtversion); #if PY_VERSION_HEX < 0x02050000 return PyErr_Warn(NULL, message); #else return PyErr_WarnEx(NULL, message, 1); #endif } return 0; } static int __Pyx_SetVtable(PyObject *dict, void *vtable) { #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0) PyObject *ob = PyCapsule_New(vtable, 0, 0); #else PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); #endif if (!ob) goto bad; if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0) goto bad; Py_DECREF(ob); return 0; bad: Py_XDECREF(ob); return -1; } #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict) { PyObject *py_module = 0; PyObject *result = 0; PyObject *py_name = 0; char warning[200]; py_module = __Pyx_ImportModule(module_name); if (!py_module) goto bad; #if PY_MAJOR_VERSION < 3 py_name = PyString_FromString(class_name); #else py_name = PyUnicode_FromString(class_name); #endif if (!py_name) goto bad; result = PyObject_GetAttr(py_module, py_name); Py_DECREF(py_name); py_name = 0; Py_DECREF(py_module); py_module = 0; if (!result) goto bad; if (!PyType_Check(result)) { PyErr_Format(PyExc_TypeError, "%s.%s is not a type object", module_name, class_name); goto bad; } if (!strict && ((PyTypeObject *)result)->tp_basicsize > (Py_ssize_t)size) { PyOS_snprintf(warning, sizeof(warning), "%s.%s size changed, may indicate binary incompatibility", module_name, class_name); #if PY_VERSION_HEX < 0x02050000 if (PyErr_Warn(NULL, warning) < 0) goto bad; #else if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; #endif } else if (((PyTypeObject *)result)->tp_basicsize != (Py_ssize_t)size) { PyErr_Format(PyExc_ValueError, "%s.%s has the wrong size, try recompiling", module_name, class_name); goto bad; } return (PyTypeObject *)result; bad: Py_XDECREF(py_module); Py_XDECREF(result); return NULL; } #endif #ifndef __PYX_HAVE_RT_ImportModule #define __PYX_HAVE_RT_ImportModule static PyObject *__Pyx_ImportModule(const char *name) { PyObject *py_name = 0; PyObject *py_module = 0; #if PY_MAJOR_VERSION < 3 py_name = PyString_FromString(name); #else py_name = PyUnicode_FromString(name); #endif if (!py_name) goto bad; py_module = PyImport_Import(py_name); Py_DECREF(py_name); return py_module; bad: Py_XDECREF(py_name); return 0; } #endif #include "compile.h" #include "frameobject.h" #include "traceback.h" static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno, int __pyx_lineno, const char *__pyx_filename) { PyObject *py_srcfile = 0; PyObject *py_funcname = 0; PyObject *py_globals = 0; PyCodeObject *py_code = 0; PyFrameObject *py_frame = 0; #if PY_MAJOR_VERSION < 3 py_srcfile = PyString_FromString(__pyx_filename); #else py_srcfile = PyUnicode_FromString(__pyx_filename); #endif if (!py_srcfile) goto bad; if (__pyx_clineno) { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno); #else py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno); #endif } else { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromString(funcname); #else py_funcname = PyUnicode_FromString(funcname); #endif } if (!py_funcname) goto bad; py_globals = PyModule_GetDict(__pyx_m); if (!py_globals) goto bad; py_code = PyCode_New( 0, /*int argcount,*/ #if PY_MAJOR_VERSION >= 3 0, /*int kwonlyargcount,*/ #endif 0, /*int nlocals,*/ 0, /*int stacksize,*/ 0, /*int flags,*/ __pyx_empty_bytes, /*PyObject *code,*/ __pyx_empty_tuple, /*PyObject *consts,*/ __pyx_empty_tuple, /*PyObject *names,*/ __pyx_empty_tuple, /*PyObject *varnames,*/ __pyx_empty_tuple, /*PyObject *freevars,*/ __pyx_empty_tuple, /*PyObject *cellvars,*/ py_srcfile, /*PyObject *filename,*/ py_funcname, /*PyObject *name,*/ __pyx_lineno, /*int firstlineno,*/ __pyx_empty_bytes /*PyObject *lnotab*/ ); if (!py_code) goto bad; py_frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate,*/ py_code, /*PyCodeObject *code,*/ py_globals, /*PyObject *globals,*/ 0 /*PyObject *locals*/ ); if (!py_frame) goto bad; py_frame->f_lineno = __pyx_lineno; PyTraceBack_Here(py_frame); bad: Py_XDECREF(py_srcfile); Py_XDECREF(py_funcname); Py_XDECREF(py_code); Py_XDECREF(py_frame); } static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { while (t->p) { #if PY_MAJOR_VERSION < 3 if (t->is_unicode) { *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); } else if (t->intern) { *t->p = PyString_InternFromString(t->s); } else { *t->p = PyString_FromStringAndSize(t->s, t->n - 1); } #else /* Python 3+ has unicode identifiers */ if (t->is_unicode | t->is_str) { if (t->intern) { *t->p = PyUnicode_InternFromString(t->s); } else if (t->encoding) { *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); } else { *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); } } else { *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); } #endif if (!*t->p) return -1; ++t; } return 0; } /* Type Conversion Functions */ static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { int is_true = x == Py_True; if (is_true | (x == Py_False) | (x == Py_None)) return is_true; else return PyObject_IsTrue(x); } static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { PyNumberMethods *m; const char *name = NULL; PyObject *res = NULL; #if PY_VERSION_HEX < 0x03000000 if (PyInt_Check(x) || PyLong_Check(x)) #else if (PyLong_Check(x)) #endif return Py_INCREF(x), x; m = Py_TYPE(x)->tp_as_number; #if PY_VERSION_HEX < 0x03000000 if (m && m->nb_int) { name = "int"; res = PyNumber_Int(x); } else if (m && m->nb_long) { name = "long"; res = PyNumber_Long(x); } #else if (m && m->nb_int) { name = "int"; res = PyNumber_Long(x); } #endif if (res) { #if PY_VERSION_HEX < 0x03000000 if (!PyInt_Check(res) && !PyLong_Check(res)) { #else if (!PyLong_Check(res)) { #endif PyErr_Format(PyExc_TypeError, "__%s__ returned non-%s (type %.200s)", name, name, Py_TYPE(res)->tp_name); Py_DECREF(res); return NULL; } } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_TypeError, "an integer is required"); } return res; } static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_ssize_t ival; PyObject* x = PyNumber_Index(b); if (!x) return -1; ival = PyInt_AsSsize_t(x); Py_DECREF(x); return ival; } static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { #if PY_VERSION_HEX < 0x02050000 if (ival <= LONG_MAX) return PyInt_FromLong((long)ival); else { unsigned char *bytes = (unsigned char *) &ival; int one = 1; int little = (int)*(unsigned char*)&one; return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0); } #else return PyInt_FromSize_t(ival); #endif } static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x); if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) { return (size_t)-1; } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) { PyErr_SetString(PyExc_OverflowError, "value too large to convert to size_t"); return (size_t)-1; } return (size_t)val; } #endif /* Py_PYTHON_H */