long _Py_HashPointer(void*)
FILE* PyFile_AsFile(object)
-cdef extern from "fileobject.h":
- ctypedef class __builtin__.file [object PyFileObject]:
- pass
-
cdef extern from "razf.h":
pass
cdef extern from "stdint.h":
- ctypedef int int64_t
+ ctypedef int int8_t
+ ctypedef int int16_t
ctypedef int int32_t
- ctypedef int uint32_t
+ ctypedef int int64_t
ctypedef int uint8_t
+ ctypedef int uint16_t
+ ctypedef int uint32_t
ctypedef int uint64_t
cdef extern from "bam.h":
uint32_t bam_calend(bam1_core_t *c, uint32_t *cigar)
+ int bam_aux_type2size( int )
+
+
cdef extern from *:
ctypedef char* const_char_ptr "const char*"
int pysam_reference2tid( bam_header_t *header, char * s )
- void pysam_set_stderr( FILE * file )
+ void pysam_set_stderr( int fd )
+ void pysam_unset_stderr()
# return mapped/unmapped reads on tid
uint32_t pysam_get_mapped( bam_index_t *idx, int tid )
# void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c )
-# need to declare all C fields and methods here
+####################################################################
+# Utility types
+
+ctypedef struct __iterdata:
+ samfile_t * samfile
+ bam_iter_t iter
+ faidx_t * fastafile
+ int tid
+ char * seq
+ int seq_len
+
+####################################################################
+#
+# Exposing pysam extension classes
+#
+# Note: need to declare all C fields and methods here
+#
+cdef class Fastafile:
+ cdef char * _filename
+ # pointer to fastafile
+ cdef faidx_t * fastafile
+
+ cdef char * _fetch( self, char * reference, int start, int end, int * length )
+
cdef class AlignedRead:
# object that this AlignedRead represents
cdef char * _getrname( self, int tid )
+cdef class PileupProxy:
+ cdef bam_pileup1_t ** plp
+ cdef int tid
+ cdef int pos
+ cdef int n_pu
+
+cdef class PileupRead:
+ cdef AlignedRead _alignment
+ cdef int32_t _qpos
+ cdef int _indel
+ cdef int _level
+ cdef uint32_t _is_del
+ cdef uint32_t _is_head
+ cdef uint32_t _is_tail
+
cdef class IteratorRow:
pass
+cdef class IteratorRowRegion(IteratorRow):
+ cdef bam_iter_t iter # iterator state object
+ cdef bam1_t * b
+ cdef int retval
+ cdef Samfile samfile
+ cdef samfile_t * fp
+ # true if samfile belongs to this object
+ cdef int owns_samfile
+
+ cdef bam1_t * getCurrent( self )
+
+ cdef int cnext(self)
+
cdef class IteratorRowAll(IteratorRow):
cdef bam1_t * b
cdef samfile_t * fp
+ cdef int owns_samfile
+ cdef bam1_t * getCurrent( self )
+ cdef int cnext(self)
+
+cdef class IteratorRowAllRefs(IteratorRow):
+ cdef Samfile samfile
+ cdef int tid
+ cdef IteratorRowRegion rowiter
+
+cdef class IteratorRowSelection(IteratorRow):
+ cdef bam1_t * b
+ cdef int current_pos
+ cdef samfile_t * fp
+ cdef positions
# true if samfile belongs to this object
cdef int owns_samfile
cdef int cnext(self)
+cdef class IteratorColumn:
+
+ # result of the last plbuf_push
+ cdef IteratorRowRegion iter
+ cdef int tid
+ cdef int pos
+ cdef int n_plp
+ cdef int mask
+ cdef const_bam_pileup1_t_ptr plp
+ cdef bam_plp_t pileup_iter
+ cdef __iterdata iterdata
+ cdef Samfile samfile
+ cdef Fastafile fastafile
+ cdef stepper
+ cdef int max_depth
+
+ cdef int cnext(self)
+ cdef char * getSequence( self )
+ cdef setMask( self, mask )
+ cdef setupIteratorData( self,
+ int tid,
+ int start,
+ int end,
+ int reopen = ? )
+
+ cdef reset( self, tid, start, end )
+
+cdef class IteratorColumnRegion(IteratorColumn):
+ cdef int start
+ cdef int end
+ cdef int truncate
+
+cdef class IteratorColumnAllRefs(IteratorColumn):
+ pass
+
+cdef class IndexedReads:
+ cdef Samfile samfile
+ cdef samfile_t * fp
+ cdef index
+ # true if samfile belongs to this object
+ cdef int owns_samfile
+