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- # cython: language_level=3
- from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
- from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
- from libc.stdlib cimport malloc, calloc, realloc, free
- from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup
- from libc.stdio cimport FILE, printf
-
- from pysam.libcfaidx cimport faidx_t, FastaFile
- from pysam.libcalignedsegment cimport AlignedSegment
- from pysam.libchtslib cimport *
-
- from cpython cimport array
- cimport cython
-
- cdef extern from *:
- ctypedef char* const_char_ptr "const char*"
-
- cdef extern from "htslib_util.h":
-
- char * pysam_bam_get_qname(bam1_t * b)
-
- ####################################################################
- # Utility types
-
- ctypedef struct __iterdata:
- htsFile * htsfile
- bam_hdr_t * header
- hts_itr_t * iter
- faidx_t * fastafile
- int tid
- char * seq
- int seq_len
- int min_mapping_quality
- int flag_require
- int flag_filter
- bint compute_baq
- bint redo_baq
- bint ignore_orphans
- int adjust_capq_threshold
-
-
- cdef class AlignmentHeader(object):
- cdef bam_hdr_t *ptr
-
- cdef class AlignmentFile(HTSFile):
- cdef readonly object reference_filename
- cdef readonly AlignmentHeader header
-
- # pointer to index
- cdef hts_idx_t *index
-
- # current read within iteration
- cdef bam1_t * b
-
- cdef bam1_t * getCurrent(self)
- cdef int cnext(self)
-
- # write an aligned read
- cpdef int write(self, AlignedSegment read) except -1
-
-
- cdef class IteratorRow:
- cdef int retval
- cdef bam1_t * b
- cdef AlignmentFile samfile
- cdef htsFile * htsfile
- cdef hts_idx_t * index
- cdef AlignmentHeader header
- cdef int owns_samfile
-
-
- cdef class IteratorRowRegion(IteratorRow):
- cdef hts_itr_t * iter
- cdef bam1_t * getCurrent(self)
- cdef int cnext(self)
-
-
- cdef class IteratorRowHead(IteratorRow):
- cdef int max_rows
- cdef int current_row
- cdef bam1_t * getCurrent(self)
- cdef int cnext(self)
-
-
- cdef class IteratorRowAll(IteratorRow):
- cdef bam1_t * getCurrent(self)
- cdef int cnext(self)
-
-
- cdef class IteratorRowAllRefs(IteratorRow):
- cdef int tid
- cdef IteratorRowRegion rowiter
-
-
- cdef class IteratorRowSelection(IteratorRow):
- cdef int current_pos
- cdef positions
- cdef bam1_t * getCurrent(self)
- 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 uint32_t min_base_quality
- cdef const bam_pileup1_t * plp
- cdef bam_mplp_t pileup_iter
- cdef __iterdata iterdata
- cdef AlignmentFile samfile
- cdef FastaFile fastafile
- cdef stepper
- cdef int max_depth
- cdef bint ignore_overlaps
-
- cdef int cnext(self)
- cdef char * get_sequence(self)
- cdef _setup_iterator(self,
- int tid,
- int start,
- int stop,
- int multiple_iterators=?)
- cdef _setup_raw_rest_iterator(self)
-
- cdef reset(self, tid, start, stop)
- cdef _free_pileup_iter(self)
- # backwards compatibility
- cdef char * getSequence(self)
-
-
- cdef class IteratorColumnRegion(IteratorColumn):
- cdef int start
- cdef int stop
- cdef int truncate
-
-
- cdef class IteratorColumnAllRefs(IteratorColumn):
- pass
-
-
- cdef class IteratorColumnAll(IteratorColumn):
- pass
-
-
- cdef class IndexedReads:
- cdef AlignmentFile samfile
- cdef htsFile * htsfile
- cdef object index
- cdef int owns_samfile
- cdef AlignmentHeader header
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