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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)
cdef extern from "samfile_util.h":
int bam_cap_mapQ(bam1_t *b, char *ref, int thres)
int bam_prob_realn(bam1_t *b, const char *ref)
####################################################################
# 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
cdef class AlignmentFile(HTSFile):
cdef readonly object reference_filename
# pointer to index
cdef hts_idx_t *index
# header structure
cdef bam_hdr_t * header
# 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 PileupColumn:
cdef bam_pileup1_t ** plp
cdef int tid
cdef int pos
cdef int n_pu
cdef class PileupRead:
cdef AlignedSegment _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 uint32_t _is_refskip
cdef class IteratorRow:
cdef int retval
cdef bam1_t * b
cdef AlignmentFile samfile
cdef htsFile * htsfile
cdef bam_hdr_t * 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 int mask
cdef bam_pileup1_t * plp
cdef bam_plp_t pileup_iter
cdef __iterdata iterdata
cdef AlignmentFile 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 multiple_iterators=?)
cdef reset(self, tid, start, end)
cdef _free_pileup_iter(self)
cdef class IteratorColumnRegion(IteratorColumn):
cdef int start
cdef int end
cdef int truncate
cdef class IteratorColumnAllRefs(IteratorColumn):
pass
cdef class IndexedReads:
cdef AlignmentFile samfile
cdef htsFile * htsfile
cdef index
cdef int owns_samfile
cdef bam_hdr_t * header
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