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- from pysam.libchtslib cimport *
-
- cdef extern from "htslib_util.h":
-
- # add *nbytes* into the variable length data of *src* at *pos*
- bam1_t * pysam_bam_update(bam1_t * b,
- size_t nbytes_old,
- size_t nbytes_new,
- uint8_t * pos)
-
- # now: static
- int aux_type2size(int)
-
- char * pysam_bam_get_qname(bam1_t * b)
- uint32_t * pysam_bam_get_cigar(bam1_t * b)
- uint8_t * pysam_bam_get_seq(bam1_t * b)
- uint8_t * pysam_bam_get_qual(bam1_t * b)
- uint8_t * pysam_bam_get_aux(bam1_t * b)
- int pysam_bam_get_l_aux(bam1_t * b)
- char pysam_bam_seqi(uint8_t * s, int i)
-
- uint8_t pysam_get_qual(bam1_t * b)
- uint32_t pysam_get_n_cigar(bam1_t * b)
- void pysam_set_qual(bam1_t * b, uint8_t v)
- void pysam_set_n_cigar(bam1_t * b, uint32_t v)
- void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag)
-
-
- from pysam.libcalignmentfile cimport AlignmentFile, AlignmentHeader
- ctypedef AlignmentFile AlignmentFile_t
-
-
- # Note: need to declare all C fields and methods here
- cdef class AlignedSegment:
-
- # object that this AlignedSegment represents
- cdef bam1_t * _delegate
-
- # the header that a read is associated with
- cdef readonly AlignmentHeader header
-
- # caching of array properties for quick access
- cdef object cache_query_qualities
- cdef object cache_query_alignment_qualities
- cdef object cache_query_sequence
- cdef object cache_query_alignment_sequence
-
- # add an alignment tag with value to the AlignedSegment
- # an existing tag of the same name will be replaced.
- cpdef set_tag(self, tag, value, value_type=?, replace=?)
-
- # add an alignment tag with value to the AlignedSegment
- # an existing tag of the same name will be replaced.
- cpdef get_tag(self, tag, with_value_type=?)
-
- # return true if tag exists
- cpdef has_tag(self, tag)
-
- # returns a valid sam alignment string
- cpdef to_string(self)
-
- # returns a valid sam alignment string (deprecated)
- cpdef tostring(self, htsfile=*)
-
-
- cdef class PileupColumn:
- cdef const bam_pileup1_t ** plp
- cdef int tid
- cdef int pos
- cdef int n_pu
- cdef AlignmentHeader header
- cdef uint32_t min_base_quality
- cdef kstring_t buf
- cdef char * reference_sequence
-
- cdef class PileupRead:
- cdef int32_t _qpos
- cdef AlignedSegment _alignment
- 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
-
- # factory methods
- cdef AlignedSegment makeAlignedSegment(
- bam1_t * src,
- AlignmentHeader header)
-
- cdef PileupColumn makePileupColumn(
- const bam_pileup1_t ** plp,
- int tid,
- int pos,
- int n_pu,
- uint32_t min_base_quality,
- char * reference_sequence,
- AlignmentHeader header)
-
- cdef PileupRead makePileupRead(const bam_pileup1_t * src,
- AlignmentHeader header)
-
- cdef uint32_t get_alignment_length(bam1_t * src)
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