jpayne@69: # cython: language_level=3
jpayne@69: from pysam.libchtslib cimport *
jpayne@69: 
jpayne@69: cdef extern from "htslib_util.h":
jpayne@69: 
jpayne@69:     # add *nbytes* into the variable length data of *src* at *pos*
jpayne@69:     bam1_t * pysam_bam_update(bam1_t * b,
jpayne@69:            	         size_t nbytes_old,
jpayne@69:                          size_t nbytes_new,
jpayne@69:                          uint8_t * pos)
jpayne@69: 
jpayne@69:     # now: static
jpayne@69:     int aux_type2size(int)
jpayne@69: 
jpayne@69:     char * pysam_bam_get_qname(bam1_t * b)
jpayne@69:     uint32_t * pysam_bam_get_cigar(bam1_t * b)
jpayne@69:     uint8_t * pysam_bam_get_seq(bam1_t * b)
jpayne@69:     uint8_t * pysam_bam_get_qual(bam1_t * b)
jpayne@69:     uint8_t * pysam_bam_get_aux(bam1_t * b)
jpayne@69:     int pysam_bam_get_l_aux(bam1_t * b)
jpayne@69:     char pysam_bam_seqi(uint8_t * s, int i)
jpayne@69: 
jpayne@69:     uint8_t pysam_get_qual(bam1_t * b)
jpayne@69:     uint32_t pysam_get_n_cigar(bam1_t * b)
jpayne@69:     void pysam_set_qual(bam1_t * b, uint8_t v)
jpayne@69:     void pysam_set_n_cigar(bam1_t * b, uint32_t v)
jpayne@69:     void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag)
jpayne@69: 
jpayne@69: 
jpayne@69: from pysam.libcalignmentfile cimport AlignmentFile, AlignmentHeader
jpayne@69: ctypedef AlignmentFile AlignmentFile_t
jpayne@69: 
jpayne@69: 
jpayne@69: # Note: need to declare all C fields and methods here
jpayne@69: cdef class AlignedSegment:
jpayne@69: 
jpayne@69:     # object that this AlignedSegment represents
jpayne@69:     cdef bam1_t * _delegate
jpayne@69: 
jpayne@69:     # the header that a read is associated with
jpayne@69:     cdef readonly AlignmentHeader header
jpayne@69: 
jpayne@69:     # caching of array properties for quick access
jpayne@69:     cdef object cache_query_qualities
jpayne@69:     cdef object cache_query_alignment_qualities
jpayne@69:     cdef object cache_query_sequence
jpayne@69:     cdef object cache_query_alignment_sequence
jpayne@69: 
jpayne@69:     # add an alignment tag with value to the AlignedSegment
jpayne@69:     # an existing tag of the same name will be replaced.
jpayne@69:     cpdef set_tag(self, tag, value, value_type=?, replace=?)
jpayne@69: 
jpayne@69:     # get an alignment tag from the AlignedSegment
jpayne@69:     cpdef get_tag(self, tag, with_value_type=?)
jpayne@69: 
jpayne@69:     # return true if tag exists
jpayne@69:     cpdef has_tag(self, tag)
jpayne@69: 
jpayne@69:     # returns a valid sam alignment string
jpayne@69:     cpdef to_string(self)
jpayne@69: 
jpayne@69:     # returns a valid sam alignment string (deprecated)
jpayne@69:     cpdef tostring(self, htsfile=*)
jpayne@69: 
jpayne@69: 
jpayne@69: cdef class PileupColumn:
jpayne@69:     cdef const bam_pileup1_t ** plp
jpayne@69:     cdef int tid
jpayne@69:     cdef int pos
jpayne@69:     cdef int n_pu
jpayne@69:     cdef AlignmentHeader header
jpayne@69:     cdef uint32_t min_base_quality
jpayne@69:     cdef kstring_t buf
jpayne@69:     cdef char * reference_sequence
jpayne@69: 
jpayne@69: cdef class PileupRead:
jpayne@69:     cdef int32_t  _qpos
jpayne@69:     cdef AlignedSegment _alignment
jpayne@69:     cdef int _indel
jpayne@69:     cdef int _level
jpayne@69:     cdef uint32_t _is_del
jpayne@69:     cdef uint32_t _is_head
jpayne@69:     cdef uint32_t _is_tail
jpayne@69:     cdef uint32_t _is_refskip
jpayne@69: 
jpayne@69: # factory methods
jpayne@69: cdef AlignedSegment makeAlignedSegment(
jpayne@69:     bam1_t * src,
jpayne@69:     AlignmentHeader header)
jpayne@69: 
jpayne@69: cdef PileupColumn makePileupColumn(
jpayne@69:     const bam_pileup1_t ** plp,
jpayne@69:     int tid,
jpayne@69:     int pos,
jpayne@69:     int n_pu,
jpayne@69:     uint32_t min_base_quality,
jpayne@69:     char * reference_sequence,
jpayne@69:     AlignmentHeader header)
jpayne@69: 
jpayne@69: cdef PileupRead makePileupRead(const bam_pileup1_t * src,
jpayne@69: 		               AlignmentHeader header)
jpayne@69: 
jpayne@69: cdef uint32_t get_alignment_length(bam1_t * src)