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# cython: language_level=3
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
cdef class _AlignedSegment_Cache: # For internal use only
cdef clear_query_sequences(self)
cdef clear_query_qualities(self)
cdef object query_sequence
cdef object query_alignment_sequence
cdef object query_qualities
cdef object query_qualities_str
cdef object query_alignment_qualities
cdef object query_alignment_qualities_str
# 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 _AlignedSegment_Cache cache
cdef object unused1
cdef object unused2
cdef object unused3
# 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=?)
# get an alignment tag from the AlignedSegment
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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