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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)
uint16_t pysam_get_bin(bam1_t * b)
uint8_t pysam_get_qual(bam1_t * b)
uint8_t pysam_get_l_qname(bam1_t * b)
uint16_t pysam_get_flag(bam1_t * b)
uint16_t pysam_get_n_cigar(bam1_t * b)
void pysam_set_bin(bam1_t * b, uint16_t v)
void pysam_set_qual(bam1_t * b, uint8_t v)
void pysam_set_l_qname(bam1_t * b, uint8_t v)
void pysam_set_flag(bam1_t * b, uint16_t v)
void pysam_set_n_cigar(bam1_t * b, uint16_t v)
void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag)
from pysam.libcalignmentfile cimport AlignmentFile
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 file from which this AlignedSegment originates (can be None)
cdef AlignmentFile _alignment_file
# 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 tostring(self, AlignmentFile_t handle)
cdef class PileupColumn:
cdef bam_pileup1_t ** plp
cdef int tid
cdef int pos
cdef int n_pu
cdef AlignmentFile _alignment_file
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
# factor methods
cdef makeAlignedSegment(bam1_t * src, AlignmentFile alignment_file)
cdef makePileupColumn(bam_pileup1_t ** plp, int tid, int pos, int n_pu, AlignmentFile alignment_file)
cdef inline makePileupRead(bam_pileup1_t * src, AlignmentFile alignment_file)
cdef inline uint32_t get_alignment_length(bam1_t * src)
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