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from pysam.libcalignmentfile cimport AlignedSegment, AlignmentFile
#################################################
# Compatibility Layer for pysam < 0.8
# import all declarations from htslib
from pysam.libchtslib cimport *
cdef class AlignedRead(AlignedSegment):
pass
cdef class Samfile(AlignmentFile):
pass
# import the conversion functions
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)
uint32_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, uint32_t v)
void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag)
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