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- # cython: language_level=3
- 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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