jpayne@69: # cython: language_level=3
jpayne@69: from pysam.libcalignmentfile cimport AlignedSegment, AlignmentFile
jpayne@69: 
jpayne@69: #################################################
jpayne@69: # Compatibility Layer for pysam < 0.8
jpayne@69: 
jpayne@69: # import all declarations from htslib
jpayne@69: from pysam.libchtslib cimport *
jpayne@69: 
jpayne@69: cdef class AlignedRead(AlignedSegment):
jpayne@69:     pass
jpayne@69: 
jpayne@69: cdef class Samfile(AlignmentFile):
jpayne@69:     pass
jpayne@69: 
jpayne@69: # import the conversion functions
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:     uint16_t pysam_get_bin(bam1_t * b)
jpayne@69:     uint8_t pysam_get_qual(bam1_t * b)
jpayne@69:     uint8_t pysam_get_l_qname(bam1_t * b)
jpayne@69:     uint16_t pysam_get_flag(bam1_t * b)
jpayne@69:     uint32_t pysam_get_n_cigar(bam1_t * b)
jpayne@69:     void pysam_set_bin(bam1_t * b, uint16_t v)
jpayne@69:     void pysam_set_qual(bam1_t * b, uint8_t v)
jpayne@69:     void pysam_set_l_qname(bam1_t * b, uint8_t v)
jpayne@69:     void pysam_set_flag(bam1_t * b, uint16_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)