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    bam.h


Introduction

Functions

      sam_open
      sam_close
      sam_read1
      sam_header_read2
      sam_header_read
      sam_header_parse
      sam_header_parse_rg
      bam_header_init
      bam_header_destroy
      bam_header_read
      bam_header_write
      bam_read1
      bam_write1_core
      bam_write1
      bam_format1
      bam_plbuf_reset
      bam_plbuf_init
      bam_plbuf_destroy
      bam_plbuf_push
      bam_lplbuf_init
      bam_lplbuf_destroy
      bam_lplbuf_push
      bam_lpileup_file
      bam_index_build
      bam_index_load
      bam_index_destroy
      bam_fetch
      bam_parse_region
      bam_aux_get
      bam_calend
      bam_cigar2qlen
      bam_reg2bin
      bam_copy1
      bam_dup1

Defined Types

      bamFile
      bamFile
      bamFile
      bam_header_t
      bam1_core_t
      bam1_t
      tamFile
      bam_pileup1_t
      bam_plbuf_t
      bam_pileup_f
      bam_fetch_f

#defines

      BAM_FPAIRED
      BAM_FPROPER_PAIR
      BAM_FUNMAP
      BAM_FMUNMAP
      BAM_FREVERSE
      BAM_FMREVERSE
      BAM_FREAD1
      BAM_FREAD2
      BAM_FSECONDARY
      BAM_FQCFAIL
      BAM_FDUP
      BAM_DEF_MASK
      BAM_CMATCH
      BAM_CINS
      BAM_CDEL
      BAM_CREF_SKIP
      BAM_CSOFT_CLIP
      BAM_CHARD_CLIP
      BAM_CPAD
      bam1_cigar
      bam1_qname
      bam1_seq
      bam1_qual
      bam1_seqi
      bam1_aux
      kroundup32
      bam_init1
      bam_destroy1

Globals

      bam_is_be
      bam_nt16_table
      bam_nt16_rev_table


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