76 lines
2.8 KiB
C
76 lines
2.8 KiB
C
/*
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Copyright (c) 2010-2013, 2018, 2020 Genome Research Ltd.
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Author: James Bonfield <jkb@sanger.ac.uk>
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice,
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this list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
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Institute nor the names of its contributors may be used to endorse or promote
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products derived from this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
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ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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#ifndef CRAM_SAMTOOLS_H
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#define CRAM_SAMTOOLS_H
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/* Samtools compatible API */
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#define bam_blk_size(b) ((b)->l_data)
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#define bam_set_blk_size(b,v) ((b)->data_len = (v))
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#define bam_ref(b) (b)->core.tid
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#define bam_pos(b) (b)->core.pos
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#define bam_mate_pos(b) (b)->core.mpos
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#define bam_mate_ref(b) (b)->core.mtid
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#define bam_ins_size(b) (b)->core.isize
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#define bam_seq_len(b) (b)->core.l_qseq
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#define bam_cigar_len(b) (b)->core.n_cigar
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#define bam_flag(b) (b)->core.flag
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#define bam_bin(b) (b)->core.bin
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#define bam_map_qual(b) (b)->core.qual
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#define bam_name_len(b) ((b)->core.l_qname - (b)->core.l_extranul)
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#define bam_name(b) bam_get_qname((b))
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#define bam_qual(b) bam_get_qual((b))
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#define bam_seq(b) bam_get_seq((b))
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#define bam_cigar(b) bam_get_cigar((b))
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#define bam_aux(b) bam_get_aux((b))
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#define bam_free(b) bam_destroy1((b))
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#define bam_reg2bin(beg,end) hts_reg2bin((beg),(end),14,5)
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#include "../htslib/sam.h"
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enum cigar_op {
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BAM_CMATCH_=BAM_CMATCH,
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BAM_CINS_=BAM_CINS,
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BAM_CDEL_=BAM_CDEL,
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BAM_CREF_SKIP_=BAM_CREF_SKIP,
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BAM_CSOFT_CLIP_=BAM_CSOFT_CLIP,
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BAM_CHARD_CLIP_=BAM_CHARD_CLIP,
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BAM_CPAD_=BAM_CPAD,
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BAM_CBASE_MATCH=BAM_CEQUAL,
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BAM_CBASE_MISMATCH=BAM_CDIFF
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};
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typedef bam1_t bam_seq_t;
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#endif /* CRAM_SAMTOOLS_H */
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