1 /* 2 Copyright (c) 2010-2013, 2018, 2020 Genome Research Ltd. 3 Author: James Bonfield <jkb@sanger.ac.uk> 4 5 Redistribution and use in source and binary forms, with or without 6 modification, are permitted provided that the following conditions are met: 7 8 1. Redistributions of source code must retain the above copyright notice, 9 this list of conditions and the following disclaimer. 10 11 2. Redistributions in binary form must reproduce the above copyright notice, 12 this list of conditions and the following disclaimer in the documentation 13 and/or other materials provided with the distribution. 14 15 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger 16 Institute nor the names of its contributors may be used to endorse or promote 17 products derived from this software without specific prior written permission. 18 19 THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 20 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 21 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 22 DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE 23 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 24 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 25 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 26 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 27 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 28 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 29 */ 30 31 #ifndef CRAM_SAMTOOLS_H 32 #define CRAM_SAMTOOLS_H 33 34 /* Samtools compatible API */ 35 #define bam_blk_size(b) ((b)->l_data) 36 #define bam_set_blk_size(b,v) ((b)->data_len = (v)) 37 38 #define bam_ref(b) (b)->core.tid 39 #define bam_pos(b) (b)->core.pos 40 #define bam_mate_pos(b) (b)->core.mpos 41 #define bam_mate_ref(b) (b)->core.mtid 42 #define bam_ins_size(b) (b)->core.isize 43 #define bam_seq_len(b) (b)->core.l_qseq 44 #define bam_cigar_len(b) (b)->core.n_cigar 45 #define bam_flag(b) (b)->core.flag 46 #define bam_bin(b) (b)->core.bin 47 #define bam_map_qual(b) (b)->core.qual 48 #define bam_name_len(b) ((b)->core.l_qname - (b)->core.l_extranul) 49 #define bam_name(b) bam_get_qname((b)) 50 #define bam_qual(b) bam_get_qual((b)) 51 #define bam_seq(b) bam_get_seq((b)) 52 #define bam_cigar(b) bam_get_cigar((b)) 53 #define bam_aux(b) bam_get_aux((b)) 54 55 #define bam_free(b) bam_destroy1((b)) 56 57 #define bam_reg2bin(beg,end) hts_reg2bin((beg),(end),14,5) 58 59 #include "../htslib/sam.h" 60 61 enum cigar_op { 62 BAM_CMATCH_=BAM_CMATCH, 63 BAM_CINS_=BAM_CINS, 64 BAM_CDEL_=BAM_CDEL, 65 BAM_CREF_SKIP_=BAM_CREF_SKIP, 66 BAM_CSOFT_CLIP_=BAM_CSOFT_CLIP, 67 BAM_CHARD_CLIP_=BAM_CHARD_CLIP, 68 BAM_CPAD_=BAM_CPAD, 69 BAM_CBASE_MATCH=BAM_CEQUAL, 70 BAM_CBASE_MISMATCH=BAM_CDIFF 71 }; 72 73 typedef bam1_t bam_seq_t; 74 75 #endif /* CRAM_SAMTOOLS_H */ 76