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1 /*
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2 Copyright (c) 2010-2013 Genome Research Ltd.
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3 Author: James Bonfield <jkb@sanger.ac.uk>
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4
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5 Redistribution and use in source and binary forms, with or without
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6 modification, are permitted provided that the following conditions are met:
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7
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8 1. Redistributions of source code must retain the above copyright notice,
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9 this list of conditions and the following disclaimer.
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10
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11 2. Redistributions in binary form must reproduce the above copyright notice,
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12 this list of conditions and the following disclaimer in the documentation
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13 and/or other materials provided with the distribution.
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14
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15 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
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16 Institute nor the names of its contributors may be used to endorse or promote
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17 products derived from this software without specific prior written permission.
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18
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19 THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
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20 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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21 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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22 DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
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23 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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24 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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25 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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26 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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27 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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28 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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29 */
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30
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31 #ifndef _CRAM_SAMTOOLS_H_
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32 #define _CRAM_SAMTOOLS_H_
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33
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34 /* Samtools compatible API */
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35 #define bam_blk_size(b) ((b)->l_data)
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36 #define bam_set_blk_size(b,v) ((b)->data_len = (v))
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37
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38 #define bam_ref(b) (b)->core.tid
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39 #define bam_pos(b) (b)->core.pos
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40 #define bam_mate_pos(b) (b)->core.mpos
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41 #define bam_mate_ref(b) (b)->core.mtid
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42 #define bam_ins_size(b) (b)->core.isize
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43 #define bam_seq_len(b) (b)->core.l_qseq
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44 #define bam_cigar_len(b) (b)->core.n_cigar
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45 #define bam_flag(b) (b)->core.flag
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46 #define bam_bin(b) (b)->core.bin
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47 #define bam_map_qual(b) (b)->core.qual
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48 #define bam_name_len(b) (b)->core.l_qname
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49 #define bam_name(b) bam_get_qname((b))
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50 #define bam_qual(b) bam_get_qual((b))
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51 #define bam_seq(b) bam_get_seq((b))
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52 #define bam_cigar(b) bam_get_cigar((b))
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53 #define bam_aux(b) bam_get_aux((b))
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54
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55 #define bam_dup(b) bam_copy1(bam_init1(), (b))
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56
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57 #define bam_free(b) bam_destroy1((b))
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58
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59 #define bam_reg2bin(beg,end) hts_reg2bin((beg),(end),14,5)
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60
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61 #include "htslib/sam.h"
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62
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63 enum cigar_op {
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64 BAM_CMATCH_=BAM_CMATCH,
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65 BAM_CINS_=BAM_CINS,
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66 BAM_CDEL_=BAM_CDEL,
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67 BAM_CREF_SKIP_=BAM_CREF_SKIP,
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68 BAM_CSOFT_CLIP_=BAM_CSOFT_CLIP,
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69 BAM_CHARD_CLIP_=BAM_CHARD_CLIP,
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70 BAM_CPAD_=BAM_CPAD,
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71 BAM_CBASE_MATCH=BAM_CEQUAL,
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72 BAM_CBASE_MISMATCH=BAM_CDIFF
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73 };
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74
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75 typedef bam1_t bam_seq_t;
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76
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77 #include "cram/sam_header.h"
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78
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79 bam_hdr_t *cram_header_to_bam(SAM_hdr *h);
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80 SAM_hdr *bam_header_to_cram(bam_hdr_t *h);
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81
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82 int bam_construct_seq(bam_seq_t **bp, size_t extra_len,
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83 const char *qname, size_t qname_len,
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84 int flag,
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85 int rname, // Ref ID
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86 int pos,
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87 int end, // aligned start/end coords
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88 int mapq,
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89 uint32_t ncigar, const uint32_t *cigar,
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90 int mrnm, // Mate Ref ID
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91 int mpos,
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92 int isize,
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93 int len,
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94 const char *seq,
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95 const char *qual);
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96
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97 #endif /* _CRAM_SAMTOOLS_H_ */
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