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1 #include <stdio.h>
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2 #include "sam.h"
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3 static int fetch_func(const bam1_t *b, void *data)
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4 {
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5 samfile_t *fp = (samfile_t*)data;
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6 uint32_t *cigar = bam1_cigar(b);
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7 const bam1_core_t *c = &b->core;
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8 int i, l;
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9 if (b->core.tid < 0) return 0;
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10 for (i = l = 0; i < c->n_cigar; ++i) {
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11 int op = cigar[i]&0xf;
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12 if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP)
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13 l += cigar[i]>>4;
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14 }
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15 printf("%s\t%d\t%d\t%s\t%d\t%c\n", fp->header->target_name[c->tid],
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16 c->pos, c->pos + l, bam1_qname(b), c->qual, (c->flag&BAM_FREVERSE)? '-' : '+');
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17 return 0;
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18 }
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19 int main(int argc, char *argv[])
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20 {
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21 samfile_t *fp;
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22 if (argc == 1) {
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23 fprintf(stderr, "Usage: bam2bed <in.bam> [region]\n");
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24 return 1;
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25 }
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26 if ((fp = samopen(argv[1], "rb", 0)) == 0) {
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27 fprintf(stderr, "bam2bed: Fail to open BAM file %s\n", argv[1]);
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28 return 1;
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29 }
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30 if (argc == 2) { /* if a region is not specified */
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31 bam1_t *b = bam_init1();
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32 while (samread(fp, b) >= 0) fetch_func(b, fp);
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33 bam_destroy1(b);
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34 } else {
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35 int ref, beg, end;
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36 bam_index_t *idx;
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37 if ((idx = bam_index_load(argv[1])) == 0) {
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38 fprintf(stderr, "bam2bed: BAM indexing file is not available.\n");
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39 return 1;
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40 }
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41 bam_parse_region(fp->header, argv[2], &ref, &beg, &end);
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42 if (ref < 0) {
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43 fprintf(stderr, "bam2bed: Invalid region %s\n", argv[2]);
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44 return 1;
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45 }
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46 bam_fetch(fp->x.bam, idx, ref, beg, end, fp, fetch_func);
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47 bam_index_destroy(idx);
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48 }
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49 samclose(fp);
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50 return 0;
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51 }
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