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comparison pyPRADA_1.2/tools/samtools-0.1.16/examples/bam2bed.c @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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-1:000000000000 0:acc2ca1a3ba4
1 #include <stdio.h>
2 #include "sam.h"
3 static int fetch_func(const bam1_t *b, void *data)
4 {
5 samfile_t *fp = (samfile_t*)data;
6 uint32_t *cigar = bam1_cigar(b);
7 const bam1_core_t *c = &b->core;
8 int i, l;
9 if (b->core.tid < 0) return 0;
10 for (i = l = 0; i < c->n_cigar; ++i) {
11 int op = cigar[i]&0xf;
12 if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP)
13 l += cigar[i]>>4;
14 }
15 printf("%s\t%d\t%d\t%s\t%d\t%c\n", fp->header->target_name[c->tid],
16 c->pos, c->pos + l, bam1_qname(b), c->qual, (c->flag&BAM_FREVERSE)? '-' : '+');
17 return 0;
18 }
19 int main(int argc, char *argv[])
20 {
21 samfile_t *fp;
22 if (argc == 1) {
23 fprintf(stderr, "Usage: bam2bed <in.bam> [region]\n");
24 return 1;
25 }
26 if ((fp = samopen(argv[1], "rb", 0)) == 0) {
27 fprintf(stderr, "bam2bed: Fail to open BAM file %s\n", argv[1]);
28 return 1;
29 }
30 if (argc == 2) { /* if a region is not specified */
31 bam1_t *b = bam_init1();
32 while (samread(fp, b) >= 0) fetch_func(b, fp);
33 bam_destroy1(b);
34 } else {
35 int ref, beg, end;
36 bam_index_t *idx;
37 if ((idx = bam_index_load(argv[1])) == 0) {
38 fprintf(stderr, "bam2bed: BAM indexing file is not available.\n");
39 return 1;
40 }
41 bam_parse_region(fp->header, argv[2], &ref, &beg, &end);
42 if (ref < 0) {
43 fprintf(stderr, "bam2bed: Invalid region %s\n", argv[2]);
44 return 1;
45 }
46 bam_fetch(fp->x.bam, idx, ref, beg, end, fp, fetch_func);
47 bam_index_destroy(idx);
48 }
49 samclose(fp);
50 return 0;
51 }