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root/gclib/bamread/bam2bed.c
Revision: 123
Committed: Mon Dec 5 22:21:21 2011 UTC (7 years, 11 months ago) by gpertea
File size: 1746 byte(s)
Log Message:
bamread files

Line File contents
1 #include <stdio.h>
2 #include "bam/sam.h"
3
4 /* callback for bam_fetch() */
5 static int fetch_func(const bam1_t *b, void *data)
6 {
7 samfile_t *fp = (samfile_t*)data;
8 uint32_t *cigar = bam1_cigar(b);
9 const bam1_core_t *c = &b->core;
10 int i, l;
11 if (c->flag&BAM_FUNMAP) return 0; /* skip unmapped reads */
12 for (i = l = 0; i < c->n_cigar; ++i) {
13 int op = cigar[i]&0xf;
14 if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP)
15 l += cigar[i]>>4;
16 }
17 printf("%s\t%d\t%d\t%s\t%d\t%c\n", fp->header->target_name[c->tid],
18 c->pos, c->pos + l, bam1_qname(b), c->qual, (c->flag&BAM_FREVERSE)? '-' : '+');
19 return 0;
20 }
21 int main(int argc, char *argv[])
22 {
23 samfile_t *fp;
24 if (argc == 1) {
25 fprintf(stderr, "Usage: bam2bed <in.bam> [region]\n");
26 return 1;
27 }
28 if ((fp = samopen(argv[1], "rb", 0)) == 0) {
29 fprintf(stderr, "bam2bed: Fail to open BAM file %s\n", argv[1]);
30 return 1;
31 }
32 if (argc == 2) { /* if a region is not specified */
33 bam1_t *b = bam_init1();
34 while (samread(fp, b) >= 0) fetch_func(b, fp);
35 bam_destroy1(b);
36 } else {
37 int ref, beg, end;
38 bam_index_t *idx;
39 if ((idx = bam_index_load(argv[1])) == 0) { /* load BAM index */
40 fprintf(stderr, "bam2bed: BAM index file is not available.\n");
41 return 1;
42 }
43 bam_parse_region(fp->header, argv[2], &ref, &beg, &end); /* parse region */
44 if (ref < 0) {
45 fprintf(stderr, "bam2bed: Invalid region %s\n", argv[2]);
46 return 1;
47 }
48 bam_fetch(fp->x.bam, idx, ref, beg, end, fp, fetch_func);
49 bam_index_destroy(idx);
50 }
51 samclose(fp);
52 return 0;
53 }