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#include <stdio.h>
#include "sam.h"
static int fetch_func(const bam1_t *b, void *data)
{
samfile_t *fp = (samfile_t*)data;
uint32_t *cigar = bam1_cigar(b);
const bam1_core_t *c = &b->core;
int i, l;
if (b->core.tid < 0) return 0;
for (i = l = 0; i < c->n_cigar; ++i) {
int op = cigar[i]&0xf;
if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP)
l += cigar[i]>>4;
}
printf("%s\t%d\t%d\t%s\t%d\t%c\n", fp->header->target_name[c->tid],
c->pos, c->pos + l, bam1_qname(b), c->qual, (c->flag&BAM_FREVERSE)? '-' : '+');
return 0;
}
int main(int argc, char *argv[])
{
samfile_t *fp;
if (argc == 1) {
fprintf(stderr, "Usage: bam2bed <in.bam> [region]\n");
return 1;
}
if ((fp = samopen(argv[1], "rb", 0)) == 0) {
fprintf(stderr, "bam2bed: Fail to open BAM file %s\n", argv[1]);
return 1;
}
if (argc == 2) { /* if a region is not specified */
bam1_t *b = bam_init1();
while (samread(fp, b) >= 0) fetch_func(b, fp);
bam_destroy1(b);
} else {
int ref, beg, end;
bam_index_t *idx;
if ((idx = bam_index_load(argv[1])) == 0) {
fprintf(stderr, "bam2bed: BAM indexing file is not available.\n");
return 1;
}
bam_parse_region(fp->header, argv[2], &ref, &beg, &end);
if (ref < 0) {
fprintf(stderr, "bam2bed: Invalid region %s\n", argv[2]);
return 1;
}
bam_fetch(fp->x.bam, idx, ref, beg, end, fp, fetch_func);
bam_index_destroy(idx);
}
samclose(fp);
return 0;
}
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