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bam2bed.c

#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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