Imported Upstream version 0.1.8

[samtools.git] / examples / bam2bed.c

diff --git a/examples/bam2bed.c b/examples/bam2bed.c
new file mode 100644 (file)
index 0000000..bb937d1
--- /dev/null
+++ b/examples/bam2bed.c
@@ -0,0 +1,51 @@
+#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;
+}