X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=examples%2Fbam2bed.c;fp=examples%2Fbam2bed.c;h=bb937d1f9fa71bd7ec335e5c40569298c957b09f;hp=0000000000000000000000000000000000000000;hb=cb12a866906ec4ac644de0e658679261c82ab098;hpb=3a3b72190c04cb076438f5027e13fcf5ddee77be

diff --git a/examples/bam2bed.c b/examples/bam2bed.c
new file mode 100644
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;
+}