diff pyPRADA_1.2/tools/samtools-0.1.16/examples/bam2bed.c @ 0:acc2ca1a3ba4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/examples/bam2bed.c	Thu Feb 20 00:44:58 2014 -0500
@@ -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;
+}