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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/examples/calDepth.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,62 @@
+#include <stdio.h>
+#include "sam.h"
+
+typedef struct {
+	int beg, end;
+	samfile_t *in;
+} tmpstruct_t;
+
+// callback for bam_fetch()
+static int fetch_func(const bam1_t *b, void *data)
+{
+	bam_plbuf_t *buf = (bam_plbuf_t*)data;
+	bam_plbuf_push(b, buf);
+	return 0;
+}
+// callback for bam_plbuf_init()
+static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
+{
+	tmpstruct_t *tmp = (tmpstruct_t*)data;
+	if ((int)pos >= tmp->beg && (int)pos < tmp->end)
+		printf("%s\t%d\t%d\n", tmp->in->header->target_name[tid], pos + 1, n);
+	return 0;
+}
+
+int main(int argc, char *argv[])
+{
+	tmpstruct_t tmp;
+	if (argc == 1) {
+		fprintf(stderr, "Usage: calDepth <in.bam> [region]\n");
+		return 1;
+	}
+	tmp.beg = 0; tmp.end = 0x7fffffff;
+	tmp.in = samopen(argv[1], "rb", 0);
+	if (tmp.in == 0) {
+		fprintf(stderr, "Fail to open BAM file %s\n", argv[1]);
+		return 1;
+	}
+	if (argc == 2) { // if a region is not specified
+		sampileup(tmp.in, -1, pileup_func, &tmp);
+	} else {
+		int ref;
+		bam_index_t *idx;
+		bam_plbuf_t *buf;
+		idx = bam_index_load(argv[1]); // load BAM index
+		if (idx == 0) {
+			fprintf(stderr, "BAM indexing file is not available.\n");
+			return 1;
+		}
+		bam_parse_region(tmp.in->header, argv[2], &ref, &tmp.beg, &tmp.end); // parse the region
+		if (ref < 0) {
+			fprintf(stderr, "Invalid region %s\n", argv[2]);
+			return 1;
+		}
+		buf = bam_plbuf_init(pileup_func, &tmp); // initialize pileup
+		bam_fetch(tmp.in->x.bam, idx, ref, tmp.beg, tmp.end, buf, fetch_func);
+		bam_plbuf_push(0, buf); // finalize pileup
+		bam_index_destroy(idx);
+		bam_plbuf_destroy(buf);
+	}
+	samclose(tmp.in);
+	return 0;
+}