#include <stdio.h>

#define BAM_LITE
#include "bam.h"

// callback for bam_plbuf_init()
static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
{
	bam_header_t *header = (bam_header_t*)data;
	printf("%s\t%d\t%d\n", header->target_name[tid], pos + 1, n);
	return 0;
}

int main(int argc, char *argv[])
{
	bamFile fp;
	bam_header_t *header;
	if (argc == 1) {
		fprintf(stderr, "Usage: calDepth <in.bam>\n");
		return 1;
	}
	fp = bam_open(argv[1], "r");
	if (fp == 0) {
		fprintf(stderr, "Fail to open BAM file %s\n", argv[1]);
		return 1;
	}
	header = bam_header_read(fp);
	bam_pileup_file(fp, 0, pileup_func, header);
	bam_header_destroy(header);
	bam_close(fp);
	return 0;
}