bam_fetch example

fetch.c

#include <stdio.h>
#include "sam.h"

// callback for bam_fetch()
static int fetch_func(const bam1_t *b, void *data)
{
	printf("%s %d %d %d\n", b->data, b->core.tid, b->core.pos, b->core.l_qseq);
	return 0;
}

int main(int argc, char *argv[])
{
	samfile_t *sf;
	sf = samopen("test-sort.bam", "rb", 0);
	if (sf == 0) {
		fprintf(stderr, "Fail to open BAM file %s\n", argv[1]);
		return 1;
	}
	int ref;
	bam_index_t *idx;
	idx = bam_index_load("test-sort.bam"); // load BAM index
	if (idx == 0) {
		fprintf(stderr, "BAM indexing file is not available.\n");
		return 1;
	}
	bam_fetch(sf->x.bam, idx, 0, 3597710, 3597711, 0, fetch_func);
	bam_index_destroy(idx);
	samclose(sf);
	return 0;
}