Quick test for vcf/bcf loading using htslib

hts_test.c

#include <stdlib.h>
#include <unistd.h>
#include <stdio.h>
#include "htslib/vcf.h"

int main(int argc, char *argv[])
{
    int c, is_sam = 0, is_copy = 0;
    long cnt = 0;
    vcfFile *fp;
    bcf_hdr_t *h;
    bcf1_t *b;

    while ((c = getopt(argc, argv, "Sc")) >= 0) {
        if (c == 'S') is_sam = 1;
        else if (c == 'c') is_copy = 1;
    }
    if (argc == optind) {
        fprintf(stderr, "Usage: test-dup [-Sc] <in.sam> | <in.bam>\n");
        return 1;
    }

    fp = bcf_open(argv[optind], is_sam? "r" : "rb");
    h = bcf_hdr_read(fp);
    b = bcf_init1();
    while (bcf_read1(fp, h, b) >= 0) {
        if (is_copy) {
            bcf1_t *b2;
            b2 = bcf_dup(b);
            bcf_destroy1(b2);
        }
        ++cnt;
    }
    bcf_destroy1(b);
    bcf_close(fp);

    fprintf(stderr, "%ld records processed.\n", cnt);

    return 0;
}