// test.c
#include <stdio.h>
#include <stdlib.h>
#include "htslib/sam.h"
#include "htslib/thread_pool.h"

int main(int argc, char *argv[]) {
    // Open BAM file
    samFile *bam_file = sam_open(argv[1], "r");
    if (bam_file == NULL) {
        fprintf(stderr, "Failed to open BAM file\n");
        return 1;
    }
    hts_tpool *p = hts_tpool_init(1);
    htsThreadPool thread_pool = {p, 0};
    if (hts_set_thread_pool(bam_file, &thread_pool) != 0) {
        fprintf(stderr, "Failed to set thread pool.\n");
        return 1;
    }
    // Load BAM header
    bam_hdr_t *header = sam_hdr_read(bam_file);
    if (header == NULL) {
        fprintf(stderr, "Failed to read BAM header\n");
        sam_close(bam_file);
        return 1;
    }

    // Initialize the alignment data structure
    bam1_t *aln = bam_init1();

    // Iterate through the BAM file
    while (sam_read1(bam_file, header, aln) >= 0);
    int r;
    r = sam_read1(bam_file, header, aln);
    printf("r: %d\n", r);

    // Cleanup
    bam_destroy1(aln);
    bam_hdr_destroy(header);
    sam_close(bam_file);

    return 0;
}

HTSLIB_DIR=
gcc test.c -I$HTSLIB_DIR $HTSLIB_DIR/libhts.a -lm -lz -lpthread -llzma -lbz2 -lcurl -lcrypto; ./a.out input.sam