int main(int argc, char *argv[])
{
char *progname;
char *bamfilename;
int32_t tid;
samfile_t *bamin;
bam_index_t *bamidx;
bam_plbuf_t *buf;
bam1_t *bam_read;
uint32_t next_pos = 1;
progname = *argv;
argv++; argc--;
if (argc < 2) {
printf("Usage: %s bam_file tid\n", progname);
exit(1);
}
else {
bamfilename = argv[0];
tid = strtol(argv[1], NULL, 10);
}
/* try to open bam file */
bamin = samopen(bamfilename, "rb", NULL);
if (!bamin) {
fprintf(stderr, "Error opening bamfile %s\n", bamfilename);
exit(1);
}
/* try to open index */
bamidx = bam_index_load(bamfilename);
if (!bamidx) {
fprintf(stderr, "Error opening index for %s\n", bamfilename);
exit(1);
}
bam_read = bam_init1();
buf = bam_plbuf_init(&pileup_func, &next_pos);
/* disable maximum pileup depth */
bam_plp_set_maxcnt(buf->iter, INT_MAX);
bam_fetch(bamin->x.bam, bamidx,
tid, 0, INT_MAX,
buf, &fetch_func);
bam_plbuf_push(0, buf); /* finish pileup */
bam_plbuf_destroy(buf);
bam_destroy1(bam_read);
bam_index_destroy(bamidx);
samclose(bamin);
return 0;
}
loci_stats *bam_access_get_position_base_counts(char *chr, int posn){
char *region = NULL;
hts_itr_t *iter = NULL;
bam1_t* b = NULL;
bam_plp_t buf;
loci_stats *stats = malloc(sizeof(loci_stats *));
check_mem(stats);
stats->base_counts = malloc(sizeof(int) * 4);
check_mem(stats->base_counts);
stats->base_counts[0] = 0;
stats->base_counts[1] = 0;
stats->base_counts[2] = 0;
stats->base_counts[3] = 0;
fholder->stats = stats;
region = malloc((sizeof(char *) * (strlen(chr)+1))+sizeof(":")+sizeof("-")+(sizeof(char)*((no_of_digits(posn)*2)+1)));
sprintf(region,"%s:%d-%d",chr,posn,posn);
fholder->beg = posn;
fholder->end = posn;
// initialize pileup
buf = bam_plp_init(pileup_func, (void *)fholder);
bam_plp_set_maxcnt(buf,maxitercnt);
/*
sam_fetch(fholder->in, fholder->idx, ref, fholder->beg, fholder->end, buf, fetch_algo_func);
*/
//Replace fetch with iterator for htslib compatibility.
b = bam_init1();
iter = sam_itr_querys(fholder->idx, fholder->head, region);
int result;
int count = 0;
while ((result = sam_itr_next(fholder->in, iter, b)) >= 0) {
if(b->core.qual < min_map_qual || (b->core.flag & BAM_FUNMAP)
|| !(b->core.flag & BAM_FPROPER_PAIR) || (b->core.flag & BAM_FMUNMAP)//Proper pair and mate unmapped
|| (b->core.flag & BAM_FDUP)//1024 is PCR/optical duplicate
|| (b->core.flag & BAM_FSECONDARY) || (b->core.flag & BAM_FQCFAIL)//Secondary alignment, quality fail
|| (b->core.flag & BAM_FSUPPLEMENTARY) ) continue;
count++;
bam_plp_push(buf, b);
}
sam_itr_destroy(iter);
bam_plp_push(buf, 0);
int tid, pos, n_plp = -1;
const bam_pileup1_t *pil;
while ( (pil=bam_plp_next(buf, &tid, &pos, &n_plp)) > 0) {
if((pos+1) != posn) continue;
int i=0;
for(i=0;i<n_plp;i++){
const bam_pileup1_t *p = pil + i;
int qual = bam_get_qual(p->b)[p->qpos];
uint8_t c = bam_seqi(bam_get_seq(p->b), p->qpos);
if(!(p->is_del) && qual >= min_base_qual
&& p->b->core.qual >= min_map_qual){
//&& (c == 1 /*A*/|| c == 2 /*C*/|| c == 4 /*G*/|| c == 8 /*T*/)){
//Now we add a new read pos struct to the list since the read is valid.
//char cbase = toupper(bam_nt16_rev_table[c]);
switch(c){
case 1:
fholder->stats->base_counts[0]++;
break;
case 2:
fholder->stats->base_counts[1]++;
break;
case 4:
fholder->stats->base_counts[2]++;
break;
case 8:
fholder->stats->base_counts[3]++;
break;
default:
break;
}; // End of args switch statement */
}
}
} //End of iteration through pileup
//bam_plp_push(buf, 0); // finalize pileup
bam_plp_destroy(buf);
free(region);
return fholder->stats;
error:
//if(region) free(region);
if(fholder->stats){
if(fholder->stats->base_counts) free(fholder->stats->base_counts);
free(fholder->stats);
}
if(iter) sam_itr_destroy(iter);
if(b) bam_destroy1(b);
if(region) free(region);
return NULL;
}