static void * downloadBamFile(void * args) {
BamReaderData * data = (BamReaderData *) args;
int j, tid, cnt, pos, n_plp;
const bam_pileup1_t *plp;
while (bam_mplp_auto(data->iter, &tid, &pos, &n_plp, &plp) > 0) {
// Count reads in pileup
cnt = 0;
const bam_pileup1_t *p = plp;
for (j = 0; j < n_plp; ++j) {
//if (bam1_qual(p->b)[p->qpos] >= data->conf->min_baseQ)
cnt++;
p++;
}
// Its a wrap:
char * chrom = data->data->h->target_name[tid];
if (data->stop > 0 && (strcmp(chrom, data->chrom) == 0 && pos >= data->stop))
break;
// +1 to account for 0-based indexing in BAMs:
if (pushValuesToBuffer(data->bufferedReaderData, chrom, pos+1, pos+2, cnt))
break;
}
bam_iter_destroy(data->data->iter);
endBufferedSignal(data->bufferedReaderData);
return NULL;
}
static void * downloadTabixFile(void * args) {
BCFReaderData * data = (BCFReaderData *) args;
char * line;
char * last_chrom = "";
while ((line = nextLine(data))) {
if (line[0] == '#')
continue;
char * chrom = strtok(line, "\t");
if (strcmp(chrom, last_chrom)) {
last_chrom = calloc(strlen(chrom) + 1, sizeof(char));
strcpy(last_chrom, chrom);
}
int pos = atoi(strtok(NULL, "\t"));
if (data->tabix_iterator)
free(line);
if (pushValuesToBuffer(data->bufferedReaderData, last_chrom, pos, pos+1, 1))
break;
}
if (data->tabix_iterator)
ti_iter_destroy(data->tabix_iterator);
endBufferedSignal(data->bufferedReaderData);
return NULL;
}
void * downloadBigFile(void * args) {
BigFileReaderData * data = (BigFileReaderData *) args;
if (!data->chrom)
downloadFullGenome(data);
else
downloadBigRegion(data, data->chrom, data->start, data->stop);
endBufferedSignal(data->bufferedReaderData);
return NULL;
}
void * readBigBed(void * ptr) {
BigBedReaderData * data = (BigBedReaderData *) ptr;
if (data->chrom)
readBigBedRegion(data, data->chrom, data->start, data->stop);
else {
int chrom_index;
for (chrom_index = 0; chrom_index < data->fp->cl->nKeys; chrom_index++)
if (readBigBedRegion(data, data->fp->cl->chrom[chrom_index], 0, data->fp->cl->len[chrom_index]))
break;
}
endBufferedSignal(data->bufferedReaderData);
return NULL;
}