static int _reader_seek(bcf_sr_t *reader, const char *seq, int start, int end)
{
if ( end>=MAX_CSI_COOR )
{
fprintf(stderr,"The coordinate is out of csi index limit: %d\n", end+1);
exit(1);
}
if ( reader->itr )
{
hts_itr_destroy(reader->itr);
reader->itr = NULL;
}
reader->nbuffer = 0;
if ( reader->tbx_idx )
{
int tid = tbx_name2id(reader->tbx_idx, seq);
if ( tid==-1 ) return -1; // the sequence not present in this file
reader->itr = tbx_itr_queryi(reader->tbx_idx,tid,start,end+1);
}
else
{
int tid = bcf_hdr_name2id(reader->header, seq);
if ( tid==-1 ) return -1; // the sequence not present in this file
reader->itr = bcf_itr_queryi(reader->bcf_idx,tid,start,end+1);
}
if ( !reader->itr ) fprintf(stderr,"Could not seek: %s:%d-%d\n",seq,start+1,end+1);
assert(reader->itr);
return 0;
}
int beds_fill_buffer(struct beds_anno_file *file, bcf_hdr_t *hdr_out, bcf1_t *line)
{
assert(file->idx);
int tid = tbx_name2id(file->idx, bcf_seqname(hdr_out, line));
// if cached this region already, just skip refill. this is different from vcfs_fill_buffer()
if ( tid == file->last_id && file->last_start <= line->pos + 1 && file->last_end > line->pos)
return -1;
if ( tid == -1 ) {
if ( file->no_such_chrom == 0 ) {
warnings("no chromosome %s found in databases %s.", bcf_seqname(hdr_out, line), file->fname);
file->no_such_chrom = 1;
}
return 1;
} else {
file->no_such_chrom = 0;
}
// empty cache
file->cached = 0;
int i;
hts_itr_t *itr = tbx_itr_queryi(file->idx, tid, line->pos, line->pos + line->rlen);
if ( itr == NULL )
return 1;
// if buffer refilled, init last start and end
file->last_id = tid;
file->last_start = -1;
file->last_end = -1;
while (1) {
if ( file->cached == file->max ) {
file->max += 8;
file->buffer = (struct beds_anno_tsv**)realloc(file->buffer, sizeof(struct beds_anno_tsv*)*file->max);
for (i = 8; i > 0; --i)
file->buffer[file->max - i] = beds_anno_tsv_init();
}
if ( tbx_itr_next(file->fp, file->idx, itr, &file->buffer[file->cached]->string) < 0)
break;
struct beds_anno_tsv *tsv = file->buffer[file->cached];
convert_string_tsv(tsv);
// Skip if variant located outside of region.
if (line->pos < tsv->start || line->pos >= tsv->end)
continue;
if (tsv->end - tsv->start == 1 && line->pos != tsv->start)
continue;
file->cached++;
if ( file->last_end == -1 ) {
file->last_end = tsv->end;
file->last_start = tsv->start;
continue;
}
if ( file->last_end < tsv->end )
file->last_end = tsv->end;
if ( file->last_start > tsv->start )
file->last_start = tsv->start;
}
// if buffer is filled return 0, else return 1
return file->cached ? 0 : 1;
}