/**
* Initialize buffer for next interval.
* This should only be invoked if the buffer is empty.
* Returns true if successful.
*/
bool BCFSyncedReader::initialize_next_interval()
{
if (random_access)
{
while (intervals_index < intervals.size())
{
GenomeInterval interval = intervals[intervals_index++];
for (size_t i=0; i<nfiles; ++i)
{
hts_itr_destroy(itrs[i]);
itrs[i] = 0;
interval.to_string(&s);
if (ftypes[i].format==bcf)
{
itrs[i] = bcf_itr_querys(idxs[i], hdrs[i], s.s);
}
else if (ftypes[i].format==vcf)
{
itrs[i] = tbx_itr_querys(tbxs[i], s.s);
}
fill_buffer(i);
}
//make sure pq is not empty
//it is possible for the pq to be empty as iterators may be returned
//as the sequence might be a valid sequence stated in the header
if (pq.size()!=0)
{
return true;
}
}
return false;
}
else
{
for (size_t i=0; i<nfiles; ++i)
{
fill_buffer(i);
}
if (pq.size()!=0)
{
return true;
}
return false;
}
}
/**
* Initialize buffer for next interval.
* This should only be invoked if the buffer is empty.
* Returns true if successful.
*/
bool BCFSyncedStreamReader::initialize_next_interval()
{
while (intervals_index < intervals.size())
{
GenomeInterval interval = intervals[intervals_index++];
for (int32_t i = 0; i<nfiles; ++i)
{
int32_t ftype = hts_file_type(vcf_files[i].c_str());
hts_itr_destroy(itrs[i]);
itrs[i] = 0;
interval.to_string(&s);
if (ftype==FT_BCF_GZ)
{
itrs[i] = bcf_itr_querys(idxs[i], hdrs[i], s.s);
}
else if (ftype==FT_VCF_GZ)
{
itrs[i] = tbx_itr_querys(tbxs[i], s.s);
}
fill_buffer(i);
}
//make sure pq is not empty
//it is possible for the pq to be empty as iterators may be returned
//as the sequence might be a valid sequence stated in the header
if (pq.size()!=0)
{
return true;
}
}
return false;
}
