void
bam_streamer::
set_new_region(const int ref, const int beg, const int end)
{
if (nullptr != _hitr) hts_itr_destroy(_hitr);
_load_index();
if (ref < 0)
{
log_os << "ERROR: Invalid region specified for BAM/CRAM file: " << name() << "\n";
exit(EXIT_FAILURE);
}
_hitr = sam_itr_queryi(_hidx,ref,beg,end);
_is_region = true;
_region.clear();
_is_record_set = false;
_record_no = 0;
}
void
bam_streamer::
set_new_region(const int ref, const int beg, const int end)
{
if (NULL != _biter) bam_iter_destroy(_biter);
_load_index();
if (ref < 0)
{
log_os << "ERROR: Invalid region specified for BAM file: " << name() << "\n";
exit(EXIT_FAILURE);
}
_biter = bam_iter_query(_bidx,ref,beg,end);
_is_region = true;
_region.clear();
_is_record_set = false;
_record_no = 0;
}
hts_streamer::
hts_streamer(
const char* filename,
const char* region) :
_is_record_set(false),
_is_stream_end(false),
_record_no(0),
_stream_name(filename),
_hfp(nullptr),
_tidx(nullptr),
_titr(nullptr),
_kstr(kinit)
{
if (! filename)
{
BOOST_THROW_EXCEPTION(illumina::common::GeneralException("hts filename is null ptr"));
}
if ('\0' == *filename)
{
BOOST_THROW_EXCEPTION(illumina::common::GeneralException("hts filename is empty string"));
}
_hfp = hts_open(filename, "r");
if (! _hfp)
{
std::ostringstream oss;
oss << "Failed to open hts file: '" << filename << "'";
BOOST_THROW_EXCEPTION(illumina::common::GeneralException(oss.str()));
}
_load_index();
// read only a region of HTS file:
if (region)
{
resetRegion(region);
}
}
