void
bam_streamer::
report_state(std::ostream& os) const
{
const bam_record* bamp(get_record_ptr());
os << "\tbam_stream_label: " << name() << "\n";
if (_is_region && (! _region.empty()))
{
os << "\tbam_stream_selected_region: " << _region << "\n";
}
if (nullptr != bamp)
{
os << "\tbam_stream_record_no: " << record_no() << "\n";
os << "\tbam_record QNAME/read_number: " << bamp->qname() << "/" << bamp->read_no() << "\n";
const char* chrom_name(target_id_to_name(bamp->target_id()));
os << "\tbam record RNAME: " << chrom_name << "\n";
os << "\tbam record POS: " << bamp->pos() << "\n";
}
else
{
os << "\tno bam record currently set\n";
}
}
bam_streamer::
bam_streamer(
const char* filename,
const char* region)
: _is_record_set(false),
_bfp(nullptr),
_hidx(nullptr),
_hitr(nullptr),
_record_no(0),
_stream_name(filename),
_is_region(false)
{
assert(nullptr != filename);
if ('\0' == *filename)
{
throw blt_exception("Can't initialize bam_streamer with empty filename\n");
}
_bfp = samopen(filename, "rb", 0);
if (nullptr == _bfp)
{
log_os << "ERROR: Failed to open SAM/BAM/CRAM file: " << filename << "\n";
exit(EXIT_FAILURE);
}
if (nullptr == region)
{
// read the whole BAM file:
if (_bfp->header->n_targets)
{
// parse a fake region so that header->hash is created
std::string fake_region(target_id_to_name(0));
fake_region += ":1-1";
int ref,beg,end;
bam_parse_region(_bfp->header, fake_region.c_str(), &ref, &beg, &end);
}
return;
}
// read a specific region of the bam file:
set_new_region(region);
}
bam_streamer::
bam_streamer(const char* filename,
const char* region)
: _is_record_set(false), _bfp(NULL), _bidx(NULL), _biter(NULL),
_record_no(0), _stream_name(filename), _is_region(false)
{
assert(NULL != filename);
assert('\0' != *filename);
_bfp = samopen(filename, "rb", 0);
if (NULL == _bfp)
{
log_os << "ERROR: Failed to open SAM/BAM file: " << filename << "\n";
exit(EXIT_FAILURE);
}
if (NULL == region)
{
// read the whole BAM file:
if (_bfp->header->n_targets)
{
// parse a fake region so that header->hash is created
std::string fake_region(target_id_to_name(0));
fake_region += ":1-1";
int ref,beg,end;
bam_parse_region(_bfp->header, fake_region.c_str(), &ref, &beg, &end);
}
return;
}
// read a specific region of the bam file:
set_new_region(region);
}
