/**
* Populate sequence names from files.
* Searches headers first folllowed by tabix.
*/
void BCFSyncedStreamReader::add_interval(int32_t i)
{
int32_t nseqs = 0;
const char **seq_names = NULL;
if (hdrs[i])
{
seq_names = bcf_hdr_seqnames(hdrs[i], &nseqs);
for (uint32_t j=0; j<nseqs; ++j)
{
std::string seq(seq_names[j]);
if (intervals_map.find(seq)==intervals_map.end())
{
intervals_map[seq] = intervals_map.size();
intervals.push_back(GenomeInterval(seq));
}
}
if(seq_names) free(seq_names);
}
if (tbxs[i])
{
seq_names = tbx_seqnames(tbxs[i], &nseqs);
for (uint32_t j=0; j<nseqs; ++j)
{
std::string seq(seq_names[j]);
if (intervals_map.find(seq)==intervals_map.end())
{
intervals_map[seq] = intervals_map.size();
intervals.push_back(GenomeInterval(seq));
}
}
if(seq_names) free(seq_names);
}
}
/**
* Populate sequence names from files.
*/
void BCFSyncedStreamReader::remove_interval(std::string& interval)
{
if (intervals_map.find(interval)!=intervals_map.end())
{
intervals_map[interval] = intervals_map.size();
intervals.push_back(GenomeInterval(interval));
}
}
static
unsigned
testOverlap(
SVLocusSet& locusSet,
const int32_t tid,
const int32_t beginPos,
const int32_t endPos)
{
std::set<SVLocusSet::NodeAddressType> intersect;
locusSet.getRegionIntersect(GenomeInterval(tid,beginPos,endPos),intersect);
return intersect.size();
}
static
void
runDSL(const DSLOptions& opt)
{
SVLocusSet set;
set.load(opt.graphFilename.c_str());
const SVLocusSet& cset(set);
std::ostream& os(std::cout);
// add this handy map of chromosome id to chromosome label at the start of all output types:
os << cset.header << "\n";
if (! opt.region.empty())
{
int32_t tid,beginPos,endPos;
parse_bam_region(set.header, opt.region, tid, beginPos, endPos); // parse the region
set.dumpRegion(os,GenomeInterval(tid,beginPos,endPos));
}
else if (opt.isLocusIndex)
{
const SVLocus& locus(cset.getLocus(opt.locusIndex));
if (opt.locusFilename.empty())
{
os << locus;
}
else
{
std::ofstream ofs(opt.locusFilename.c_str(), std::ios::binary);
boost::archive::binary_oarchive oa(ofs);
oa << locus;
}
}
else
{
cset.dump(os);
}
}