static
void
addDebugInfo(
const bool isFirstOfPair,
const SVCandidate& sv,
const SVCandidateAssemblyData& assemblyData,
VcfWriterSV::InfoTag_t& infotags)
{
if (!assemblyData.isSpanning) return;
const bool isFirst = (assemblyData.bporient.isBp1First == isFirstOfPair);
const bool isRightOpen = (isFirstOfPair ? sv.bp1.state : sv.bp2.state) == SVBreakendState::RIGHT_OPEN;
infotags.push_back(str(boost::format("FOOBAR_FW=%1%") % (isFirst == isRightOpen)));
if (!isFirst) return; // only the first breakpoint gets the alignments attached to its VCF entry
infotags.push_back(str(boost::format("FOOBAR_bp1=%i;bp2=%i") % sv.bp1.interval.tid % sv.bp2.interval.tid));
// there can be several contigs per breakend, so we iterate over all of them.
const unsigned numContigs(assemblyData.contigs.size());
infotags.push_back(str(boost::format("FOOBAR_NCONTIGS=%i") % numContigs));
if (numContigs > 0)
{
if (numContigs != assemblyData.spanningAlignments.size())
infotags.push_back(str(boost::format("FOOBAR_ERROR=%i;%i") % numContigs % assemblyData.spanningAlignments.size()));
if (numContigs <= assemblyData.bestAlignmentIndex)
infotags.push_back(str(boost::format("FOOBAR_ERROR2=%i;%i") % numContigs % assemblyData.bestAlignmentIndex));
infotags.push_back(str(boost::format("FOOBAR_BEST=%i") % assemblyData.bestAlignmentIndex));
//infotags.push_back(str(boost::format("FOOBAR_EXTCONTIG=%s") % assemblyData.extendedContigs[assemblyData.bestAlignmentIndex]));
infotags.push_back(str(boost::format("FOOBAR_CONTIGcount=%i") % assemblyData.contigs[assemblyData.bestAlignmentIndex].supportReads.size()));
}
}
static
void
addSharedInfo(
const EventInfo& event,
VcfWriterSV::InfoTag_t& infoTags)
{
if (event.isEvent())
{
infoTags.push_back( str(boost::format("EVENT=%i") % event.label));
}
}