void
VcfWriterCandidateSV::
writeSV(
const SVCandidateSetData& svData,
const SVCandidateAssemblyData& adata,
const SVCandidate& sv,
const SVId& svId)
{
static const EventInfo event;
writeSVCore( svData, adata, sv, svId, event);
}
void
VcfWriterSomaticSV::
writeSV(
const EdgeInfo& edge,
const SVCandidateData& ,
const unsigned svIndex,
const SVCandidate& sv,
const SomaticSVScoreInfo& ssInfo)
{
if (ssInfo.somaticScore < _somaticOpt.minOutputSomaticScore) return;
//TODO: this is a lame way to customize subclass behavior:
_ssInfoPtr=&ssInfo;
writeSVCore(edge, svIndex, sv);
_ssInfoPtr=NULL;
}
void
VcfWriterRnaSV::
writeSV(
const SVCandidateSetData& svData,
const SVCandidateAssemblyData& adata,
const SVCandidate& sv,
const SVId& svId,
const SVScoreInfo& baseInfo,
const SVScoreInfoRna& rnaInfo,
const EventInfo& event)
{
//TODO: this is a lame way to customize subclass behavior:
setScoreInfo(baseInfo);
_rnaInfoPtr =&rnaInfo;
writeSVCore(svData, adata, sv, svId, event, true);
clearScoreInfo();
_rnaInfoPtr =nullptr;
}
void
VcfWriterSomaticSV::
writeSV(
const SVCandidateSetData& svData,
const SVCandidateAssemblyData& adata,
const SVCandidate& sv,
const SVId& svId,
const SVScoreInfo& baseInfo,
const SVScoreInfoSomatic& somaticInfo,
const EventInfo& event,
const SVScoreInfoSomatic& singleJunctionSomaticInfo)
{
//TODO: this is a lame way to customize subclass behavior:
setScoreInfo(baseInfo);
_somaticInfoPtr=&somaticInfo;
_singleJunctionSomaticInfoPtr=&singleJunctionSomaticInfo;
writeSVCore(svData, adata, sv, svId, event);
clearScoreInfo();
_somaticInfoPtr=NULL;
_singleJunctionSomaticInfoPtr=NULL;
}
