void
VcfWriterRnaSV::
modifySample(
const SVCandidate& sv,
SampleTag_t& sampletags) const
{
const SVScoreInfo& baseInfo(getBaseInfo());
const unsigned sampleCount(baseInfo.samples.size());
std::vector<std::string> values(sampleCount);
for (unsigned sampleIndex(0); sampleIndex<sampleCount; ++sampleIndex)
{
const SVSampleInfo& sampleInfo(baseInfo.samples[sampleIndex]);
values[sampleIndex] = str(boost::format("%i,%i")
% sampleInfo.ref.spanningPairCount
% sampleInfo.alt.spanningPairCount);
}
sampletags.push_back(std::make_pair("PR", values));
if (sv.isImprecise()) return;
for (unsigned sampleIndex(0); sampleIndex<sampleCount; ++sampleIndex)
{
const SVSampleInfo& sampleInfo(baseInfo.samples[sampleIndex]);
values[sampleIndex] = str( boost::format("%i,%i")
% sampleInfo.ref.splitReadCount
% sampleInfo.alt.splitReadCount);
}
sampletags.push_back(std::make_pair("SR",values));
}
void
VcfWriterSomaticSV::
modifySample(
const SVCandidate& sv,
SampleTag_t& sampletags) const
{
const SVScoreInfo& baseInfo(getBaseInfo());
std::vector<std::string> values(2);
static const std::string pairTag("PR");
values[0] = str( boost::format("%i,%i") % baseInfo.normal.ref.confidentSpanningPairCount % baseInfo.normal.alt.confidentSpanningPairCount);
values[1] = str( boost::format("%i,%i") % baseInfo.tumor.ref.confidentSpanningPairCount % baseInfo.tumor.alt.confidentSpanningPairCount);
sampletags.push_back(std::make_pair(pairTag,values));
if (sv.isImprecise()) return;
static const std::string srTag("SR");
values[0] = str( boost::format("%i,%i") % baseInfo.normal.ref.confidentSplitReadCount % baseInfo.normal.alt.confidentSplitReadCount);
values[1] = str( boost::format("%i,%i") % baseInfo.tumor.ref.confidentSplitReadCount % baseInfo.tumor.alt.confidentSplitReadCount);
sampletags.push_back(std::make_pair(srTag,values));
}
