void CHPQuantificationFileBufferWriter::FlushBuffer()
{
if(m_BufferSize > 0) {
for (int target=0; target<m_CHPFileNames->size(); target++)
{
CalvinCHPFileUpdater updater;
updater.OpenCHPFile((*m_CHPFileNames)[target].c_str());
updater.UpdateExpressionQuantificationBuffer(m_TargetQuantificationRowIndexes[target], m_TargetQuantificationBuffers[target]);
updater.CloseCHPFile();
m_TargetQuantificationRowIndexes[target] += m_TargetQuantificationBuffers[target].size();
m_TargetQuantificationBuffers[target].clear();
}
}
m_BufferSize = 0;
}
void CHPMultiDataFileBufferWriter::FlushBuffer()
{
if(m_BufferSize > 0)
{
MultiDataType segmentTypes[] = {
SegmentCNMultiDataType,
SegmentLOHMultiDataType,
SegmentCNNeutralLOHMultiDataType,
SegmentNormalDiploidMultiDataType,
SegmentMosaicismMultiDataType,
SegmentNoCallMultiDataType,
SegmentGenotypeConcordanceMultiDataType,
SegmentGenotypeDiscordanceMultiDataType,
SegmentCNLossLOHConcordanceMultiDataType,
SegmentCNNeutralLOHConcordanceMultiDataType,
SegmentHeteroUPDMultiDataType,
SegmentIsoUPDMultiDataType,
SegmentDenovoCopyNumberMultiDataType,
SegmentHemizygousParentOfOriginMultiDataType
};
int nSegmentTypes = sizeof(segmentTypes) / sizeof(MultiDataType);
for (int target = 0; target < (int)chpFileNames->size(); target++)
{
CalvinCHPFileUpdater updater;
updater.OpenCHPFile((*chpFileNames)[target].c_str());
MultiDataType dataType;
dataType = GenotypeMultiDataType;
if (dataBuffers.find(dataType) != dataBuffers.end() && dataBuffers[dataType][target].size() > 0)
{
updater.UpdateMultiDataGenotypeEntryBuffer(dataType,
rowIndexes[dataType][target],
dataBufferSz[dataType],
dataBuffers[dataType][target]);
rowIndexes[dataType][target] += (int) dataBuffers[dataType][target].size();
ClearBuffer(dataBuffers[dataType][target]);
}
dataType = CopyNumberMultiDataType;
if (dataBuffers.find(dataType) != dataBuffers.end() && dataBuffers[dataType][target].size() > 0)
{
updater.UpdateMultiDataCopyNumberEntryBuffer(dataType,
rowIndexes[dataType][target],
dataBufferSz[dataType],
dataBuffers[dataType][target]);
rowIndexes[dataType][target] += (int) dataBuffers[dataType][target].size();
ClearBuffer(dataBuffers[dataType][target]);
}
dataType = CytoMultiDataType;
if (dataBuffers.find(dataType) != dataBuffers.end() && dataBuffers[dataType][target].size() > 0)
{
updater.UpdateMultiDataCytoRegionEntryBuffer(dataType,
rowIndexes[dataType][target],
dataBufferSz[dataType],
dataBuffers[dataType][target]);
rowIndexes[dataType][target] += (int) dataBuffers[dataType][target].size();
ClearBuffer(dataBuffers[dataType][target]);
}
dataType = ExpressionMultiDataType;
if (dataBuffers.find(dataType) != dataBuffers.end() && dataBuffers[dataType][target].size() > 0)
{
updater.UpdateMultiDataExpressionEntryBuffer(dataType,
rowIndexes[dataType][target],
dataBufferSz[dataType],
dataBuffers[dataType][target]);
rowIndexes[dataType][target] += (int) dataBuffers[dataType][target].size();
ClearBuffer(dataBuffers[dataType][target]);
}
dataType = CopyNumberVariationMultiDataType;
if (dataBuffers.find(dataType) != dataBuffers.end() && dataBuffers[dataType][target].size() > 0)
{
updater.UpdateMultiDataCopyNumberVariationRegionEntryBuffer(dataType,
rowIndexes[dataType][target],
dataBufferSz[dataType],
dataBuffers[dataType][target]);
rowIndexes[dataType][target] += (int) dataBuffers[dataType][target].size();
ClearBuffer(dataBuffers[dataType][target]);
}
dataType = DmetBiAllelicMultiDataType;
if (dataBuffers.find(dataType) != dataBuffers.end() && dataBuffers[dataType][target].size() > 0)
{
updater.UpdateDmetBiAllelicEntryBuffer(dataType,
rowIndexes[dataType][target],
dataBufferSz[dataType],
dataBuffers[dataType][target]);
rowIndexes[dataType][target] += (int) dataBuffers[dataType][target].size();
ClearBuffer(dataBuffers[dataType][target]);
}
dataType = DmetMultiAllelicMultiDataType;
if (dataBuffers.find(dataType) != dataBuffers.end() && dataBuffers[dataType][target].size() > 0)
{
updater.UpdateDmetMultiAllelicEntryBuffer(dataType,
rowIndexes[dataType][target],
dataBufferSz[dataType],
dataBuffers[dataType][target]);
rowIndexes[dataType][target] += (int) dataBuffers[dataType][target].size();
ClearBuffer(dataBuffers[dataType][target]);
}
dataType = DmetCopyNumberMultiDataType;
if (dataBuffers.find(dataType) != dataBuffers.end() && dataBuffers[dataType][target].size() > 0)
{
updater.UpdateDmetCopyNumberEntryBuffer(dataType,
rowIndexes[dataType][target],
dataBufferSz[dataType],
dataBuffers[dataType][target]);
rowIndexes[dataType][target] += (int) dataBuffers[dataType][target].size();
ClearBuffer(dataBuffers[dataType][target]);
}
dataType = ChromosomeSummaryMultiDataType;
if (dataBuffers.find(dataType) != dataBuffers.end() && dataBuffers[dataType][target].size() > 0)
{
updater.UpdateChromosomeSummaryEntryBuffer(dataType,
rowIndexes[dataType][target],
dataBufferSz[dataType],
dataBuffers[dataType][target]);
rowIndexes[dataType][target] += (int) dataBuffers[dataType][target].size();
ClearBuffer(dataBuffers[dataType][target]);
}
dataType = CytoGenotypeCallMultiDataType;
if (dataBuffers.find(dataType) != dataBuffers.end() && dataBuffers[dataType][target].size() > 0)
{
updater.UpdateMultiDataCytoGenotypeEntryBuffer(dataType,
rowIndexes[dataType][target],
dataBufferSz[dataType],
dataBuffers[dataType][target]);
rowIndexes[dataType][target] += (int) dataBuffers[dataType][target].size();
ClearBuffer(dataBuffers[dataType][target]);
}
for (int iseg=0; iseg<nSegmentTypes; iseg++)
{
dataType = segmentTypes[iseg];
if (dataBuffers.find(dataType) != dataBuffers.end() && dataBuffers[dataType][target].size() > 0)
{
updater.UpdateChromosomeSegmentEntryBuffer(dataType,
rowIndexes[dataType][target],
dataBufferSz[dataType],
dataBuffers[dataType][target]);
rowIndexes[dataType][target] += (int) dataBuffers[dataType][target].size();
ClearBuffer(dataBuffers[dataType][target]);
}
}
dataType = FamilialSegmentOverlapsMultiDataType;
if (dataBuffers.find(dataType) != dataBuffers.end() && dataBuffers[dataType][target].size() > 0)
{
updater.UpdateFamilialSegmentOverlapEntryBuffer(dataType,
rowIndexes[dataType][target],
dataBufferSz[dataType],
dataBuffers[dataType][target]);
rowIndexes[dataType][target] += (int) dataBuffers[dataType][target].size();
ClearBuffer(dataBuffers[dataType][target]);
}
dataType = FamilialSamplesMultiDataType;
if (dataBuffers.find(dataType) != dataBuffers.end() && dataBuffers[dataType][target].size() > 0)
{
updater.UpdateFamilialSampleEntryBuffer(dataType,
rowIndexes[dataType][target],
dataBufferSz[dataType],
dataBuffers[dataType][target]);
rowIndexes[dataType][target] += (int) dataBuffers[dataType][target].size();
ClearBuffer(dataBuffers[dataType][target]);
}
dataType = AllelePeaksMultiDataType;
if (dataBuffers.find(dataType) != dataBuffers.end() && dataBuffers[dataType][target].size() > 0)
{
updater.UpdateMultiDataAllelePeaksEntryBuffer(dataType,
rowIndexes[dataType][target],
dataBufferSz[dataType],
dataBuffers[dataType][target]);
rowIndexes[dataType][target] += (int) dataBuffers[dataType][target].size();
ClearBuffer(dataBuffers[dataType][target]);
}
dataType = MarkerABSignalsMultiDataType;
if (dataBuffers.find(dataType) != dataBuffers.end() && dataBuffers[dataType][target].size() > 0)
{
updater.UpdateMultiDataMarkerABSignalsEntryBuffer(dataType,
rowIndexes[dataType][target],
dataBufferSz[dataType],
dataBuffers[dataType][target]);
rowIndexes[dataType][target] += (int) dataBuffers[dataType][target].size();
ClearBuffer(dataBuffers[dataType][target]);
}
updater.CloseCHPFile();
}
}
m_BufferSize = 0;
}