/////////////// BclBaseCallsSource Implementation
BclBaseCallsSource::BclBaseCallsSource(
const flowcell::Layout &flowcell,
const bool ignoreMissingBcls,
const bool ignoreMissingFilters,
common::ThreadVector &bclLoadThreads,
const unsigned inputLoadersMax,
const bool extractClusterXy):
flowcell_(flowcell),
tileSource_(flowcell_),
bclLoadThreads_(bclLoadThreads),
filterFilePath_(flowcell_.getLongestAttribute<flowcell::Layout::Bcl, flowcell::FiltersFilePathAttributeTag>()),
positionsFilePath_(flowcell_.getLongestAttribute<flowcell::Layout::Bcl, flowcell::PositionsFilePathAttributeTag>()),
threadReaders_(bclLoadThreads_.size(), rta::BclReader(
flowcell_.getLongestAttribute<flowcell::Layout::Bcl, flowcell::BclFilePathAttributeTag>().string().size(),
ignoreMissingBcls, tileSource_.getMaxTileClusters())),
bclMapper_(flowcell::getTotalReadLength(flowcell_.getReadMetadataList()) + flowcell_.getBarcodeLength(),
bclLoadThreads_, threadReaders_,
inputLoadersMax, tileSource_.getMaxTileClusters()),
filtersMapper_(ignoreMissingFilters),
clocsMapper_(),
locsMapper_(),
barcodeLoader_(bclLoadThreads, inputLoadersMax, tileSource_.getMaxTileClusters(), threadReaders_)
{
ISAAC_TRACE_STAT("SelectMatchesTransition::SelectMatchesTransitions before filtersMapper_.reserveBuffer ")
filtersMapper_.reserveBuffers(filterFilePath_.string().size(), tileSource_.getMaxTileClusters());
ISAAC_TRACE_STAT("SelectMatchesTransition::SelectMatchesTransitions after filtersMapper_.reserveBuffer ")
if (extractClusterXy)
{
clocsMapper_.reserveBuffers(positionsFilePath_.string().size(), tileSource_.getMaxTileClusters());
locsMapper_.reserveBuffers(positionsFilePath_.string().size(), tileSource_.getMaxTileClusters());
ISAAC_TRACE_STAT("SelectMatchesTransition::SelectMatchesTransitions after filtersMapper_.reserveBuffer ")
}
}
void AlignWorkflow::selectMatches(
alignment::matchSelector::FragmentStorage &fragmentStorage,
std::vector<alignment::TemplateLengthStatistics> &barcodeTemplateLengthStatistics) const
{
ISAAC_TRACE_STAT("AlignWorkflow::selectMatches fragmentStorage ")
workflow::alignWorkflow::SelectMatchesTransition transition(
(bufferBins_ ? 3 : 2),
fragmentStorage, foundMatchesMetadata_.matchDistribution_,
sortedReferenceMetadataList_, tempDirectory_, coresMax_,
foundMatchesMetadata_.tileMetadataList_, barcodeMetadataList_,
flowcellLayoutList_, repeatThreshold_, mateDriftRange_,
allowVariableFastqLength_,
cleanupIntermediary_,
ignoreMissingBcls_, ignoreMissingFilters_,
inputLoadersMax_, tempLoadersMax_, tempSaversMax_,
foundMatchesMetadata_.matchTally_,
userTemplateLengthStatistics_, mapqThreshold_, perTileTls_, pfOnly_, baseQualityCutoff_,
keepUnaligned_, clipSemialigned_, clipOverlapping_,
scatterRepeats_, gappedMismatchesMax_, avoidSmithWaterman_,
gapMatchScore_, gapMismatchScore_, gapOpenScore_, gapExtendScore_, minGapExtendScore_, semialignedGapLimit_,
dodgyAlignmentScore_, qScoreBin_, fullBclQScoreTable_, optionalFeatures_ & BamZX);
transition.selectMatches(memoryControl_, matchSelectorStatsXmlPath_, barcodeTemplateLengthStatistics);
}
