public void Execute() { Read read; if (_alignmentSource.SourceIsStitched) { Logger.WriteToLog("Stitched reads detected"); } while ((read = _alignmentSource.GetNextRead()) != null) { // find candidate variants var candidateVariants = _variantFinder.FindCandidates(read, _chrReference.Sequence, _chrReference.Name); // track in state manager _stateManager.AddCandidates(candidateVariants); _stateManager.AddAlleleCounts(read); // call anything possible to call Call(_alignmentSource.LastClearedPosition); } Call(); // call everything left if (_regionMapper != null) { _vcfWriter.WriteRemaining(_regionMapper); // pad any remaining intervals if necessary } Logger.WriteToLog("Totals: {0} alleles called. {1} variants collapsed.", _alleleCaller.TotalNumCalled, _alleleCaller.TotalNumCollapsed); }
public void Execute() { AlignmentSet alignmentSet; while ((alignmentSet = _alignmentSource.GetNextAlignmentSet()) != null) { // find candidate variants var candidateVariants = _variantFinder.FindCandidates(alignmentSet, _chrReference.Sequence, _chrReference.Name); // track in state manager _stateManager.AddCandidates(candidateVariants); _stateManager.AddAlleleCounts(alignmentSet); // call anything possible to call Call(_alignmentSource.LastClearedPosition); } Call(); // call everything left Logger.WriteToLog("Totals: {0} alleles called.", _numCalledAlleles); }