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);
}
