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);
}
private IEnumerable <BaseCalledAllele> CallForPositions(IEnumerable <CandidateAllele> candidates, IStateManager source, int?maxPosition)
{
var calledAlleles = new List <BaseCalledAllele>();
var failedMnvs = new List <BaseCalledAllele>();
var callableAlleles = new List <BaseCalledAllele>();
foreach (var candidate in candidates)
{
var variant = Map(candidate);
if (variant.Type == AlleleCategory.Mnv)
{
ProcessVariant(source, variant);
if (IsCallable(variant))
{
callableAlleles.Add(variant);
}
else
{
failedMnvs.Add(variant);
}
}
else
{
callableAlleles.Add(variant);
}
}
var leftoversInNextBlock = MnvReallocator.ReallocateFailedMnvs(failedMnvs, callableAlleles, maxPosition);
source.AddCandidates(leftoversInNextBlock.Select(Map));
source.AddGappedMnvRefCount(GetRefSupportFromGappedMnvs(callableAlleles));
// need to re-process variants since they may have additional support
foreach (var baseCalledAllele in callableAlleles)
{
ProcessVariant(source, baseCalledAllele);
if (IsCallable(baseCalledAllele) && ShouldReport(baseCalledAllele))
{
calledAlleles.Add(baseCalledAllele);
}
}
// prune reference call if variants were found
var allPositions = calledAlleles.Select(c => c.Coordinate).Distinct().ToList();
foreach (var position in allPositions)
{
var allelesAtPosition = calledAlleles.Where(x => x.Coordinate == position);
var referenceCall = allelesAtPosition.FirstOrDefault(v => v is CalledReference);
if (referenceCall != null && allelesAtPosition.Any(v => v is CalledVariant))
{
calledAlleles.Remove(referenceCall);
}
}
return(calledAlleles);
}
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);
}
