public void CallRefs(IVcfNeighborhood completedNbhd)
{
var suckedUpRefCalls = completedNbhd.UsedRefCountsLookup;
Dictionary <int, CalledAllele> possibleRefs = new Dictionary <int, CalledAllele>();
var variantsRecalledByMnvCaller = completedNbhd.GetOriginalVcfVariants();
foreach (var allele in variantsRecalledByMnvCaller)
{
int suckedUpRefCallCount = 0;
if (suckedUpRefCalls.ContainsKey(allele.ReferencePosition))
{
suckedUpRefCallCount = suckedUpRefCalls[allele.ReferencePosition].Counts;
}
var newRef = ReCallAsRef(allele, suckedUpRefCallCount);
if (!possibleRefs.ContainsKey(newRef.ReferencePosition))
{
completedNbhd.NbhdGTcalculator.SetGenotypes(new List <CalledAllele> {
newRef
});
possibleRefs.Add(newRef.ReferencePosition, newRef);
}
}
completedNbhd.CalledRefs = possibleRefs;
}
private static int OrderWithNeighborhood(IVcfNeighborhood nbhdWithMNVs, CalledAllele originalVariant)
{
if (originalVariant.Chromosome != nbhdWithMNVs.ReferenceName)
{
return(1);
}
if (originalVariant.ReferencePosition > nbhdWithMNVs.LastPositionOfInterestInVcf)
{
return(1);
}
if ((originalVariant.ReferencePosition <= nbhdWithMNVs.LastPositionOfInterestInVcf) && (originalVariant.ReferencePosition >= nbhdWithMNVs.FirstPositionOfInterest))
{
return(0);
}
return(-1);
}
public void CallMNVs(IVcfNeighborhood completedNbhd)
{
var foundMNVs = new Dictionary <int, List <CalledAllele> >();
foreach (var mnv in completedNbhd.CandidateVariants)
{
bool isReference = (mnv.Type == Pisces.Domain.Types.AlleleCategory.Reference);
CallCandidate(mnv, isReference);
AddFilters(mnv, isReference);
if (!foundMNVs.ContainsKey(mnv.Coordinate))
{
foundMNVs.Add(mnv.Coordinate, new List <CalledAllele>());
}
foundMNVs[mnv.Coordinate].Add(mnv);
}
completedNbhd.CalledVariants = foundMNVs;
}
public void CallRefs(IVcfNeighborhood completedNbhd)
{
var suckedUpRefCalls = completedNbhd.UsedRefCountsLookup;
Dictionary <int, CalledAllele> possibleRefs = new Dictionary <int, CalledAllele>();
var variantsRecalledByMnvCaller = completedNbhd.GetOriginalVcfVariants();
foreach (var allele in variantsRecalledByMnvCaller)
{
int suckedUpRefCallCount = 0;
if (suckedUpRefCalls.ContainsKey(allele.Coordinate))
{
suckedUpRefCallCount = suckedUpRefCalls[allele.Coordinate];
}
var newRef = ReCallAsRef(allele, suckedUpRefCallCount);
if (!possibleRefs.ContainsKey(newRef.Coordinate))
{
possibleRefs.Add(newRef.Coordinate, newRef);
}
}
completedNbhd.CalledRefs = possibleRefs;
}
public List <CalledAllele> WriteVariantsUptoIncludingNbhd(
IVcfNeighborhood nbhdWithMNVs,
IVcfFileWriter <CalledAllele> writer, List <CalledAllele> leftoverAlleles)
{
var calledMNVs = nbhdWithMNVs.CalledVariants;
var allelesReadyToWrite = new List <CalledAllele>();
var allelesInCurrentVcfNbhd = new List <CalledAllele>();
var allelesToGoupWithNextNbhd = new List <CalledAllele>();
var allelesInProcess = new List <CalledAllele>();
int orderWithRespectToNbhd = -1;
bool quittingNbhd = false;
bool takenCareOfLeftOvers = (leftoverAlleles.Count() == 0);
while (true)
{
if (quittingNbhd)
{
break;
}
if (takenCareOfLeftOvers)
{
allelesInProcess = GetNextBlockOfOriginalAllelesFromVcfVar().ToList();
}
else
{
allelesInProcess = GetNextSetOfAllelesToProcess(leftoverAlleles, nbhdWithMNVs.ReferenceName, writer);
takenCareOfLeftOvers = true;
}
if (allelesInProcess.Count() == 0)
{
break;
}
foreach (var originalAllele in allelesInProcess)
{
if (quittingNbhd)
{
allelesReadyToWrite.Add(originalAllele);
continue;
}
orderWithRespectToNbhd = OrderWithNeighborhood(nbhdWithMNVs, originalAllele);
switch (orderWithRespectToNbhd)
{
case (-1): //if we are before the nbhd, write straight to vcf
allelesReadyToWrite.Add(originalAllele);
break;
case (0): //in the nbhd
allelesInCurrentVcfNbhd.Add(originalAllele);
break;
default:
//if we are either ahead of our nbhd, or gone into the wrong chr)
//Close out the nbhd and finish up.
var mergedVariants = GetMergedListOfVariants(nbhdWithMNVs, allelesInCurrentVcfNbhd);
allelesReadyToWrite.AddRange(mergedVariants);
allelesToGoupWithNextNbhd.Add(originalAllele);
quittingNbhd = true;
break;
}
}
}
//close out any remaining nbhd
if (orderWithRespectToNbhd == 0)
{
var mergedVariants = GetMergedListOfVariants(nbhdWithMNVs, allelesInCurrentVcfNbhd);
allelesReadyToWrite.AddRange(mergedVariants);
}
var alleleAfterAdjustment = VcfMergerUtils.AdjustForcedAllele(allelesReadyToWrite);
writer.Write(alleleAfterAdjustment);
return(allelesToGoupWithNextNbhd);
}
public static List <CalledAllele> GetMergedListOfVariants(IVcfNeighborhood completedNbhd, List <CalledAllele> originalVariantsInsideRange)
{
var mergedVariantList = new List <CalledAllele>();
Dictionary <int, List <CalledAllele> > foundMNVS = completedNbhd.CalledVariants;
//track which variants got used for MNV phasing.
var indexesOfVariantsRecalledByMnvCaller = completedNbhd.GetOriginalVcfVariants();
//decide which of the original variants we keep, and which get replaced.
for (int i = 0; i < originalVariantsInsideRange.Count; i++)
{
var originalCall = originalVariantsInsideRange[i];
var currentPosition = originalCall.ReferencePosition;
bool variantWasAlreadyUsed = CheckIfUsed(indexesOfVariantsRecalledByMnvCaller, originalCall);
if (foundMNVS.ContainsKey(currentPosition))
{
//add all the MNVs
mergedVariantList.AddRange(foundMNVS[currentPosition]);
foundMNVS[currentPosition] = new List <CalledAllele>();//empty out the list, but leave the fact that there were MNVs here.
//add back any original variants,
//so long as they were not used by the caller, and not reference
if (!(variantWasAlreadyUsed) &&
(originalCall.Type != Pisces.Domain.Types.AlleleCategory.Reference))
{
mergedVariantList.Add(originalCall);
}
continue;
}
//Else, we did not find any MNVs here.
//Then this position should be either the original call from the vcf,
//or a new reference call converted from a variant that got used by the MNV caller.
if (variantWasAlreadyUsed)
{
var newRef = completedNbhd.CalledRefs[originalCall.ReferencePosition];
//sometimes several variants were used, all at the same position. we dont need to add new references for all of them.
if ((mergedVariantList.Count == 0) || (mergedVariantList.Last().ReferencePosition != currentPosition))
{
mergedVariantList.Add(newRef);
}
}
else //wasnt used for MNV calling
{
mergedVariantList.Add(originalVariantsInsideRange[i]);
}
}
//incase we called any MNVs past the edge of the input VCF.
foreach (var mnvsLeft in foundMNVS)
{
mergedVariantList.AddRange(mnvsLeft.Value);
}
var comparer = new AlleleCompareByLoci();
mergedVariantList.Sort(comparer);
return(mergedVariantList);
}
