private List <CalledAllele> GetNextSetOfAllelesToProcess(List <CalledAllele> leftoverAlleles,
string thisChr, IVcfFileWriter <CalledAllele> writer)
{
var originalAlleles = new List <CalledAllele>();
//if alleles are left over from the last nbhd, do them first.
if (leftoverAlleles.Count > 0)
{
if (leftoverAlleles[0].Chromosome != thisChr)
{
//we have already gone into the wrong chr. This cant possibly be in our nbhd.
//write straight to vcf.
writer.Write(leftoverAlleles);
return(GetNextSetOfAllelesToProcess(new List <CalledAllele>(), thisChr, writer));
}
else //they might be in our nbhd, so send them through the process
{
originalAlleles.AddRange(leftoverAlleles);
}
leftoverAlleles = new List <CalledAllele>();
return(originalAlleles);
}
else
{
originalAlleles = GetNextBlockOfOriginalAllelesFromVcfVar().ToList();
return(originalAlleles);
}
}
public List <Tuple <CalledAllele, string> > WriteVariantsUptoChr(
IVcfFileWriter <CalledAllele> writer, List <Tuple <CalledAllele, string> > alleleTuplesLeftoverList, string stopChr)
{
WriteDistinctVcfLines(writer, alleleTuplesLeftoverList);
while (true)
{
var alleleTuplesInProcessList = GetNextBlockOfOriginalAlleleTuplesFromVcfVar();
if (alleleTuplesInProcessList.Count == 0)
{
return(new List <Tuple <CalledAllele, string> >());
}
if (alleleTuplesInProcessList[0].Item1.Chromosome != stopChr)
{
//still not in the right nbhd
WriteDistinctVcfLines(writer, alleleTuplesInProcessList);
}
else
{
return(alleleTuplesInProcessList);
}
}
}
private List <Tuple <CalledAllele, string> > GetNextSetOfAlleleTuplesToProcess(
IVcfFileWriter <CalledAllele> writer, List <Tuple <CalledAllele, string> > alleleTuplesLeftoverList, string thisChr)
{
var alleleTuplesOriginalList = new List <Tuple <CalledAllele, string> >();
//if alleles are left over from the last nbhd, do them first.
if (alleleTuplesLeftoverList.Count > 0)
{
if (alleleTuplesLeftoverList[0].Item1.Chromosome != thisChr)
{
//we have already gone into the wrong chr. This cant possibly be in our nbhd.
//write straight to vcf.
WriteDistinctVcfLines(writer, alleleTuplesLeftoverList);
return(GetNextSetOfAlleleTuplesToProcess(writer, new List <Tuple <CalledAllele, string> >(), thisChr));
}
else //they might be in our nbhd, so send them through the process
{
alleleTuplesOriginalList.AddRange(alleleTuplesLeftoverList);
}
return(alleleTuplesOriginalList);
}
else
{
alleleTuplesOriginalList = GetNextBlockOfOriginalAlleleTuplesFromVcfVar();
return(alleleTuplesOriginalList);
}
}
public void WriteRemainingVariants(IVcfFileWriter <CalledAllele> writer, List <CalledAllele> allelesPastNbhd)
{
writer.Write(allelesPastNbhd);
while (true)
{
var alleles = GetNextBlockOfOriginalAllelesFromVcfVar();
if (alleles.Count() == 0)
{
return;
}
writer.Write(alleles);
}
}
public void WriteRemainingVariants(IVcfFileWriter <CalledAllele> writer, List <Tuple <CalledAllele, string> > alleleTuplesPastNbhd)
{
WriteDistinctVcfLines(writer, alleleTuplesPastNbhd);
while (true)
{
var alleleTuplesOriginalFromVcfVarList = GetNextBlockOfOriginalAlleleTuplesFromVcfVar();
if (!alleleTuplesOriginalFromVcfVarList.Any())
{
return;
}
WriteDistinctVcfLines(writer, alleleTuplesOriginalFromVcfVarList);
}
}
private void WriteDistinctVcfLines(IVcfFileWriter <CalledAllele> writer, List <Tuple <CalledAllele, string> > alleleTuples)
{
var distinctVcfLines = new HashSet <string>();
foreach (var alleleTuple in alleleTuples)
{
if (alleleTuple.Item2 == "")
{
writer.Write(new List <CalledAllele> {
alleleTuple.Item1
});
}
else
{
if (!distinctVcfLines.Contains(alleleTuple.Item2))
{
distinctVcfLines.Add(alleleTuple.Item2);
writer.Write(alleleTuple.Item2);
}
}
}
}
public List <CalledAllele> WriteVariantsUptoChr(IVcfFileWriter <CalledAllele> writer, List <CalledAllele> leftoverAlleles, string stopChr)
{
writer.Write(leftoverAlleles);
while (true)
{
var allelesInProcess = GetNextBlockOfOriginalAllelesFromVcfVar().ToList();
if (allelesInProcess == null || allelesInProcess.Count == 0)
{
return(new List <CalledAllele>());
}
if (allelesInProcess[0].Chromosome != stopChr)
{
//still not in the right nbhd
writer.Write(allelesInProcess);
}
else
{
return(allelesInProcess);
}
}
}
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 List <Tuple <CalledAllele, string> > WriteVariantsUptoIncludingNbhd(
IVcfFileWriter <CalledAllele> writer, List <Tuple <CalledAllele, string> > alleleTuplesLeftoverList, ICallableNeighborhood nbhdWithMNVs)
{
var alleleTuplesInProcessList = new List <Tuple <CalledAllele, string> >();
var alleleTuplesReadyToWriteList = new List <Tuple <CalledAllele, string> >();
var alleleTuplesInCurrentVcfNbhdList = new List <Tuple <CalledAllele, string> >();
var alleleTuplesToGroupWithNextNbhdList = new List <Tuple <CalledAllele, string> >();
int orderWithRespectToNbhd = -1;
bool quittingNbhd = false;
bool takenCareOfLeftOvers = !alleleTuplesLeftoverList.Any();
while (true)
{
if (quittingNbhd)
{
break;
}
if (takenCareOfLeftOvers)
{
alleleTuplesInProcessList = GetNextBlockOfOriginalAlleleTuplesFromVcfVar();
}
else
{
alleleTuplesInProcessList = GetNextSetOfAlleleTuplesToProcess(
writer, alleleTuplesLeftoverList, nbhdWithMNVs.ReferenceName);
takenCareOfLeftOvers = true;
}
if (!alleleTuplesInProcessList.Any())
{
break;
}
foreach (var originalAlleleTuple in alleleTuplesInProcessList)
{
if (quittingNbhd)
{
alleleTuplesToGroupWithNextNbhdList.Add(originalAlleleTuple);
continue;
}
orderWithRespectToNbhd = OrderWithNeighborhood(nbhdWithMNVs, originalAlleleTuple.Item1);
switch (orderWithRespectToNbhd)
{
case (-1): //if we are before the nbhd, write straight to vcf
alleleTuplesReadyToWriteList.Add(originalAlleleTuple);
break;
case (0): //in the nbhd
alleleTuplesInCurrentVcfNbhdList.Add(originalAlleleTuple);
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, alleleTuplesInCurrentVcfNbhdList);
alleleTuplesReadyToWriteList.AddRange(mergedVariants);
alleleTuplesToGroupWithNextNbhdList.Add(originalAlleleTuple);
quittingNbhd = true;
break;
}
}
}
//close out any remaining nbhd
if (orderWithRespectToNbhd == 0)
{
var mergedVariants = GetMergedListOfVariants(nbhdWithMNVs, alleleTuplesInCurrentVcfNbhdList);
alleleTuplesReadyToWriteList.AddRange(mergedVariants);
}
var alleleTuplesAfterAdjustmentList = VcfMergerUtils.AdjustForcedAllele(alleleTuplesReadyToWriteList);
WriteDistinctVcfLines(writer, alleleTuplesAfterAdjustmentList);
return(alleleTuplesToGroupWithNextNbhdList);
}
