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);
}