private IEnumerable <CalledAllele> GetNextBlockOfOriginalAllelesFromVcfVar()
{
var vcfVar = new VcfVariant();
bool worked = _variantSource.GetNextVariant(vcfVar);
if (!worked)
{
return(new List <CalledAllele>());
}
return(VcfVariantUtilities.Convert(new List <VcfVariant> {
vcfVar
}));
}
public IEnumerable <VcfNeighborhood> GetBatchOfNeighborhoods(int numNbhdsSoFar)
{
_nextBatchOfNeighborhoods.Clear();
_nextBatchOfNeighborhoods.AddRange(_unfinshedNeighborhoods);
_unfinshedNeighborhoods.Clear();
bool keepAddingNbhdsToTheBatch = true;
while (keepAddingNbhdsToTheBatch)
{
keepAddingNbhdsToTheBatch = _vcfVariantSource.GetNextVariant(_tempRawVcfVariant);
//only loose _tempRawVcfVariant if it was null. We are done with the file.
if (!keepAddingNbhdsToTheBatch)
{
break;
}
var allelesUnpackedFromVcfVariant = VcfVariantUtilities.Convert(new List <VcfVariant> {
_tempRawVcfVariant
});
foreach (var currentAllele in allelesUnpackedFromVcfVariant)
{
if (currentAllele.Filters.Contains(FilterType.ForcedReport))
{
continue;
}
var currentVariantSite = new VariantSite(currentAllele);
var refBase = currentVariantSite.VcfReferenceAllele.Substring(0, 1);
//append the next base, unless we have a repeated variant.
if (currentVariantSite.VcfReferencePosition != _lastVariantSite.VcfReferencePosition)
{
_referenceStringBetweenVariants += refBase;
}
//check its not reference or otherwise useless
if (!IsEligibleVariant(currentAllele))
{
continue;
}
//the current variant is close to the last one
if (IsProximal(currentVariantSite, _lastVariantSite, _phasableVariantCriteria.PhasingDistance))
{
keepAddingNbhdsToTheBatch = FitVariantsInNeighborhood(_lastVariantSite, currentVariantSite,
_referenceStringBetweenVariants, numNbhdsSoFar);
_referenceStringBetweenVariants = "";
}
else
{
_referenceStringBetweenVariants = "";
}
_lastVariantSite = currentVariantSite;
}
}
PrepNbhdsForUse(_nextBatchOfNeighborhoods);
return(_nextBatchOfNeighborhoods);
}