public override void Write(IEnumerable <CalledAllele> calledAlleles, IRegionMapper mapper = null)
{
//this is a cheap hack, to be removed as soon as I merge another change.
var comparer = new AlleleComparer();
var sortedVariants = calledAlleles.OrderBy(a => a, comparer).ThenBy(a => a.Reference).ThenBy(a => a.Alternate);
base.Write(sortedVariants);
}
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.Coordinate;
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.Coordinate];
//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().Coordinate != 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 AlleleComparer();
mergedVariantList.Sort(comparer);
return(mergedVariantList);
}
