public IEnumerable <ISimplePosition> Recompose(List <ISimplePosition> simplePositions, List <int> functionBlockRanges)
{
var positionSet = PositionSet.CreatePositionSet(simplePositions, functionBlockRanges);
var alleleSet = positionSet.AlleleSet;
var alleleIndexBlockToSampleIndex = positionSet.AlleleBlockToSampleHaplotype;
int numSamples = positionSet.NumSamples;
_sequenceProvider.LoadChromosome(alleleSet.Chromosome);
int regionStart = alleleSet.Starts[0];
string lastRefAllele = alleleSet.VariantArrays.Last()[0];
int regionEnd = alleleSet.Starts.Last() + lastRefAllele.Length + 100; // make it long enough
if (regionEnd > _sequenceProvider.Sequence.Length)
{
regionEnd = _sequenceProvider.Sequence.Length;
}
string totalRefSequence = _sequenceProvider.Sequence.Substring(regionStart - 1, regionEnd - regionStart); // VCF positions are 1-based
var recomposedAlleleSet = new RecomposedAlleleSet(positionSet.ChrName, numSamples);
foreach (var(alleleIndexBlock, sampleAlleles) in alleleIndexBlockToSampleIndex)
{
(int start, _, string refAllele, string altAllele, var varPosIndexesInAlleleBlock, List <string> decomposedVids) = GetPositionsAndRefAltAlleles(alleleIndexBlock, alleleSet, totalRefSequence, regionStart, simplePositions);
var variantSite = new VariantSite(start, refAllele);
if (!recomposedAlleleSet.RecomposedAlleles.TryGetValue(variantSite, out var variantInfo))
{
variantInfo = GetVariantInfo(positionSet, alleleIndexBlock);
recomposedAlleleSet.RecomposedAlleles[variantSite] = variantInfo;
}
variantInfo.AddAllele(altAllele, sampleAlleles, decomposedVids);
variantInfo.UpdateSampleFilters(varPosIndexesInAlleleBlock, sampleAlleles);
}
return(recomposedAlleleSet.GetRecomposedPositions(_sequenceProvider.RefNameToChromosome));
}
public IEnumerable <ISimplePosition> Recompose(List <ISimplePosition> recomposablePositions, List <int> functionBlockRanges)
{
var positionSet = PositionSet.CreatePositionSet(recomposablePositions, functionBlockRanges);
var alleleSet = positionSet.AlleleSet;
var alleleIndexBlockToSampleIndex = positionSet.AlleleIndexBlockToSampleIndex;
var numSamples = positionSet.NumSamples;
_sequenceProvider.LoadChromosome(alleleSet.Chromosome);
int regionStart = alleleSet.Starts[0];
string lastRefAllele = alleleSet.VariantArrays.Last()[0];
int regionEnd = alleleSet.Starts.Last() + lastRefAllele.Length + 100; // make it long enough
if (regionEnd > _sequenceProvider.Sequence.Length)
{
regionEnd = _sequenceProvider.Sequence.Length;
}
string totalRefSequence = _sequenceProvider.Sequence.Substring(regionStart - 1, regionEnd - regionStart); // VCF positions are 1-based
var recomposedAlleleSet = new RecomposedAlleleSet(positionSet.ChrName, numSamples);
var decomposedPosVarIndex = new HashSet <(int PosIndex, int VarIndex)>();
foreach (var(alleleIndexBlock, sampleAlleles) in alleleIndexBlockToSampleIndex)
{
var(start, _, refAllele, altAllele) = GetPositionsAndRefAltAlleles(alleleIndexBlock, alleleSet, totalRefSequence, regionStart, decomposedPosVarIndex);
var variantSite = new VariantSite(start, refAllele);
if (!recomposedAlleleSet.RecomposedAlleles.TryGetValue(variantSite, out var variantInfo))
{
variantInfo = GetVariantInfo(positionSet, alleleIndexBlock);
recomposedAlleleSet.RecomposedAlleles[variantSite] = variantInfo;
}
variantInfo.AddAllele(altAllele, sampleAlleles);
}
// Set decomposed tag to positions used for recomposition
foreach (var indexTuple in decomposedPosVarIndex)
{
recomposablePositions[indexTuple.PosIndex].IsDecomposed[indexTuple.VarIndex] = true;
}
return(recomposedAlleleSet.GetRecomposedVcfRecords().Select(x => SimplePosition.GetSimplePosition(x, _sequenceProvider.RefNameToChromosome, true)));
}