public List <CalledAllele> SetGenotypes(IEnumerable <CalledAllele> alleles)
{
var allelesToPrune = new List <CalledAllele>();
var singleGTForLoci = CalculateDiploidGenotype(alleles, MinDepthToGenotype,
_diploidSnvThresholdingParameters, _diploidIndelThresholdingParameters, out allelesToPrune);
int phaseSetIndex = 1; //reserve -1 for unset, and 0 for reference, and 1 and 2 for alts
foreach (var allele in alleles)
{
allele.Genotype = singleGTForLoci;
allele.GenotypeQscore = DiploidGenotypeQualityCalculator.Compute(allele, MinGQScore, MaxGQScore);
if (allele.IsRefType)
{
allele.PhaseSetIndex = 0;
}
else
{
allele.PhaseSetIndex = phaseSetIndex;
phaseSetIndex++;
}
}
return(allelesToPrune);
}
public List <CalledAllele> SetGenotypes(IEnumerable <CalledAllele> alleles)
{
var allelesToPrune = new List <CalledAllele>();
var singleGTForLoci = CalculateDiploidGenotype(alleles, MinDepthToGenotype, _diploidThresholdingParameters, out allelesToPrune);
foreach (var allele in alleles)
{
allele.Genotype = singleGTForLoci;
allele.GenotypeQscore = DiploidGenotypeQualityCalculator.Compute(allele, MinGQScore, MaxGQScore);
}
return(allelesToPrune);
}
