private static CalledAllele UpdateGenotype(CalledAllele allele, SimplifiedDiploidGenotype category)
{
if (category == SimplifiedDiploidGenotype.HomozygousRef)
{
allele.Genotype = Genotype.HomozygousRef;
}
else if (category == SimplifiedDiploidGenotype.HeterozygousAltRef)
{
if (allele.IsRefType)
{
allele.Genotype = Genotype.HomozygousRef;
}
else if (VariantReader.GetVariantType(allele) == VariantType.Snv)
{
allele.Genotype = Genotype.HeterozygousAltRef;
}
else if (VariantReader.GetVariantType(allele) == VariantType.Indel)
{
allele.Genotype = Genotype.HeterozygousAltRef;
}
}
else if (category == SimplifiedDiploidGenotype.HomozygousAlt)
{
if (allele.IsRefType)
{
allele.Genotype = Genotype.HomozygousRef;
}
else if (VariantReader.GetVariantType(allele) == VariantType.Snv)
{
allele.Genotype = Genotype.HomozygousAlt;
}
else if (VariantReader.GetVariantType(allele) == VariantType.Indel)
{
allele.Genotype = Genotype.HomozygousAlt;
}
}
return(allele);
}
public static int GenotypeCategoryToInt(SimplifiedDiploidGenotype genotype)
{
return((int)genotype);
}
public static Genotype ConvertSimpleGenotypeToComplexGenotype(IEnumerable <CalledAllele> alleles,
List <CalledAllele> orderedVariants, double referenceFrequency, bool refExists, bool depthIssue, bool refCall,
float minVarFrequency, float sumVFforMultiAllelicSite, SimplifiedDiploidGenotype preliminaryGenotype)
{
if (depthIssue)
{
if (refCall)
{
return(Genotype.RefLikeNoCall);
}
else
{
return(Genotype.AltLikeNoCall);
}
}
else
{
switch (preliminaryGenotype)
{
case SimplifiedDiploidGenotype.HomozygousRef: //obvious reference call
if (!refExists)
{
return(Genotype.RefLikeNoCall); //there might have been an upstream deletion
}
else
{
var firstAllele = alleles.First();
//we see too much of something else (unknown) for a clean ref call.
if ((firstAllele.Type == AlleleCategory.Reference) && ((1 - firstAllele.Frequency) > minVarFrequency))
{
return(Genotype.RefAndNoCall);
}
else
{
return(Genotype.HomozygousRef); // being explicit for readability
}
}
case SimplifiedDiploidGenotype.HeterozygousAltRef: //else, types of alt calls...
if (orderedVariants.Count == 1)
{
if (refExists)
{
return(Genotype.HeterozygousAltRef);
}
else
{
return(Genotype.AltAndNoCall);
}
}
else
{
//is this 0/1, 1/2, or 0/1/2 or 1/2/3/...
bool diploidModelFail = CheckForTriAllelicIssue(refExists, referenceFrequency, orderedVariants, sumVFforMultiAllelicSite);
if (diploidModelFail)
{
SetMultiAllelicFilter(alleles);
if (refExists)
{
return(Genotype.AltLikeNoCall);
}
else
{
return(Genotype.Alt12LikeNoCall);
}
}
}
if (refExists)
{
return(Genotype.HeterozygousAltRef);
}
else
{
return(Genotype.HeterozygousAlt1Alt2);
}
default:
case SimplifiedDiploidGenotype.HomozygousAlt:
return(Genotype.HomozygousAlt);
}
}
}
