private static RecalibrationResult GetModelFromType(CalledAllele allele, RecalibrationResults results)
{
var variantType = VariantReader.GetVariantType(allele);
RecalibrationResult resultForVariant;
if (variantType == VariantType.NoVariant || variantType == VariantType.Snv)
{
resultForVariant = results.SnvResults;
}
else if (variantType == VariantType.Indel)
{
resultForVariant = results.IndelResults;
}
else
{
throw new ArgumentException("Variant type unrecognized.");
}
return(resultForVariant);
}
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);
}
