private static List <CalledAllele> ProcessMultiAllelicLocus(List <CalledAllele> orderedVariants,
RecalibrationResults results)
{
RecalibrationResult resultForVariant = GetModelFromType(orderedVariants[0], results);
MixtureModelResult mixtureModelResult = GetModelResult(orderedVariants[0], resultForVariant);
switch (mixtureModelResult.GenotypeCategory)
{
case SimplifiedDiploidGenotype.HomozygousRef:
case SimplifiedDiploidGenotype.HomozygousAlt:
var allele = UpdateGenotypeAndQScore(orderedVariants[0], mixtureModelResult);
return(new List <CalledAllele> {
allele
});
case SimplifiedDiploidGenotype.HeterozygousAltRef:
orderedVariants[0].Genotype = Genotype.HeterozygousAlt1Alt2;
orderedVariants[1].Genotype = Genotype.HeterozygousAlt1Alt2;
orderedVariants = UpdateMultiAllelicQScores(orderedVariants, results);
return(orderedVariants);
default:
throw new ArgumentException("Invalid model results");
}
}
private static CalledAllele UpdateGenotypeAndQScore(CalledAllele allele, MixtureModelResult mixtureModelResult)
{
allele = UpdateGenotype(allele, mixtureModelResult.GenotypeCategory);
allele.GenotypePosteriors = mixtureModelResult.GenotypePosteriors;
allele.GenotypeQscore = mixtureModelResult.QScore;
return(allele);
}
public RecalibratedVariant(int dp, int ad, int category, int qScore, float[] gp)
{
Dp = dp;
Ad = ad;
MixtureModelResult = new MixtureModelResult();
MixtureModelResult.GenotypeCategory = MixtureModelResult.IntToGenotypeCategory(category);
MixtureModelResult.QScore = qScore;
MixtureModelResult.GenotypePosteriors = gp;
}
public void GetMultiAllelicQScores()
{
CalledAllele variant1 = TestHelper.CreateDummyAllele("chr1", 1000, "A", "C", 30, 12);
CalledAllele variant2 = TestHelper.CreateDummyAllele("chr1", 1000, "A", "T", 30, 11);
MixtureModelResult result = AdaptiveGenotyperCalculator.GetMultiAllelicQScores(variant1, variant2,
new List <double[]> {
Means, Means
});
// The 4th GP should always be the minimum because that reflects the 1/2 call
Assert.Equal(4, result.GenotypePosteriors.ToList().IndexOf(result.GenotypePosteriors.Min()));
}
private void TestCalculation(CalledAllele variant, double frequency, double depth, int expectedValue)
{
variant.TotalCoverage = (int)depth;
variant.AlleleSupport = (int)(depth * frequency);
if (variant.Genotype == Genotype.HomozygousRef)
{
variant.AlleleSupport = (int)(depth * (1.0 - frequency));
}
MixtureModelResult result = AdaptiveGenotyperCalculator.GetGenotypeAndQScore(variant, Means, Priors);
Assert.Equal(expectedValue, result.QScore);
}
public void GenotypeCategoryTests()
{
var mm = new MixtureModelResult {
GenotypeCategory = SimplifiedDiploidGenotype.HeterozygousAltRef
};
Assert.Equal(1, mm.GenotypeCategoryAsInt);
mm.GenotypeCategory = SimplifiedDiploidGenotype.HomozygousAlt;
Assert.Equal(2, mm.GenotypeCategoryAsInt);
mm.GenotypeCategoryAsInt = 0;
Assert.Equal(SimplifiedDiploidGenotype.HomozygousRef, mm.GenotypeCategory);
Assert.Throws <ArgumentException>(() => mm.GenotypeCategoryAsInt = 3);
}
