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 AddLocus(CalledAllele variant)
{
ReferenceName.Add(variant.Chromosome);
ReferencePosition.Add(variant.ReferencePosition);
ChrIndexer.Add(variant.Chromosome + ":" + variant.ReferencePosition.ToString(), Count);
NumIndexer.Add(Count, variant.Chromosome + ":" + variant.ReferencePosition.ToString());
int dp = variant.TotalCoverage;
if (dp < AdaptiveGenotyperCalculator.MaxEffectiveDepth)
{
Dp.Add(dp);
Ad.Add(VariantReader.GetAlternateAlleleSupport(variant));
}
else
{
var(ad, depth) = AdaptiveGenotyperCalculator.DownsampleVariant(
VariantReader.GetAlternateAlleleSupport(variant), dp);
Dp.Add(depth);
Ad.Add(ad);
}
Count++;
}
