private static void CheckSimpleCombinations(
CalledAllele VarA, CalledAllele VarB, ConsensusBuilder cb,
Genotype ExpectedGT, string ExpectedAlt,
VariantComparisonCase ComparisonCase)
{
var AandB = cb.CombineVariants(VarA, VarB, ComparisonCase);
var BandA = cb.CombineVariants(VarB, VarA, ComparisonCase);
var AandNull = cb.CombineVariants(VarA, null, VariantComparisonCase.CanNotCombine);
var NullAndB = cb.CombineVariants(null, VarB, VariantComparisonCase.CanNotCombine);
int ExpectedAlleleCount = VarA.AlleleSupport + VarB.AlleleSupport;
if (ComparisonCase == VariantComparisonCase.OneReferenceOneAlternate)
{
//for this test, we presume we are calling alternate.
ExpectedAlleleCount = (VarA.Type == AlleleCategory.Snv) ? VarA.AlleleSupport : VarB.AlleleSupport;
}
//check alt-and-nocalls
Assert.Equal(ExpectedGT, AandB.Genotype);
Assert.Equal(VarA.ReferenceAllele, AandB.ReferenceAllele);
Assert.Equal(ExpectedAlt, AandB.AlternateAllele);
Assert.Equal(VarA.TotalCoverage + VarB.TotalCoverage, AandB.TotalCoverage);
Assert.Equal(ExpectedAlleleCount, AandB.AlleleSupport);
Assert.Equal(ExpectedGT, BandA.Genotype);
Assert.Equal(VarA.ReferenceAllele, BandA.ReferenceAllele);
Assert.Equal(ExpectedAlt, BandA.AlternateAllele);
Assert.Equal(VarA.TotalCoverage + VarB.TotalCoverage, BandA.TotalCoverage);
Assert.Equal(ExpectedAlleleCount, BandA.AlleleSupport);
Assert.Equal(ConsensusBuilder.DoDefensiveGenotyping(VarA), AandNull.Genotype);
Assert.Equal(VarA.ReferenceAllele, AandNull.ReferenceAllele);
Assert.Equal(VarA.AlternateAllele, AandNull.AlternateAllele);
Assert.Equal(VarA.TotalCoverage, AandNull.TotalCoverage);
Assert.Equal(VarA.AlleleSupport, AandNull.AlleleSupport);
Assert.Equal(ConsensusBuilder.DoDefensiveGenotyping(VarB), NullAndB.Genotype);
Assert.Equal(VarB.ReferenceAllele, NullAndB.ReferenceAllele);
Assert.Equal(VarB.AlternateAllele, NullAndB.AlternateAllele);
Assert.Equal(VarB.TotalCoverage, NullAndB.TotalCoverage);
Assert.Equal(VarB.AlleleSupport, NullAndB.AlleleSupport);
}
