private void ExecuteDiploidGenotypeTest(
Genotype expectedGenotype, int expectedNumAllelesToPrune,
List <float> refFrequencies, List <float> altFrequencies, List <FilterType> filters, int coverage)
{
var alleles = new List <CalledAllele>();
double refFreq = 0;
foreach (float rf in refFrequencies)
{
var variant = TestHelper.CreatePassingVariant(true);
variant.AlleleSupport = (int)(rf * coverage);
variant.TotalCoverage = (int)coverage;
variant.ReferenceSupport = variant.AlleleSupport;
alleles.Add(variant);
refFreq = rf;
}
if (refFreq == 0)
{
refFreq = (1.0 - altFrequencies.Sum());
}
foreach (float vf in altFrequencies)
{
var variant = TestHelper.CreatePassingVariant(false);
variant.AlleleSupport = (int)(vf * coverage);
variant.TotalCoverage = (int)coverage;
variant.ReferenceSupport = (int)(refFreq * coverage);
alleles.Add(variant);
}
//set filters for at least one allele. they should affect all results.
alleles[0].Filters = filters;
DiploidGenotypeCalculator GTC = GetOriginalSettings();
GTC.MinDepthToGenotype = 100;
var allelesToPrune = GTC.SetGenotypes(alleles);
Assert.Equal(expectedNumAllelesToPrune, allelesToPrune.Count);
foreach (var allele in alleles)
{
Assert.Equal(expectedGenotype, allele.Genotype);
}
}
private void ExecuteDiploidIndelGenotypeTest()
{
//test cases:
// (1) SNP + indel + indel
// (2) indel + SNP + SNP
// (3) 3 indels (OK)
// (4) 3 indels - ploidy violation
Genotype expectedGenotype = Genotype.HeterozygousAlt1Alt2;
int expectedNumAllelesToPrune = 1;
// (1) SNP + indel + indel
// should be 1/2 with the lowest freq thrown out
List <float> refFrequencies = new List <float>()
{
0.40F, 0.60F, 0.90F
};
List <float> altFrequencies = new List <float>()
{
0.60F, 0.40F, 0.10F
};
List <string> refAllele = new List <string>()
{
"A", "A", "ACT"
};
List <string> altAllele = new List <string>()
{
"C", "AGGG", "A"
};
double coverage = 1000;
var alleles = new List <CalledAllele>();
for (int i = 0; i < 3; i++)
{
var variant = TestHelper.CreatePassingVariant(false);
variant.AlleleSupport = (int)(altFrequencies[i] * coverage);
variant.TotalCoverage = (int)coverage;
variant.ReferenceSupport = (int)(refFrequencies[i] * coverage);
variant.AlternateAllele = altAllele[i];
variant.ReferenceAllele = refAllele[i];
alleles.Add(variant);
}
alleles[1].Type = AlleleCategory.Insertion;
alleles[2].Type = AlleleCategory.Deletion;
var GTC = new DiploidGenotypeCalculator();
GTC.MinDepthToGenotype = 100;
var allelesToPrune = GTC.SetGenotypes(alleles);
Assert.Equal(expectedNumAllelesToPrune, allelesToPrune.Count);
foreach (var allele in alleles)
{
Assert.Equal(expectedGenotype, allele.Genotype);
Assert.Equal(0, allele.Filters.Count());
}
Assert.Equal(allelesToPrune[0].ReferenceAllele, "ACT");
Assert.Equal(allelesToPrune[0].AlternateAllele, "A");
Assert.Equal(allelesToPrune[0].Frequency, 0.10F);
// (2) indel + SNP + SNP
// should be 1/2 with the lowest freq thrown out
refFrequencies = new List <float>()
{
0.40F, 0.20F, 0.20F
};
altFrequencies = new List <float>()
{
0.60F, 0.10F, 0.40F
};
refAllele = new List <string>()
{
"A", "A", "A"
};
altAllele = new List <string>()
{
"ACCAT", "G", "C"
};
alleles = new List <CalledAllele>();
for (int i = 0; i < 3; i++)
{
var variant = TestHelper.CreatePassingVariant(false);
variant.AlleleSupport = (int)(altFrequencies[i] * coverage);
variant.TotalCoverage = (int)coverage;
variant.ReferenceSupport = (int)(refFrequencies[i] * coverage);
variant.AlternateAllele = altAllele[i];
variant.ReferenceAllele = refAllele[i];
alleles.Add(variant);
}
alleles[0].Type = AlleleCategory.Insertion;
GTC = new DiploidGenotypeCalculator();
GTC.MinDepthToGenotype = 100;
allelesToPrune = GTC.SetGenotypes(alleles);
Assert.Equal(expectedNumAllelesToPrune, allelesToPrune.Count);
foreach (var allele in alleles)
{
Assert.Equal(expectedGenotype, allele.Genotype);
Assert.Equal(0, allele.Filters.Count());
}
Assert.Equal(allelesToPrune[0].ReferenceAllele, "A");
Assert.Equal(allelesToPrune[0].AlternateAllele, "G");
Assert.Equal(allelesToPrune[0].Frequency, 0.10F);
// (3) 3 indels (OK)
// should be 1/2 with the lowest freq thrown out
refFrequencies = new List <float>()
{
0.40F, 0.90F, 0.60F
};
altFrequencies = new List <float>()
{
0.60F, 0.10F, 0.40F
};
refAllele = new List <string>()
{
"A", "ACT", "A"
};
altAllele = new List <string>()
{
"ACCAT", "A", "CC"
};
alleles = new List <CalledAllele>();
for (int i = 0; i < 3; i++)
{
var variant = TestHelper.CreatePassingVariant(false);
variant.AlleleSupport = (int)(altFrequencies[i] * coverage);
variant.TotalCoverage = (int)coverage;
variant.ReferenceSupport = (int)(refFrequencies[i] * coverage);
variant.AlternateAllele = altAllele[i];
variant.ReferenceAllele = refAllele[i];
alleles.Add(variant);
}
alleles[0].Type = AlleleCategory.Insertion;
alleles[1].Type = AlleleCategory.Deletion;
alleles[2].Type = AlleleCategory.Insertion;
GTC = new DiploidGenotypeCalculator();
GTC.MinDepthToGenotype = 100;
allelesToPrune = GTC.SetGenotypes(alleles);
Assert.Equal(expectedNumAllelesToPrune, allelesToPrune.Count);
foreach (var allele in alleles)
{
Assert.Equal(expectedGenotype, allele.Genotype);
Assert.Equal(0, allele.Filters.Count());
}
Assert.Equal(allelesToPrune[0].ReferenceAllele, "ACT");
Assert.Equal(allelesToPrune[0].AlternateAllele, "A");
Assert.Equal(allelesToPrune[0].Frequency, 0.10F);
// (4) 3 indels - ploidy violation
// should be ./. with the lowest freq thrown out
refFrequencies = new List <float>()
{
0.60F, 0.60F, 0.60F
};
altFrequencies = new List <float>()
{
0.31F, 0.30F, 0.31F
};
refAllele = new List <string>()
{
"A", "ACT", "A"
};
altAllele = new List <string>()
{
"ACCAT", "A", "AC"
};
expectedGenotype = Genotype.Alt12LikeNoCall;
alleles = new List <CalledAllele>();
for (int i = 0; i < 3; i++)
{
var variant = TestHelper.CreatePassingVariant(false);
variant.AlleleSupport = (int)(altFrequencies[i] * coverage);
variant.TotalCoverage = (int)coverage;
variant.ReferenceSupport = (int)(refFrequencies[i] * coverage);
variant.AlternateAllele = altAllele[i];
variant.ReferenceAllele = refAllele[i];
alleles.Add(variant);
}
alleles[0].Type = AlleleCategory.Insertion;
alleles[1].Type = AlleleCategory.Deletion;
alleles[2].Type = AlleleCategory.Insertion;
GTC = new DiploidGenotypeCalculator();
GTC.MinDepthToGenotype = 100;
allelesToPrune = GTC.SetGenotypes(alleles);
Assert.Equal(expectedNumAllelesToPrune, allelesToPrune.Count);
foreach (var allele in alleles)
{
Assert.Equal(expectedGenotype, allele.Genotype);
Assert.Equal(FilterType.MultiAllelicSite, allele.Filters[0]);
}
Assert.Equal(allelesToPrune[0].ReferenceAllele, "ACT");
Assert.Equal(allelesToPrune[0].AlternateAllele, "A");
Assert.Equal(allelesToPrune[0].Frequency, 0.30F);
}