private void ExecuteRepeatTest(string variantBases, string repeatUnit, int repeatsInReference, int repeatThreshold, bool shouldBeFlagged)
{
var offset = 5 * repeatUnit.Length * repeatsInReference;
offset = 10;
// Test with insertion
var variant = CreateRepeatVariant(variantBases);
variant.Coordinate = offset + repeatUnit.Length;
var chrReference = new ChrReference
{
Sequence = CreateRepeat(repeatUnit, repeatsInReference, variant.Coordinate)
};
AlleleProcessor.Process(variant, 0.01f, 0, 0,
true, 0, 0, repeatThreshold, null, chrReference);
Assert.Equal(shouldBeFlagged, variant.Filters.Contains(FilterType.IndelRepeatLength));
// Test with deletion
variant = CreateRepeatVariant(variantBases, true);
variant.Coordinate = offset + repeatUnit.Length;
AlleleProcessor.Process(variant, 0.01f, 0, 0,
true, 0, 0, repeatThreshold, null, chrReference);
Assert.Equal(shouldBeFlagged, variant.Filters.Contains(FilterType.IndelRepeatLength));
}
private void ExecuteFilteringTest(int totalCoverage, int qscore, bool strandBias,
int?lowDepthFilter, int minQscore, bool singleStrandVariant, float?variantFreq,
float?lowGQ, int?indelRepeat, List <FilterType> expectedFilters, bool isRefAllele = false)
{
var variant = TestHelper.CreatePassingVariant(isRefAllele);
variant.TotalCoverage = totalCoverage;
variant.VariantQscore = qscore;
variant.StrandBiasResults.BiasAcceptable = !strandBias;
variant.StrandBiasResults.VarPresentOnBothStrands = !singleStrandVariant;
var chrRef = new ChrReference();
if (indelRepeat > 0)
{
variant.AlternateAllele = "AAAAAA";
chrRef.Sequence = "AAAAAAAA";
if (!isRefAllele)
{
variant.Type = AlleleCategory.Insertion;
}
}
AlleleProcessor.Process(variant, 0.01f, lowDepthFilter, minQscore,
true, variantFreq, lowGQ, indelRepeat, null, 0.6f, chrRef);
Assert.Equal(variant.Filters.Count, expectedFilters.Count);
foreach (var filter in variant.Filters)
{
Assert.True(expectedFilters.Contains(filter));
}
}
public void HappyPath()
{
var variant = TestHelper.CreatePassingVariant(false);
variant.ReferenceSupport = 10;
AlleleProcessor.Process(variant, 0.01f, 100, 20, false, 0f, 10f, 0, null, 0.6f, new ChrReference());
Assert.False(variant.Filters.Any());
Assert.Equal(0.02f, variant.FractionNoCalls);
Assert.Equal(Genotype.HeterozygousAltRef, variant.Genotype);
}
private void ExecuteNoCallTest(int totalCoverage, int numNoCalls, float expectedFraction)
{
var variant = CreatePassingVariant(false);
variant.NumNoCalls = numNoCalls;
variant.TotalCoverage = totalCoverage;
AlleleProcessor.Process(variant, GenotypeModel.Symmetrical, 0.01f, 100, 20, false);
Assert.Equal(expectedFraction, variant.FractionNoCalls);
}
private void ExecuteNoCallTest(int totalCoverage, int numNoCalls, float expectedFraction)
{
var variant = TestHelper.CreatePassingVariant(false);
variant.NumNoCalls = numNoCalls;
variant.TotalCoverage = totalCoverage;
AlleleProcessor.Process(variant, 0.01f, 100, 20, false, 10f, 10f, 8, null, 0.6f, new ChrReference());
Assert.Equal(expectedFraction, variant.FractionNoCalls);
}
public void HappyPath()
{
var variant = CreatePassingVariant(false);
((CalledVariant)variant).ReferenceSupport = 10;
AlleleProcessor.Process(variant, GenotypeModel.Symmetrical, 0.01f, 100, 20, false);
Assert.False(variant.Filters.Any());
Assert.Equal(0.02f, variant.FractionNoCalls);
Assert.Equal(Genotype.HeterozygousAlt, variant.Genotype);
}
private void TestRepeats(string variantBases, int repeatThreshold, bool shouldBeFlagged, int referencePosition,
ChrReference chrReferenceLong, bool isDeletion, int lengthToEnd)
{
var variant = CreateRepeatVariant(variantBases, isDeletion);
variant.ReferencePosition = referencePosition;
AlleleProcessor.Process(variant, 0.01f, 0, 0,
true, 0, 0, repeatThreshold, null, 0.6f, chrReferenceLong);
Assert.Equal(shouldBeFlagged, variant.Filters.Contains(FilterType.IndelRepeatLength));
}
private void ExecuteGenotypeTest(int totalCoverage, float refFrequency, bool isReference, GenotypeModel model, Genotype expectedGenotype)
{
var variant = CreatePassingVariant(isReference);
variant.TotalCoverage = totalCoverage;
if (!isReference)
{
var refSupport = (int)(refFrequency * totalCoverage);
variant.AlleleSupport = totalCoverage - refSupport;
((CalledVariant)variant).ReferenceSupport = refSupport;
}
AlleleProcessor.Process(variant, model, 0.01f, 100, 20, false);
Assert.Equal(expectedGenotype, variant.Genotype);
}
private void ExecuteFilteringTest(int totalCoverage, int qscore, bool strandBias, int minCoverage, int minQscore, bool singleStrandVariant,
List <FilterType> expectedFilters)
{
var variant = CreatePassingVariant(false);
variant.TotalCoverage = totalCoverage;
variant.Qscore = qscore;
variant.StrandBiasResults.BiasAcceptable = !strandBias;
variant.StrandBiasResults.VarPresentOnBothStrands = !singleStrandVariant;
AlleleProcessor.Process(variant, GenotypeModel.Symmetrical, 0.01f, minCoverage, minQscore, true);
Assert.Equal(variant.Filters.Count, expectedFilters.Count);
foreach (var filter in variant.Filters)
{
Assert.True(expectedFilters.Contains(filter));
}
}
private void ExecuteRMxNTest(string variantBases, string referenceSequence, int expectedRepeatLength, AlleleCategory category, int maxRepeatUnitLength)
{
var alleleCoordinate = referenceSequence.IndexOf('*');
var cleanReferenceSequence = referenceSequence.Replace("*", "");
var refAllele = "";
var altAllele = "";
if (category == AlleleCategory.Insertion)
{
refAllele = cleanReferenceSequence.Substring(alleleCoordinate - 1, 1);
altAllele = refAllele + variantBases;
}
else if (category == AlleleCategory.Deletion)
{
altAllele = cleanReferenceSequence.Substring(alleleCoordinate - 1, 1);
refAllele = altAllele + variantBases;
}
else
{
refAllele = cleanReferenceSequence.Substring(alleleCoordinate - 1, variantBases.Length);
altAllele = variantBases;
}
var allele = new CalledAllele(category)
{
ReferenceAllele = refAllele,
AlternateAllele = altAllele,
ReferencePosition = alleleCoordinate
};
RMxNFilterSettings rmxnFilterSettings = new RMxNFilterSettings();
rmxnFilterSettings.RMxNFilterFrequencyLimit = 1.1f;
rmxnFilterSettings.RMxNFilterMaxLengthRepeat = maxRepeatUnitLength;
rmxnFilterSettings.RMxNFilterMinRepetitions = expectedRepeatLength;
// If expected repeats == N, flag
AlleleProcessor.Process(allele, 0.01f, 0, 0,
true, 0, 0, null, rmxnFilterSettings, 0.6f, new ChrReference()
{
Sequence = cleanReferenceSequence
});
Assert.True(allele.Filters.Contains(FilterType.RMxN));
// If expected repeats > N, flag
rmxnFilterSettings.RMxNFilterMinRepetitions = expectedRepeatLength - 1;
AlleleProcessor.Process(allele, 0.01f, 0, 0,
true, 0, 0, null, rmxnFilterSettings, 0.6f, new ChrReference()
{
Sequence = cleanReferenceSequence
});
Assert.True(allele.Filters.Contains(FilterType.RMxN));
// If expected repeats < N, flag
rmxnFilterSettings.RMxNFilterMinRepetitions = expectedRepeatLength + 1;
AlleleProcessor.Process(allele, 0.01f, 0, 0,
true, 0, 0, null, rmxnFilterSettings, 0.6f, new ChrReference()
{
Sequence = cleanReferenceSequence
});
Assert.False(allele.Filters.Contains(FilterType.RMxN));
// RMxN isn't valid on reference calls
rmxnFilterSettings.RMxNFilterMinRepetitions = expectedRepeatLength + 1;
AlleleProcessor.Process(new CalledAllele()
{
}, 0.01f, 0, 0,
true, 0, 0, null, rmxnFilterSettings, 0.6f, new ChrReference()
{
Sequence = cleanReferenceSequence
});
Assert.False(allele.Filters.Contains(FilterType.RMxN));
}
public void IndelRepeat_ChromosomeEdgeCases()
{
var chrReference = new ChrReference()
{
Sequence = String.Concat(Enumerable.Repeat("A", 75))
};
// Wherever the variant is in the reference, as long as it's within it, R8 filter should be ok.
// See exception below.
for (int i = 0; i < chrReference.Sequence.Length - 1; i++)
{
var variant = TestHelper.CreatePassingVariant(false);
variant.ReferencePosition = i;
variant.Type = AlleleCategory.Insertion;
variant.ReferenceAllele = "A";
variant.AlternateAllele = "AA";
AlleleProcessor.Process(variant, 0.01f, 0, 0,
true, 0, 0, 2, null, 0.6f, chrReference);
Assert.Equal(true, variant.Filters.Contains(FilterType.IndelRepeatLength));
}
// Quirk: A variant at the last or second-to-last position of the chromosome does not get R8 filtered
// This comes from the legacy code that we implemented _only_ to maintain continuity with Isas, and it appears that this was an intentional behavior (comment in the code is "this handles cases where a deletion is larger than the number of downstream flanking bases").
// This test is here to show the behavior.
var variantAtLastPosition = TestHelper.CreatePassingVariant(false);
variantAtLastPosition.ReferencePosition = chrReference.Sequence.Length; // Last position of chrom (variant positions are 1-based)
variantAtLastPosition.Type = AlleleCategory.Insertion;
variantAtLastPosition.ReferenceAllele = "A";
variantAtLastPosition.AlternateAllele = "AA";
AlleleProcessor.Process(variantAtLastPosition, 0.01f, 0, 0,
true, 0, 0, 2, null, 0.6f, chrReference);
Assert.Equal(false, variantAtLastPosition.Filters.Contains(FilterType.IndelRepeatLength));
var variantAtSecondToLastPosition = TestHelper.CreatePassingVariant(false);
variantAtSecondToLastPosition.ReferencePosition = chrReference.Sequence.Length - 1; // Second to last position of chrom (variant positions are 1-based)
variantAtSecondToLastPosition.Type = AlleleCategory.Insertion;
variantAtSecondToLastPosition.ReferenceAllele = "A";
variantAtSecondToLastPosition.AlternateAllele = "AA";
AlleleProcessor.Process(variantAtSecondToLastPosition, 0.01f, 0, 0,
true, 0, 0, 2, null, 0.6f, chrReference);
Assert.Equal(false, variantAtSecondToLastPosition.Filters.Contains(FilterType.IndelRepeatLength));
// Variant decidedly outside of chromosome - throws exception because trying to substring at nonsensical positions of chromosome.
// This is a non-sensical scenario, just demonstrating that it throws exception.
// Note that if the variant was just one base outside of the chromosome, it wouldn't throw this exception (returns false -- again, not a real scenario, just documenting it)... .NET behavior for substring: returns empty string "if startIndex is equal to the length of this instance and length is zero."
var variantOutsideOfChromosome = TestHelper.CreatePassingVariant(false);
variantOutsideOfChromosome.ReferencePosition = chrReference.Sequence.Length + 2;
variantOutsideOfChromosome.Type = AlleleCategory.Insertion;
variantOutsideOfChromosome.ReferenceAllele = "A";
variantOutsideOfChromosome.AlternateAllele = "AA";
Assert.Throws <ArgumentOutOfRangeException>(() => AlleleProcessor.Process(variantOutsideOfChromosome, 0.01f, 0, 0,
true, 0, 0, 2, null, 0.6f, chrReference));
}
