private void ComputeCoverageTest(BaseCalledAllele variant, List <AlleleCount> stagedCounts,
int[] expectedCoverageByDirection, bool checkAux = true, int alleleSupport = 5, int expectedSnvRef = 0, int takenRefSupport = 0)
{
variant.AlleleSupport = alleleSupport;
var mockStateManager = CreateMockStateManager(stagedCounts, takenRefSupport);
var expectedCoverage = expectedCoverageByDirection.Sum();
CoverageCalculator.Compute(variant, mockStateManager);
Assert.Equal(expectedCoverage, variant.TotalCoverage);
for (var i = 0; i < expectedCoverageByDirection.Length; i++)
{
Assert.Equal(expectedCoverageByDirection[i], variant.TotalCoverageByDirection[i]);
}
if (checkAux)
{
//"Reference" Support should be the coverage less the variant support, if we don't have an SNV
if (variant is CalledVariant && variant.Type != AlleleCategory.Snv)
{
Assert.Equal(expectedCoverage - variant.AlleleSupport, ((CalledVariant)variant).ReferenceSupport);
}
else
{
Assert.Equal(expectedSnvRef, ((CalledVariant)variant).ReferenceSupport);
}
//Frequency should be support/coverage
Assert.Equal((float)variant.AlleleSupport / expectedCoverage, variant.Frequency);
}
}
public static ISomaticVariantCaller CreateMockVariantCaller(VcfFileWriter vcfWriter, ApplicationOptions options, ChrReference chrRef, MockAlignmentExtractor mockAlignmentExtractor, IStrandBiasFileWriter biasFileWriter = null, string intervalFilePath = null)
{
var config = new AlignmentSourceConfig
{
MinimumMapQuality = options.MinimumMapQuality,
OnlyUseProperPairs = options.OnlyUseProperPairs,
};
//var mateFinder = options.StitchReads ? new AlignmentMateFinder() : null;
AlignmentMateFinder mateFinder = null;
var alignmentSource = new AlignmentSource(mockAlignmentExtractor, mateFinder, config);
var variantFinder = new CandidateVariantFinder(options.MinimumBaseCallQuality, options.MaxSizeMNV, options.MaxGapBetweenMNV, options.CallMNVs);
var coverageCalculator = new CoverageCalculator();
var alleleCaller = new AlleleCaller(new VariantCallerConfig
{
IncludeReferenceCalls = options.OutputgVCFFiles,
MinVariantQscore = options.MinimumVariantQScore,
MaxVariantQscore = options.MaximumVariantQScore,
VariantQscoreFilterThreshold = options.FilteredVariantQScore > options.MinimumVariantQScore ? options.FilteredVariantQScore : (int?)null,
MinCoverage = options.MinimumDepth,
MinFrequency = options.MinimumFrequency,
EstimatedBaseCallQuality = options.AppliedNoiseLevel == -1 ? options.MinimumBaseCallQuality : options.AppliedNoiseLevel,
StrandBiasModel = options.StrandBiasModel,
StrandBiasFilterThreshold = options.StrandBiasAcceptanceCriteria,
FilterSingleStrandVariants = options.FilterOutVariantsPresentOnlyOneStrand,
ChrReference = chrRef
},
coverageCalculator: coverageCalculator,
variantCollapser: options.Collapse ? new VariantCollapser(null, coverageCalculator) : null);
var stateManager = new RegionStateManager(
expectStitchedReads: mockAlignmentExtractor.SourceIsStitched,
trackOpenEnded: options.Collapse, trackReadSummaries: options.CoverageMethod == CoverageMethod.Approximate);
//statmanager is an allele source
Assert.Equal(0, stateManager.GetAlleleCount(1, AlleleType.A, DirectionType.Forward));
return(new SomaticVariantCaller(
alignmentSource,
variantFinder,
alleleCaller,
vcfWriter,
stateManager,
chrRef,
null,
biasFileWriter));
}
