public void PrunedForcedAlleleShouldBeCalled()
{
var mockCandidateToBatch = new Mock <ICandidateBatch>();
var candidateAllele1 = new CandidateAllele("chr1", 10, "G", "T", AlleleCategory.Snv);
mockCandidateToBatch.Setup(s => s.GetCandidates()).Returns(new List <CandidateAllele> {
candidateAllele1
});
mockCandidateToBatch.SetupGet(s => s.MaxClearedPosition).Returns(100);
var config = new VariantCallerConfig {
MinCoverage = 20
};
var myChrRef = new ChrReference()
{
Name = "chr1",
Sequence = "ATGGCCTACGATTAGTAGGT"
};
config.ChrReference = myChrRef;
//config.MinCoverage = 20;
var mockCoverageCalculator = new Mock <ICoverageCalculator>();
mockCoverageCalculator.Setup(x => x.Compute(It.IsAny <CalledAllele>(), It.IsAny <IAlleleSource>()));
var mockGenotypeCalculator = new Mock <IGenotypeCalculator>();
mockGenotypeCalculator.Setup(x => x.SetGenotypes(It.IsAny <IEnumerable <CalledAllele> >())).Returns <List <CalledAllele> >(s => s); //note: returns allele to prune
config.GenotypeCalculator = mockGenotypeCalculator.Object;
config.LocusProcessor = new DiploidLocusProcessor();
var alleleCaller = new AlleleCaller(config, null, null, mockCoverageCalculator.Object);
var mockAlleleSource = new Mock <IAlleleSource>();
var observedAllelewithoutForcedAllele = alleleCaller.Call(mockCandidateToBatch.Object, mockAlleleSource.Object);
Assert.Equal(0, observedAllelewithoutForcedAllele.Count);
var forcedGtAlleles = new HashSet <Tuple <string, int, string, string> >
{
new Tuple <string, int, string, string>("chr1", 10, "G", "T")
};
alleleCaller.AddForcedGtAlleles(forcedGtAlleles);
var observedCalledAllele = alleleCaller.Call(mockCandidateToBatch.Object, mockAlleleSource.Object);
Assert.Equal(1, observedCalledAllele.Count);
Assert.True(observedCalledAllele.First().Value.First().IsForcedToReport);
}
protected virtual IAlleleCaller CreateVariantCaller(ChrReference chrReference, ChrIntervalSet intervalSet, IAlignmentSource alignmentSource, HashSet <Tuple <string, int, string, string> > forceGtAlleles = null)
{
var coverageCalculator = CreateCoverageCalculator(alignmentSource);
var genotypeCalculator = GenotypeCreator.CreateGenotypeCalculator(
_options.VariantCallingParameters.PloidyModel, _options.VariantCallingParameters.MinimumFrequencyFilter,
_options.VariantCallingParameters.MinimumCoverage,
_options.VariantCallingParameters.DiploidSNVThresholdingParameters,
_options.VariantCallingParameters.DiploidINDELThresholdingParameters,
_options.VariantCallingParameters.AdaptiveGenotypingParameters,
_options.VariantCallingParameters.MinimumGenotypeQScore,
_options.VariantCallingParameters.MaximumGenotypeQScore,
_options.VariantCallingParameters.TargetLODFrequency,
_options.VariantCallingParameters.MinimumFrequency,
chrReference.Name, _options.VariantCallingParameters.IsMale);
genotypeCalculator.SetMinFreqFilter(_options.VariantCallingParameters.MinimumFrequencyFilter);
var locusProcessor = _options.VariantCallingParameters.PloidyModel == PloidyModel.DiploidByThresholding
? (ILocusProcessor) new DiploidLocusProcessor()
: new SomaticLocusProcessor();
var variantCallerConfig = new VariantCallerConfig
{
IncludeReferenceCalls = _options.VcfWritingParameters.OutputGvcfFile,
MinVariantQscore = _options.VariantCallingParameters.MinimumVariantQScore,
MaxVariantQscore = _options.VariantCallingParameters.MaximumVariantQScore,
MinGenotypeQscore = _options.VariantCallingParameters.MinimumGenotypeQScore,
MaxGenotypeQscore = _options.VariantCallingParameters.MaximumGenotypeQScore,
VariantQscoreFilterThreshold = _options.VariantCallingParameters.MinimumVariantQScoreFilter,
NoCallFilterThreshold = _options.VariantCallingParameters.NoCallFilterThreshold,
AmpliconBiasFilterThreshold = _options.VariantCallingParameters.AmpliconBiasFilterThreshold,
MinCoverage = _options.VariantCallingParameters.MinimumCoverage,
MinFrequency = genotypeCalculator.MinVarFrequency,
NoiseLevelUsedForQScoring = _options.VariantCallingParameters.NoiseLevelUsedForQScoring,
StrandBiasModel = _options.VariantCallingParameters.StrandBiasModel,
StrandBiasFilterThreshold = _options.VariantCallingParameters.StrandBiasAcceptanceCriteria,
FilterSingleStrandVariants = _options.VariantCallingParameters.FilterOutVariantsPresentOnlyOneStrand,
GenotypeCalculator = genotypeCalculator,
VariantFreqFilter = genotypeCalculator.MinVarFrequencyFilter,
LowGTqFilter = _options.VariantCallingParameters.LowGenotypeQualityFilter,
IndelRepeatFilter = _options.VariantCallingParameters.IndelRepeatFilter,
LowDepthFilter = _options.VariantCallingParameters.LowDepthFilter,
ChrReference = chrReference,
RMxNFilterSettings = new RMxNFilterSettings
{
RMxNFilterMaxLengthRepeat = _options.VariantCallingParameters.RMxNFilterMaxLengthRepeat,
RMxNFilterMinRepetitions = _options.VariantCallingParameters.RMxNFilterMinRepetitions,
RMxNFilterFrequencyLimit = _options.VariantCallingParameters.RMxNFilterFrequencyLimit
},
NoiseModel = _options.VariantCallingParameters.NoiseModel,
LocusProcessor = locusProcessor
};
var alleleCaller = new AlleleCaller(variantCallerConfig, intervalSet,
CreateVariantCollapser(chrReference.Name, coverageCalculator),
coverageCalculator);
alleleCaller.AddForcedGtAlleles(forceGtAlleles);
return(alleleCaller);
}