protected virtual ICoverageCalculator CreateCoverageCalculator(IAlignmentSource alignmentSource)
{
return(_options.CoverageMethod == CoverageMethod.Exact
? (ICoverageCalculator) new ExactCoverageCalculator()
: alignmentSource.SourceIsCollapsed && alignmentSource.SourceIsStitched? new CollapsedCoverageCalculator(considerAnchorInformation: _options.TrackedAnchorSize > 0) :
new CoverageCalculator(considerAnchorInformation: _options.TrackedAnchorSize > 0));
}
public SomaticVariantCaller(IAlignmentSource alignmentSource, ICandidateVariantFinder variantFinder, IAlleleCaller alleleCaller,
IVcfWriter <CalledAllele> vcfWriter, IStateManager stateManager, ChrReference chrReference, IRegionMapper regionMapper,
IStrandBiasFileWriter biasFileWriter, ChrIntervalSet intervalSet = null)
{
_alignmentSource = alignmentSource;
_variantFinder = variantFinder;
_alleleCaller = alleleCaller;
_vcfWriter = vcfWriter;
_stateManager = stateManager;
_chrReference = chrReference;
_regionMapper = regionMapper;
_biasFileWriter = biasFileWriter;
_intervalSet = intervalSet;
}
public SomaticVariantCaller(IAlignmentSource alignmentSource, ICandidateVariantFinder variantFinder, IAlleleCaller alleleCaller,
IVcfWriter <CalledAllele> vcfWriter, IStateManager stateManager, ChrReference chrReference, IRegionMapper regionMapper,
IStrandBiasFileWriter biasFileWriter, ChrIntervalSet intervalSet = null, HashSet <Tuple <string, int, string, string> > forcedGTAlleles = null)
{
_alignmentSource = alignmentSource;
_variantFinder = variantFinder;
_alleleCaller = alleleCaller;
_vcfWriter = vcfWriter;
_stateManager = stateManager;
_chrReference = chrReference;
_regionMapper = regionMapper;
_biasFileWriter = biasFileWriter;
_intervalSet = intervalSet;
_forcedGtAlleles = forcedGTAlleles;
_unProcessedForcedAllelesByPos = CreateForcedAllelePos(_forcedGtAlleles);
}
public SomaticVariantCaller(IAlignmentSource alignmentSource, ICandidateVariantFinder variantFinder, IAlleleCaller alleleCaller,
IVcfWriter vcfWriter, IStateManager stateManager, ChrReference chrReference, IRegionPadder regionMapper, IStrandBiasFileWriter biasFileWriter)
{
_alignmentSource = alignmentSource;
_variantFinder = variantFinder;
_alleleCaller = alleleCaller;
_vcfWriter = vcfWriter;
_stateManager = stateManager;
_chrReference = chrReference;
_regionMapper = regionMapper;
_biasFileWriter = biasFileWriter;
if (_alignmentSource.ChromosomeFilter != _chrReference.Name)
{
throw new ArgumentException(string.Format("Chromosome filter in alignment source '{0}' does not match to current chromosome '{1}'", _alignmentSource.ChromosomeFilter, _chrReference.Name));
}
}
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);
}
protected override IAlleleCaller CreateVariantCaller(ChrReference chrReference, ChrIntervalSet intervalSet, IAlignmentSource alignmentSource, HashSet <Tuple <string, int, string, string> > forcedGtAlleles = null)
{
return(MockVariantCaller != null ? MockVariantCaller.Object : base.CreateVariantCaller(chrReference, intervalSet, alignmentSource, forcedGtAlleles));
}