public virtual ISmallVariantCaller CreateSomaticVariantCaller( ChrReference chrReference, string bamFilePath, IVcfWriter <CalledAllele> vcfWriter, IStrandBiasFileWriter strandBiasFileWriter = null, IAmpliconBiasFileWriter ampliconBiasFileWriter = null, string intervalFilePath = null, List <string> chrToProcess = null) { var alignmentSource = CreateAlignmentSource(chrReference, bamFilePath, _options.UseStitchedXDInfo, chrToProcess); var variantFinder = CreateVariantFinder(); var intervalSet = GetIntervalSet(chrReference.Name, bamFilePath); var forceGtAlleles = SelectForcedAllele(_forcedAllelesByChrom, chrReference.Name, intervalSet); var alleleCaller = CreateVariantCaller(chrReference, intervalSet, alignmentSource, forceGtAlleles); var stateManager = CreateStateManager(intervalSet, alignmentSource.SourceIsStitched, alignmentSource.SourceIsCollapsed); var intervalPadder = CreateRegionPadder(chrReference, intervalSet, _options.VcfWritingParameters.OutputGvcfFile); return(new SmallVariantCaller(alignmentSource, variantFinder, alleleCaller, vcfWriter, stateManager, chrReference, intervalPadder, strandBiasFileWriter, ampliconBiasFileWriter, intervalSet, forceGtAlleles)); }
public SmallVariantCaller(IAlignmentSource alignmentSource, ICandidateVariantFinder variantFinder, IAlleleCaller alleleCaller, IVcfWriter <CalledAllele> vcfWriter, IStateManager stateManager, ChrReference chrReference, IRegionMapper regionMapper, IStrandBiasFileWriter strandBiasFileWriter, IAmpliconBiasFileWriter ampBiasFileWriter, 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; _strandBiasFileWriter = strandBiasFileWriter; _ampliconBiasFileWriter = ampBiasFileWriter; _intervalSet = intervalSet; _forcedGtAlleles = forcedGTAlleles; _unProcessedForcedAllelesByPos = CreateForcedAllelePos(_forcedGtAlleles); _writeBiasFiles = (strandBiasFileWriter != null && ampBiasFileWriter != null); }
public override ISmallVariantCaller CreateSomaticVariantCaller(ChrReference chrReference, string bamFilePath, IVcfWriter <CalledAllele> vcfWriter, IStrandBiasFileWriter strandBiasFileWriter = null, IAmpliconBiasFileWriter ampliconBiasFileWriter = null, string intervalFilePath = null, List <string> chrToProcess = null) { return(MockSomaticVariantCaller != null ? MockSomaticVariantCaller.Object : base.CreateSomaticVariantCaller(chrReference, bamFilePath, vcfWriter, strandBiasFileWriter, ampliconBiasFileWriter, intervalFilePath, chrToProcess)); }