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)); }
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 virtual ISomaticVariantCaller CreateSomaticVariantCaller( ChrReference chrReference, string bamFilePath, IVcfWriter <CalledAllele> vcfWriter, IStrandBiasFileWriter biasFileWriter = null, string intervalFilePath = null, List <string> chrToProcess = null) { var alignmentSource = CreateAlignmentSource(chrReference, bamFilePath, chrToProcess); var variantFinder = CreateVariantFinder(); var intervalSet = GetIntervalSet(chrReference.Name, bamFilePath); var alleleCaller = CreateVariantCaller(chrReference, intervalSet); var stateManager = CreateStateManager(intervalSet, alignmentSource.SourceIsStitched); var intervalPadder = CreateRegionPadder(chrReference, intervalSet, _options.OutputgVCFFiles); return(new SomaticVariantCaller(alignmentSource, variantFinder, alleleCaller, vcfWriter, stateManager, chrReference, intervalPadder, biasFileWriter, 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)); } }
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 override ISomaticVariantCaller CreateSomaticVariantCaller(ChrReference chrReference, string bamFilePath, IVcfWriter vcfWriter, IStrandBiasFileWriter biasFileWriter = null, string intervalFilePath = null) { return(MockSomaticVariantCaller != null ? MockSomaticVariantCaller.Object : base.CreateSomaticVariantCaller(chrReference, bamFilePath, vcfWriter, biasFileWriter, intervalFilePath)); }