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)); } }