Esempio n. 1
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);
 }
Esempio n. 3
0
        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));
            }
        }