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));
}
}
