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));
}