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)
{
_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));
}
}
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));
}
public static ISomaticVariantCaller CreateMockVariantCaller(VcfFileWriter vcfWriter, ApplicationOptions options, ChrReference chrRef, MockAlignmentExtractor mockAlignmentExtractor, IStrandBiasFileWriter biasFileWriter = null, string intervalFilePath = null)
{
var config = new AlignmentSourceConfig
{
MinimumMapQuality = options.MinimumMapQuality,
OnlyUseProperPairs = options.OnlyUseProperPairs,
};
//var mateFinder = options.StitchReads ? new AlignmentMateFinder() : null;
AlignmentMateFinder mateFinder = null;
var alignmentSource = new AlignmentSource(mockAlignmentExtractor, mateFinder, config);
var variantFinder = new CandidateVariantFinder(options.MinimumBaseCallQuality, options.MaxSizeMNV, options.MaxGapBetweenMNV, options.CallMNVs);
var coverageCalculator = new CoverageCalculator();
var alleleCaller = new AlleleCaller(new VariantCallerConfig
{
IncludeReferenceCalls = options.OutputgVCFFiles,
MinVariantQscore = options.MinimumVariantQScore,
MaxVariantQscore = options.MaximumVariantQScore,
VariantQscoreFilterThreshold = options.FilteredVariantQScore > options.MinimumVariantQScore ? options.FilteredVariantQScore : (int?)null,
MinCoverage = options.MinimumDepth,
MinFrequency = options.MinimumFrequency,
EstimatedBaseCallQuality = options.AppliedNoiseLevel == -1 ? options.MinimumBaseCallQuality : options.AppliedNoiseLevel,
StrandBiasModel = options.StrandBiasModel,
StrandBiasFilterThreshold = options.StrandBiasAcceptanceCriteria,
FilterSingleStrandVariants = options.FilterOutVariantsPresentOnlyOneStrand,
ChrReference = chrRef
},
coverageCalculator: coverageCalculator,
variantCollapser: options.Collapse ? new VariantCollapser(null, coverageCalculator) : null);
var stateManager = new RegionStateManager(
expectStitchedReads: mockAlignmentExtractor.SourceIsStitched,
trackOpenEnded: options.Collapse, trackReadSummaries: options.CoverageMethod == CoverageMethod.Approximate);
//statmanager is an allele source
Assert.Equal(0, stateManager.GetAlleleCount(1, AlleleType.A, DirectionType.Forward));
return(new SomaticVariantCaller(
alignmentSource,
variantFinder,
alleleCaller,
vcfWriter,
stateManager,
chrRef,
null,
biasFileWriter));
}
private ISomaticVariantCaller CreateMockVariantCaller(VcfFileWriter vcfWriter, ApplicationOptions options, ChrReference chrRef, MockAlignmentExtractor mae, IStrandBiasFileWriter biasFileWriter = null, string intervalFilePath = null)
{
var config = new AlignmentSourceConfig
{
MinimumMapQuality = options.MinimumMapQuality,
OnlyUseProperPairs = options.OnlyUseProperPairs,
};
IAlignmentStitcher stitcher = null;
if (options.StitchReads)
{
if (options.UseXCStitcher)
{
stitcher = new XCStitcher(options.MinimumBaseCallQuality);
}
else
{
stitcher = new BasicStitcher(options.MinimumBaseCallQuality);
}
}
var mateFinder = options.StitchReads ? new AlignmentMateFinder(MAX_FRAGMENT_SIZE) : null;
var RegionPadder = new RegionPadder(chrRef, null);
var alignmentSource = new AlignmentSource(mae, mateFinder, stitcher, config);
var variantFinder = new CandidateVariantFinder(options.MinimumBaseCallQuality, options.MaxSizeMNV, options.MaxGapBetweenMNV, options.CallMNVs);
var alleleCaller = new AlleleCaller(new VariantCallerConfig
{
IncludeReferenceCalls = options.OutputgVCFFiles,
MinVariantQscore = options.MinimumVariantQScore,
MaxVariantQscore = options.MaximumVariantQScore,
VariantQscoreFilterThreshold = options.FilteredVariantQScore > options.MinimumVariantQScore ? options.FilteredVariantQScore : (int?)null,
MinCoverage = options.MinimumCoverage,
MinFrequency = options.MinimumFrequency,
EstimatedBaseCallQuality = options.AppliedNoiseLevel == -1 ? options.MinimumBaseCallQuality : options.AppliedNoiseLevel,
StrandBiasModel = options.StrandBiasModel,
StrandBiasFilterThreshold = options.StrandBiasAcceptanceCriteria,
FilterSingleStrandVariants = options.FilterOutVariantsPresentOnlyOneStrand,
GenotypeModel = options.GTModel
});
var stateManager = new RegionStateManager();
return(new SomaticVariantCaller(
alignmentSource,
variantFinder,
alleleCaller,
vcfWriter,
stateManager,
chrRef,
RegionPadder,
biasFileWriter));
}
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));
}