public PairHandler(Dictionary <int, string> refIdMapping, IAlignmentStitcher stitcher, bool filterUnstitchablePairs = false, bool tryStitch = true)
{
_refIdMapping = refIdMapping;
_stitcher = stitcher;
_filterUnstitchablePairs = filterUnstitchablePairs;
_tryStitch = tryStitch;
}
public PairHandler(Dictionary <int, string> refIdMapping, IAlignmentStitcher stitcher, bool filterUnstitchablePairs, ReadStatusCounter statusCounter)
{
_refIdMapping = refIdMapping;
_stitcher = stitcher;
_filterUnstitchablePairs = filterUnstitchablePairs;
_statusCounter = statusCounter;
_stitcher.SetStatusCounter(_statusCounter);
}
public PairHandler(Dictionary <int, string> refIdMapping, IAlignmentStitcher stitcher, ReadStatusCounter statusCounter, bool filterUnstitchablePairs = false, bool tryStitch = true)
{
_refIdMapping = refIdMapping;
_stitcher = stitcher;
_filterUnstitchablePairs = filterUnstitchablePairs;
_masterStatusCounter = statusCounter;
_statusCounter = new ReadStatusCounter();
_stitcher.SetStatusCounter(_statusCounter);
_tryStitch = tryStitch;
}
public AlignmentSource(IAlignmentExtractor alignmentExtractor,
IAlignmentMateFinder mateFinder,
IAlignmentStitcher stitcher,
AlignmentSourceConfig config) // add intervals
{
_alignmentExtractor = alignmentExtractor;
_mateFinder = mateFinder;
_stitcher = stitcher;
_config = config;
}
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 static void TryStitchAndAssertFailed(IAlignmentStitcher stitcher, AlignmentSet alignmentSet)
{
Assert.False(stitcher.TryStitch(alignmentSet).Stitched);
}
public static void TryStitchAndAssertAddedSeparately(IAlignmentStitcher stitcher, AlignmentSet alignmentSet)
{
Assert.True(stitcher.TryStitch(alignmentSet).Stitched);
Assert.True(alignmentSet.ReadsForProcessing.Contains(alignmentSet.PartnerRead1));
Assert.True(alignmentSet.ReadsForProcessing.Contains(alignmentSet.PartnerRead2));
}
public static void TryStitchAndAssertFailed(IAlignmentStitcher stitcher, AlignmentSet alignmentSet)
{
Assert.Throws <ReadsNotStitchableException>(() => stitcher.TryStitch(alignmentSet));
}
