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));
}
private void ExecuteTest(RegionPadder mapper, CandidateBatch batch,
List <CandidateAllele> expectedAlleles, bool mapAll = false)
{
mapper.Pad(batch, mapAll);
var candidates = batch.GetCandidates();
Assert.Equal(expectedAlleles.Count, candidates.Count());
foreach (var candidate in candidates)
{
Assert.True(expectedAlleles.Contains(candidate));
}
}
public void Map()
{
// set up test
var intervals = new List <CallSomaticVariants.Logic.RegionState.Region>
{
new CallSomaticVariants.Logic.RegionState.Region(4, 10),
new CallSomaticVariants.Logic.RegionState.Region(15, 17),
new CallSomaticVariants.Logic.RegionState.Region(25, 39),
new CallSomaticVariants.Logic.RegionState.Region(50, 55),
new CallSomaticVariants.Logic.RegionState.Region(60, 70),
new CallSomaticVariants.Logic.RegionState.Region(80, 80)
};
var mapper = new RegionPadder(_chrReference, new ChrIntervalSet(intervals, "chr1"));
// ------------------------------------
// first batch starts after interval start - make sure beginning positions arent skipped
// ------------------------------------
var batch = new CandidateBatch
{
ClearedRegions = new List <CallSomaticVariants.Logic.RegionState.Region>
{
new CallSomaticVariants.Logic.RegionState.Region(5, 11)
}
};
var expectedAlleles = new List <CandidateAllele>();
AddReferenceCandidatesByRange(expectedAlleles, new List <Tuple <int, int> >()
{
new Tuple <int, int>(4, 4)
});
ExecuteTest(mapper, batch, expectedAlleles);
// ------------------------------------
// next batch and starts after the second interval, fully covers third interval and partially the fourth
// ------------------------------------
batch = new CandidateBatch
{
ClearedRegions = new List <CallSomaticVariants.Logic.RegionState.Region>
{
new CallSomaticVariants.Logic.RegionState.Region(20, 52),
}
};
expectedAlleles.Clear();
AddReferenceCandidatesByRange(expectedAlleles, new List <Tuple <int, int> >()
{
new Tuple <int, int>(15, 17)
});
ExecuteTest(mapper, batch, expectedAlleles);
// ------------------------------------
// next batch contains multiple cleared regions
// ------------------------------------
batch = new CandidateBatch
{
ClearedRegions = new List <CallSomaticVariants.Logic.RegionState.Region>
{
new CallSomaticVariants.Logic.RegionState.Region(58, 59),
new CallSomaticVariants.Logic.RegionState.Region(62, 68)
}
};
expectedAlleles.Clear();
AddReferenceCandidatesByRange(expectedAlleles, new List <Tuple <int, int> >()
{
new Tuple <int, int>(53, 55),
new Tuple <int, int>(60, 61)
});
ExecuteTest(mapper, batch, expectedAlleles);
// ------------------------------------
// empty batch
// ------------------------------------
batch = new CandidateBatch
{
ClearedRegions = null
};
expectedAlleles.Clear();
ExecuteTest(mapper, batch, expectedAlleles);
// ------------------------------------
// all the rest
// ------------------------------------
batch = new CandidateBatch
{
ClearedRegions = new List <CallSomaticVariants.Logic.RegionState.Region>
{
new CallSomaticVariants.Logic.RegionState.Region(69, 69)
}
};
expectedAlleles.Clear();
AddReferenceCandidatesByRange(expectedAlleles, new List <Tuple <int, int> >()
{
new Tuple <int, int>(70, 70),
new Tuple <int, int>(80, 80)
});
ExecuteTest(mapper, batch, expectedAlleles, true);
}