public void GenerateWhatAndWhyWorksWithCnSample(bool isAlleleMatch, uint posStart, uint posEnd, uint endStart, uint endEnd,
bool isGtMatch, uint cn, MatchEnum matchResult, FailedReason reasonResult)
{
var originalVariant = GetOriginalCnvGtVariant();
var otherVariant =
SetupBasicVariant(isAlleleMatch ? PrimaryContigAndInterval : PrimaryFailedContigAndInterval);
otherVariant.SetupGet(v => v.PosInterval).Returns(ContigAndInterval.Create(PrimaryContig, posStart, posEnd));
otherVariant.SetupGet(v => v.EndInterval).Returns(ContigAndInterval.Create(PrimaryContig, endStart, endEnd));
var otherSample = new Mock <IWittyerGenotypedCopyNumberSample>();
var gt = new Mock <IGenotypeInfo>();
if (originalVariant.Sample is IWittyerGenotypedSample gtSample)
{
gt.Setup(g => g.Equals(gtSample.Gt)).Returns(isGtMatch);
}
otherSample.SetupGet(s => s.Gt).Returns(gt.Object);
otherSample.SetupGet(s => s.Cn).Returns(cn);
otherVariant.SetupGet(v => v.Sample).Returns(otherSample.Object);
var actual = OverlappingUtils.GenerateWhatAndWhy(otherVariant.Object, new List <FailedReason>(),
originalVariant, OverlappingUtils.IsVariantAlleleMatch, false);
Assert.Equal((matchResult, reasonResult), actual);
}
internal static void Work([NotNull] TruthForest truthForest, [NotNull] IReadOnlyList <IWittyerSimpleVariant> queries)
{
foreach (var variant in queries)
{
OverlappingUtils.DoOverlapping(truthForest.Trees, variant);
}
}
public void OverlapWorks_DupDel([NotNull] string truthVar, [NotNull] string queryVar, string type, bool isTp)
{
const string sampleName = "blah";
var vcfVariantParserSettings = VcfVariantParserSettings.Create(new List <string> {
sampleName
});
var baseVariant = VcfVariant.TryParse(truthVar, vcfVariantParserSettings).GetOrThrow();
const bool isCrossTypeOn = true;
var wittyerType = WittyerType.Parse(type);
var inputSpecs = InputSpec.GenerateCustomInputSpecs(!isCrossTypeOn, new[] { wittyerType }, percentDistance: PercentDistance).ToDictionary(s => s.VariantType, s => s);
var bndSet = new Dictionary <IGeneralBnd, IVcfVariant>();
var errorList = new List <string>();
var truthV = (IMutableWittyerSimpleVariant)WittyerVcfReader.CreateVariant(baseVariant, baseVariant.Samples.First().Value, true, sampleName,
inputSpecs, bndSet, errorList, isCrossTypeOn);
baseVariant = VcfVariant.TryParse(queryVar, vcfVariantParserSettings).GetOrThrow();
var queryV = (IMutableWittyerVariant)WittyerVcfReader.CreateVariant(baseVariant, baseVariant.Samples.First().Value, false, sampleName,
inputSpecs, bndSet, errorList, isCrossTypeOn);
var tree = TruthForest.Create(sampleName, VcfHeader.CreateBuilder(VcfVersion.FourPointOne).Build());
tree.AddTarget(truthV);
OverlappingUtils.DoOverlapping(tree.VariantTrees, queryV, OverlappingUtils.IsVariantAlleleMatch, isCrossTypeOn, true);
queryV.Finalize(WitDecision.FalsePositive, EvaluationMode.CrossTypeAndSimpleCounting, null);
truthV.Finalize(WitDecision.FalseNegative, EvaluationMode.CrossTypeAndSimpleCounting, null);
Assert.Equal(isTp ? WitDecision.TruePositive : WitDecision.FalsePositive, queryV.Sample.Wit);
Assert.Equal(isTp ? WitDecision.TruePositive : WitDecision.FalseNegative, truthV.Sample.Wit);
}
