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); }
public static void ParseWittyerVariantType_AssignCorrectType([NotNull] string vcfString, bool isCrossTypeOn, [CanBeNull] string expected) { const string sampleName = "s1"; var variant = VcfVariant.TryParse(vcfString, VcfVariantParserSettings.Create(ImmutableList.Create(sampleName, "s2"), GenomeAssembly.Hg38)) .GetOrThrowDebug(); var reason = WittyerType.ParseFromVariant(variant, isCrossTypeOn, sampleName, out var assignedType); if (expected == null) { Assert.Equal(FailedReason.UndeterminedCn, reason); } else { Assert.Equal(WittyerType.Parse(expected), assignedType); } }