/// <summary>
/// Gets the truth.
/// </summary>
/// <param name="sampleName">Name of the sample.</param>
/// <returns></returns>
/// <exception cref="InvalidDataException"></exception>
internal (TruthForest forest, GenomeType genomeType) GetTruth([CanBeNull] string sampleName)
{
var truth = TruthForest.Create(sampleName, _vcfReader.Header);
var genomeType = GetResult(sampleName, truth, GenomeType.Unknown);
return(truth, genomeType ?? GenomeType.Unknown);
}
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);
}
