public void ParsingDoesntThrowException(string bedFileName) { var bedFile = Path.Combine(BedsFolder, bedFileName).ToFileInfo(); Assert.Equal(bedFile.FullName, IncludeBedFile.CreateFromBedFile(bedFile).BedFile.FullName); var bedReader = BedReader.Create(bedFile); var source = bedReader.Select(b => (b.Contig, b.Start, b.Stop)).ToList(); var actual = BedReader.Create(IncludeBedFile .CreateFromContigIntervals(bedReader, Path.GetTempFileName().ToFileInfo()).BedFile) .Select(b => (b.Contig, b.Start, b.Stop)).ToList(); // if source and count is equal, then the sequence should equal. Assert.Equal(source.Count == actual.Count, source.SequenceEqual(actual)); }
public void CrossType_Bases_Works() { var outputDirectory = Path.GetRandomFileName().ToDirectoryInfo(); var inputSpecs = InputSpec.GenerateDefaultInputSpecs(false) .Select(i => InputSpec.Create(i.VariantType, i.BinSizes, 10000, i.PercentDistance, i.ExcludedFilters, i.IncludedFilters, IncludeBedFile.CreateFromBedFile(TinyBed))) .ToDictionary(i => i.VariantType, i => i); var wittyerSettings = WittyerSettings.Create(outputDirectory, TinyTruth, TinyQuery, ImmutableList <ISamplePair> .Empty, EvaluationMode.CrossTypeAndSimpleCounting, inputSpecs); var(_, query, truth) = MainLauncher.GenerateResults(wittyerSettings) .EnumerateSuccesses().First(); var results = MainLauncher.GenerateSampleMetrics(truth, query, false, inputSpecs); MultiAssert.Equal(4U, results.OverallStats[StatsType.Event].QueryStats.TrueCount); MultiAssert.Equal(1451995U, results.OverallStats[StatsType.Base].QueryStats.TrueCount); MultiAssert.Equal(1451995U, results.OverallStats[StatsType.Base].TruthStats.TrueCount); MultiAssert.AssertAll(); }
public void CrossType_ComplexBed_Works() { var outputDirectory = Path.GetRandomFileName().ToDirectoryInfo(); var inputSpecs = InputSpec.CreateSpecsFromString( File.ReadAllText(Config.FullName), IncludeBedFile.CreateFromBedFile(Bed)) ?.ToDictionary(i => i.VariantType, i => i) ?? new Dictionary <WittyerType, InputSpec>(); var wittyerSettings = WittyerSettings.Create(outputDirectory, Truth, Query, ImmutableList <ISamplePair> .Empty, EvaluationMode.CrossTypeAndSimpleCounting, inputSpecs); var(_, query, truth) = MainLauncher.GenerateResults(wittyerSettings) .EnumerateSuccesses().First(); var results = MainLauncher .GenerateSampleMetrics(truth, query, false, inputSpecs); var baseStats = results.DetailedStats[WittyerType.Deletion].OverallStats[StatsType.Base]; MultiAssert.Equal(206678U, baseStats.QueryStats.TrueCount); MultiAssert.Equal(206678U, baseStats.TruthStats.TrueCount); MultiAssert.AssertAll(); }