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();
}