public void SkippedBinsAreIgnoredInStats()
{
var outputDirectory = Path.GetRandomFileName().ToDirectoryInfo();
var alternatingBins = ImmutableList <(uint size, bool skip)> .Empty
.Add((1, true))
.Add((100000, false))
.Add((200000, true))
.Add((300000, false));
var inputSpecs = InputSpec.GenerateDefaultInputSpecs(true)
.Select(i => InputSpec.Create(i.VariantType, alternatingBins,
1, 1, i.ExcludedFilters, i.IncludedFilters, i.IncludedRegions))
.ToDictionary(i => i.VariantType, i => i);
var wittyerSettings = WittyerSettings.Create(outputDirectory, TinyTruth, TinyQuery,
ImmutableList <ISamplePair> .Empty, EvaluationMode.SimpleCounting,
inputSpecs);
var(_, query, truth) = MainLauncher.GenerateResults(wittyerSettings).EnumerateSuccesses().First();
var results = MainLauncher.GenerateSampleMetrics(truth, query, false, inputSpecs);
Assert.Equal(1U, results.OverallStats[StatsType.Event].QueryStats.TrueCount);
Assert.Equal(1U, results.OverallStats[StatsType.Event].QueryStats.FalseCount);
Assert.Equal(0.5, results.EventLevelRecallOverall.First(typeRecallTuple => typeRecallTuple.type == WittyerType.CopyNumberGain).recall);
var numberOfBinsReportedOn = results.EventLevelRecallPerBin.First().perBinRecall.Count();
Assert.Equal(2, numberOfBinsReportedOn);
}
public void CrossType_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, i.IncludedRegions))
.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);
Assert.Equal(4U, results.OverallStats[StatsType.Event].QueryStats.TrueCount);
}
public void Bed_Counts_Bases_Of_FP_Events()
{
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(Bed)))
.ToDictionary(i => i.VariantType, i => i);
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);
// should be end of bed - start of query + 1 = 149835000 - 145395620 + 1 = 4439381
MultiAssert.Equal(4439381U, results.OverallStats[StatsType.Base].QueryStats.TrueCount);
MultiAssert.Equal(4439381U, results.OverallStats[StatsType.Base].TruthStats.TrueCount);
MultiAssert.Equal(0U, results.OverallStats[StatsType.Event].QueryStats.TrueCount);
MultiAssert.Equal(0U, results.OverallStats[StatsType.Event].TruthStats.TrueCount);
MultiAssert.AssertAll();
}
public void UsingDefaultConfigFileProducesSameInputSpecsAsCommandLineDefaults()
{
var defaultConfigFilePath = Path.Combine(Environment.CurrentDirectory, "Config-default.json");
var defaultInputSpecsCommandLine = InputSpec
.GenerateDefaultInputSpecs(true, WittyerType.AllTypes.OrderBy(s => s.Name))
.ToImmutableDictionary(x => x.VariantType, x => x);
var defaultInputSpecsConfig = JsonConvert
.DeserializeObject <IEnumerable <InputSpec> >(File.ReadAllText(defaultConfigFilePath),
InputSpecConverter.Create()).OrderBy(x => x.VariantType.Name)
.ToImmutableDictionary(x => x.VariantType, x => x);
foreach (var(key, value) in defaultInputSpecsConfig)
{
if (!defaultInputSpecsCommandLine.TryGetValue(key, out var value2))
{
MultiAssert.Equal(string.Empty, key.ToString());
}
if (!value.Equals(value2))
{
MultiAssert.Equal(value, value2);
}
}
MultiAssert.AssertAll();
}
