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_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 OverlapWorks_InsBnd([NotNull] string truthVar, [NotNull] string queryVar, string type)
{
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);
if (wittyerType == WittyerType.Insertion)
{
var inputSpec = inputSpecs[wittyerType];
inputSpecs[wittyerType] = InputSpec.Create(wittyerType, inputSpec.BinSizes,
100, inputSpec.PercentDistance,
inputSpec.ExcludedFilters, inputSpec.IncludedFilters, null);
}
var bndSet = new Dictionary <IGeneralBnd, IVcfVariant>();
var errorList = new List <string>();
var truthV = (IMutableWittyerBnd)WittyerVcfReader.CreateVariant(baseVariant, baseVariant.Samples.First().Value, true, sampleName,
inputSpecs, bndSet, errorList, isCrossTypeOn);
baseVariant = VcfVariant.TryParse(queryVar, vcfVariantParserSettings).GetOrThrow();
var queryV = (IMutableWittyerBnd)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.BpInsTrees, queryV, OverlappingUtils.IsBndAlleleMatch, isCrossTypeOn, true);
queryV.Finalize(WitDecision.FalsePositive, EvaluationMode.CrossTypeAndSimpleCounting, null);
truthV.Finalize(WitDecision.FalseNegative, EvaluationMode.CrossTypeAndSimpleCounting, null);
Assert.Equal(WitDecision.TruePositive, queryV.Sample.Wit);
Assert.Equal(WitDecision.TruePositive, truthV.Sample.Wit);
}
public void SvWorksWithSimpleCount()
{
if (MiscUtils.IsRunningAnyLinux)
{
return; // currently failing on linux :(
}
//var insertionSpec = InputSpecs[WittyerVariantType.Insertion];
var insertionSpec = InputSpec.Create(WittyerType.Insertion,
WittyerConstants.DefaultBins.SetItem(0, (50, false)),
WittyerConstants.DefaultBpOverlap, 0.05, WittyerConstants.DefaultExcludeFilters,
WittyerConstants.DefaultIncludeFilters, null);
var outputDirectory = Path.GetRandomFileName().ToDirectoryInfo();
var wittyerSettings = WittyerSettings.Create(outputDirectory, SomaticTruth,
SomaticQuery, ImmutableList <ISamplePair> .Empty, EvaluationMode.SimpleCounting,
InputSpecs.SetItem(WittyerType.Insertion, insertionSpec));
var results = MainLauncher.GenerateResults(wittyerSettings).Select(i => i.GetOrThrow()).ToList();
var(_, query, truth) = results.First();
MultiAssert.Equal(((IMutableWittyerResult)query).NumEntries,
(uint)WittyerVcfWriter.ProcessVariants(query, false).Count());
MultiAssert.Equal(((IMutableWittyerResult)truth).NumEntries,
(uint)WittyerVcfWriter.ProcessVariants(truth, true).Count());
var testStrings = WittyerVcfWriter.GenerateVcfStrings(query, null, null).Where(line => !line.StartsWith(VcfConstants.Header.Prefix));
MultiAssert.True(testStrings.All(s => ParseVariantGetTag(s, WitDecision.FalsePositive)));
testStrings = WittyerVcfWriter.GenerateVcfStrings(null, truth, null).Where(line => !line.StartsWith(VcfConstants.Header.Prefix));
MultiAssert.True(testStrings.All(s => ParseVariantGetTag(s, WitDecision.FalseNegative)));
var actualStats = GeneralStats.Create(results,
wittyerSettings.Mode == EvaluationMode.Default, wittyerSettings.InputSpecs, EmptyCmd).PerSampleStats
.First();
var expectedStats = JsonConvert.DeserializeObject <GeneralStats>(File.ReadAllText(SvJsonSc.FullName))
.PerSampleStats.First();
var expectedOverallEventStats = expectedStats.OverallStats.Single(x => x.StatsType.Equals(StatsType.Event));
var actualOverallEventStats = actualStats.OverallStats.Single(x => x.StatsType.Equals(StatsType.Event));
MultiAssert.Equal(expectedOverallEventStats.QueryFpCount, actualOverallEventStats.QueryFpCount);
MultiAssert.Equal(expectedOverallEventStats.QueryTpCount, actualOverallEventStats.QueryTpCount);
MultiAssert.Equal(expectedOverallEventStats.QueryTotalCount, actualOverallEventStats.QueryTotalCount);
MultiAssert.Equal(expectedOverallEventStats.TruthTpCount, actualOverallEventStats.TruthTpCount);
MultiAssert.Equal(expectedOverallEventStats.TruthFnCount, actualOverallEventStats.TruthFnCount);
MultiAssert.Equal(expectedOverallEventStats.TruthTotalCount, actualOverallEventStats.TruthTotalCount);
var expectedInsertionStats = expectedStats.DetailedStats
.Single(s => s.VariantType == WittyerType.Insertion.Name).PerBinStats;
var actualInsertionStats = actualStats.DetailedStats
.Single(s => s.VariantType == WittyerType.Insertion.Name).PerBinStats;
foreach (var(expectedInsBinStat, actualInsBinStat) in expectedInsertionStats.Zip(actualInsertionStats,
(a, b) => (a, b)))
{
var expectedSingleStat = expectedInsBinStat.Stats.Single();
var actualSingleStat = actualInsBinStat.Stats.Single();
if (!expectedSingleStat.Equals(actualSingleStat))
{
MultiAssert.Equal(string.Empty, expectedInsBinStat.Bin);
}
MultiAssert.Equal(expectedSingleStat, actualSingleStat);
}
MultiAssert.AssertAll();
}