public void GenerateVcfStrings_IncludeHeaders()
{
if (MiscUtils.IsRunningAnyLinux)
{
return; // currently failing on linux :(
}
var parser = VcfVariantParserSettings.Create(ImmutableList.Create(SampleName));
var variants = VcfVariant.TryParse(Bnd1, parser).FollowedBy(VcfVariant.TryParse(Bnd2, parser)).EnumerateSuccesses().ToList();
var wittyerVariant = WittyerBndInternal.Create(variants[0],
variants[0].ToTryOfGenotypedVcfVariant(VariantNormalizer.TrimCommonBases).GetOrThrow().Samples.Values.First(),
WittyerType.IntraChromosomeBreakend, new List <uint>(), uint.MinValue, null, variants[1]);
var headerLines = WittyerVcfWriter.GenerateVcfStrings(
WittyerResult.Create(VcfHeader.CreateBuilder(VcfVersion.FourPointOne).Build(), SampleName,
variants.Select(v => v.Contig).Distinct().ToList(), false,
new Dictionary <WittyerType, IReadOnlyList <IWittyerVariant> >(),
new Dictionary <WittyerType, IReadOnlyList <IWittyerBnd> >
{
{ WittyerType.IntraChromosomeBreakend, new List <IWittyerBnd> {
wittyerVariant
} }
}, new List <IVcfVariant>()), null, null)
.TakeWhile(line => line.StartsWith(VcfConstants.Header.Prefix)).ToList();
// 11 = VcfVersion, WHO, WHAT, WHERE, WHY, WIT, WIN, WOW, date, version, column names
Assert.Equal(11, headerLines.Count);
}
public void CnvWorksWithCrossType()
{
if (MiscUtils.IsRunningAnyLinux)
{
return; // currently failing on linux :(
}
var outputDirectory = Path.GetRandomFileName().ToDirectoryInfo();
var wittyerSettings = WittyerSettings.Create(outputDirectory, CnvTruth, CnvQuery,
ImmutableList <ISamplePair> .Empty, EvaluationMode.CrossTypeAndSimpleCounting, InputSpecs);
var results = MainLauncher.GenerateResults(wittyerSettings).EnumerateSuccesses().ToList();
var(_, query, truth) = results.First();
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 stats = MainLauncher
.GenerateJson(wittyerSettings, results,
EmptyCmd).GetOrThrow().PerSampleStats.First();
// make sure to check for null
MultiAssert.True(stats.QuerySampleName != null);
MultiAssert.True(stats.TruthSampleName != null);
var expectedStats = JsonConvert.DeserializeObject <GeneralStats>(File.ReadAllText(CnvJsonCts.FullName))
.PerSampleStats.First();
var expectedOverallEventStats = expectedStats.OverallStats.Single(x => x.StatsType.Equals(StatsType.Event));
var actualOverallEventStats = stats.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);
MultiAssert.AssertAll();
}
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();
}