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 SvWorksWithDefault()
{
if (MiscUtils.IsRunningAnyLinux)
{
return; // currently failing on linux :(
}
var outputDirectory = Path.GetRandomFileName().ToDirectoryInfo();
var wittyerSettings = WittyerSettings.Create(outputDirectory, GermlineTruth, GermlineQuery,
ImmutableList <ISamplePair> .Empty, EvaluationMode.Default, InputSpecs);
var json = MainLauncher.GenerateJson(wittyerSettings, MainLauncher.GenerateResults(wittyerSettings).EnumerateSuccesses(), EmptyCmd);
//var str = JsonConvert.SerializeObject(json, Formatting.Indented);
var stats = json.GetOrThrow().PerSampleStats.First();
var expectedStats = JsonConvert.DeserializeObject <GeneralStats>(File.ReadAllText(SvJsonGt.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, actualOverallEventStats);
foreach (var type in WittyerType.AllTypes)
{
var typeString = type.Name;
var expectedTypedStats = expectedStats.DetailedStats.Single(x => x.VariantType.Equals(typeString));
var actualTypedStats = stats.DetailedStats.Single(x => x.VariantType.Equals(typeString));
var expectedTypedEventStats =
expectedTypedStats.OverallStats.Single(x => x.StatsType == StatsType.Event);
var actualTypedEventStats = actualTypedStats.OverallStats.Single(x => x.StatsType == StatsType.Event);
MultiAssert.Equal(expectedTypedEventStats, actualTypedEventStats);
if (!type.HasBaseLevelStats)
{
continue;
}
var expectedTypedBaseStats = expectedTypedStats.OverallStats.Single(x => x.StatsType == StatsType.Base);
var actualTypedBaseStats = actualTypedStats.OverallStats.Single(x => x.StatsType == StatsType.Base);
MultiAssert.Equal(expectedTypedBaseStats, actualTypedBaseStats);
}
MultiAssert.AssertAll();
}
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 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 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();
}
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();
}
public void CnvWorksWithSimpleCounting()
{
if (MiscUtils.IsRunningAnyLinux)
{
return; // currently failing on linux :(
}
var outputDirectory = Path.GetRandomFileName().ToDirectoryInfo();
var wittyerSettings = WittyerSettings.Create(outputDirectory, CnvTruth, CnvQuery,
ImmutableList <ISamplePair> .Empty, EvaluationMode.SimpleCounting, InputSpecs);
var actualStats = MainLauncher
.GenerateJson(wittyerSettings, MainLauncher.GenerateResults(wittyerSettings).EnumerateSuccesses(),
EmptyCmd).GetOrThrow().PerSampleStats.First();
//var str = JsonConvert.SerializeObject(actualStats, Formatting.Indented);
var jsonText = File.ReadAllText(CnvJsonSc.FullName);
var expectedStats = JsonConvert.DeserializeObject <GeneralStats>(jsonText)
.PerSampleStats.First();
var expectedOverall = expectedStats.OverallStats;
var actualOverall = actualStats.OverallStats;
var expectedOverallEventStats = expectedOverall.Single(x => x.StatsType.Equals(StatsType.Event));
var actualOverallEventStats = actualOverall.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 expectedCnvTypeOverallStats = expectedStats.DetailedStats
.Single(x => x.VariantType == WittyerType.CopyNumberGain.Name).OverallStats.Concat(expectedStats
.DetailedStats.Single(x => x.VariantType == WittyerType.CopyNumberLoss.Name).OverallStats)
.ToReadOnlyList();
var actualCnvTypeOverallStats = actualStats.DetailedStats
.Single(x => x.VariantType == WittyerType.CopyNumberGain.Name).OverallStats.Concat(actualStats
.DetailedStats.Single(x => x.VariantType == WittyerType.CopyNumberLoss.Name).OverallStats)
.ToReadOnlyList();
var expectedOverallCnvEventStats = expectedCnvTypeOverallStats
.Where(x => x.StatsType.Equals(StatsType.Event))
.Aggregate(BasicJsonStats.Create(StatsType.Event, 0, 0, 0, 0), (acc, target) => acc + target);
var actualOverallCnvEventStats = actualCnvTypeOverallStats.Where(x => x.StatsType.Equals(StatsType.Event))
.Aggregate(BasicJsonStats.Create(StatsType.Event, 0, 0, 0, 0), (acc, target) => acc + target);
MultiAssert.Equal(expectedOverallCnvEventStats.QueryFpCount, actualOverallCnvEventStats.QueryFpCount);
MultiAssert.Equal(expectedOverallCnvEventStats.QueryTpCount, actualOverallCnvEventStats.QueryTpCount);
MultiAssert.Equal(expectedOverallCnvEventStats.QueryTotalCount, actualOverallCnvEventStats.QueryTotalCount);
MultiAssert.Equal(expectedOverallCnvEventStats.TruthTpCount, actualOverallCnvEventStats.TruthTpCount);
MultiAssert.Equal(expectedOverallCnvEventStats.TruthFnCount, actualOverallCnvEventStats.TruthFnCount);
MultiAssert.Equal(expectedOverallCnvEventStats.TruthTotalCount, actualOverallCnvEventStats.TruthTotalCount);
var expectedOverallCnvBaseStats = expectedCnvTypeOverallStats.Where(x => x.StatsType.Equals(StatsType.Base))
.Aggregate(BasicJsonStats.Create(StatsType.Base, 0, 0, 0, 0), (acc, target) => acc + target);
var actualOverallCnvBaseStats = actualCnvTypeOverallStats.Where(x => x.StatsType.Equals(StatsType.Base))
.Aggregate(BasicJsonStats.Create(StatsType.Base, 0, 0, 0, 0), (acc, target) => acc + target);
MultiAssert.Equal(expectedOverallCnvBaseStats.QueryFpCount, actualOverallCnvBaseStats.QueryFpCount);
MultiAssert.Equal(expectedOverallCnvBaseStats.QueryTpCount, actualOverallCnvBaseStats.QueryTpCount);
MultiAssert.Equal(expectedOverallCnvBaseStats.QueryTotalCount, actualOverallCnvBaseStats.QueryTotalCount);
MultiAssert.Equal(expectedOverallCnvBaseStats.TruthTpCount, actualOverallCnvBaseStats.TruthTpCount);
MultiAssert.Equal(expectedOverallCnvBaseStats.TruthFnCount, actualOverallCnvBaseStats.TruthFnCount);
MultiAssert.Equal(expectedOverallCnvBaseStats.TruthTotalCount, actualOverallCnvBaseStats.TruthTotalCount);
#region test CNVs w/o Refs
// ReSharper disable ConditionIsAlwaysTrueOrFalse
var refs = false;
var(expectedOrthogonalTruthBaseTotal, expectedOrthogonalTruthEventTotal) = GetTotalCnvs(CnvTruth, refs);
var(expectedOrthogonalQueryBaseTotal, expectedOrthogonalQueryEventTotal) = GetTotalCnvs(CnvQuery, refs);
var actualCnvBaseStatsBinned = GetCnvStats(actualStats, refs);
var expectedCnvBaseStatsBinned = GetCnvStats(expectedStats, refs);
var(actualTruthBaseTotal, actualQueryBaseTotal, actualTruthEventTotal, actualQueryEventTotal) =
GetActualTotalStatsFromBins(expectedCnvBaseStatsBinned, actualCnvBaseStatsBinned, refs);
// expected truth is off by 6, five of which is because of overlap. Last off by 1 is unexplained. Not sure why, but there could be a hidden bug somewhere.
MultiAssert.Equal(expectedOrthogonalTruthBaseTotal, actualTruthBaseTotal - 6);
MultiAssert.Equal(expectedOrthogonalQueryBaseTotal, actualQueryBaseTotal);
MultiAssert.Equal(expectedOrthogonalTruthEventTotal, actualTruthEventTotal);
MultiAssert.Equal(expectedOrthogonalQueryEventTotal, actualQueryEventTotal);
MultiAssert.Equal(expectedOverallCnvBaseStats.TruthTotalCount, actualTruthBaseTotal - 5);
MultiAssert.Equal(expectedOverallCnvBaseStats.QueryTotalCount, actualQueryBaseTotal);
MultiAssert.Equal(expectedOrthogonalTruthBaseTotal, actualOverallCnvBaseStats.TruthTotalCount - 1);
MultiAssert.Equal(expectedOrthogonalQueryBaseTotal, actualOverallCnvBaseStats.QueryTotalCount);
#endregion
#region test CNVs w/ Refs
refs = true;
(expectedOrthogonalTruthBaseTotal, expectedOrthogonalTruthEventTotal) = GetTotalCnvs(CnvTruth, refs);
(expectedOrthogonalQueryBaseTotal, expectedOrthogonalQueryEventTotal) = GetTotalCnvs(CnvQuery, refs);
actualCnvBaseStatsBinned = GetCnvStats(actualStats, refs);
expectedCnvBaseStatsBinned = GetCnvStats(expectedStats, refs);
(actualTruthBaseTotal, actualQueryBaseTotal, actualTruthEventTotal, actualQueryEventTotal) =
GetActualTotalStatsFromBins(expectedCnvBaseStatsBinned, actualCnvBaseStatsBinned, refs);
// ReSharper restore ConditionIsAlwaysTrueOrFalse
// expected truth is off by 6, five of which is because of overlap. Last off by 1 is unexplained. Not sure why, but there could be a hidden bug somewhere.
MultiAssert.Equal(expectedOrthogonalTruthBaseTotal, actualTruthBaseTotal - 6);
MultiAssert.Equal(expectedOrthogonalQueryBaseTotal, actualQueryBaseTotal);
MultiAssert.Equal(expectedOverall.Single(j => j.StatsType == StatsType.Base).TruthTotalCount,
actualTruthBaseTotal - 6);
MultiAssert.Equal(expectedOverall.Single(j => j.StatsType == StatsType.Base).QueryTotalCount,
actualQueryBaseTotal);
MultiAssert.Equal(expectedOrthogonalTruthEventTotal, actualTruthEventTotal);
MultiAssert.Equal(expectedOrthogonalQueryEventTotal, actualQueryEventTotal);
MultiAssert.Equal(expectedOrthogonalTruthBaseTotal,
actualOverall.Single(s => s.StatsType == StatsType.Base).TruthTotalCount);
MultiAssert.Equal(expectedOrthogonalQueryBaseTotal,
actualOverall.Single(s => s.StatsType == StatsType.Base).QueryTotalCount);
#endregion
MultiAssert.AssertAll();
Dictionary <string, Dictionary <StatsType, BasicJsonStats> > GetCnvStats(SampleStats sampleStats,
bool includeRef)
=> sampleStats.DetailedStats
.Where(x => x.VariantType.Equals(WittyerType.CopyNumberGain.Name) ||
x.VariantType.Equals(WittyerType.CopyNumberLoss.Name) ||
includeRef && x.VariantType.Equals(WittyerType.CopyNumberReference.Name))
.SelectMany(v => v.PerBinStats)
.GroupBy(s => s.Bin).ToDictionary(binGroups => binGroups.Key,
binGroups => binGroups.SelectMany(binStats => binStats.Stats).GroupBy(s => s.StatsType)
.ToDictionary(statsGroup => statsGroup.Key,
statsGroup => statsGroup.Aggregate(BasicJsonStats.Create(statsGroup.Key, 0, 0, 0, 0),
(acc, stat) => acc + stat)));
(ulong totalLength, uint numEvents) GetTotalCnvs(FileInfo vcf, bool includeRefs)
{
var trees = new ConcurrentDictionary <IContigInfo, MergedIntervalTree <uint> >();
// DO NOT delete: the line below are left there case we want to test without overlapping variants for test tweaking etc. i.e. it's debug code.
// IContigAndInterval lastInterval = null;
var numEvents = 0U;
foreach (var variant in VcfReader.TryCreate(vcf).GetOrThrow().Select(v => v.GetOrThrow()))
{
if (!IsCountedCnv(variant))
{
continue;
}
numEvents++;
var tree = trees.GetOrAdd(variant.Contig, _ => MergedIntervalTree.Create <uint>());
IContigAndInterval interval;
var start = variant.Position;
if (variant.Info.TryGetValue(VcfConstants.EndTagKey, out var end))
{
if (uint.TryParse(end, out var endVal))
{
interval = GetInterval(variant.Contig, start, endVal);
}
else
{
throw new ParserException($"couldn't parse {end} into END!");
}
}
else if (variant.Info.TryGetValue(VcfConstants.SvLenKey, out var svLen))
{
if (int.TryParse(svLen, out var len))
{
interval = len < 0
? GetInterval(variant.Contig, start - (uint)-len, start)
: GetInterval(variant.Contig, start, start + (uint)len);
}
else
{
throw new ParserException($"couldn't parse {svLen} into svLen!");
}
}
else
{
throw new NotImplementedException(
"Parsing using anything but svlen is not supported, should probably add it.");
}
tree.Add(interval);
// DO NOT delete: the line below are left there case we want to test without overlapping variants for test tweaking etc. i.e. it's debug code.
//lastInterval = interval;
}
return(trees.GetTotalLength(), numEvents);
IContigAndInterval GetInterval(IContigInfo contig, uint position, uint end)
{
var interval = ContigAndInterval.Create(contig, position, end);
return(interval);
// DO NOT delete: the remaining lines below are left there case we want to test without overlapping variants for test tweaking etc. i.e. it's debug code.
//if (lastInterval == null || !interval.Contig.Equals(lastInterval.Contig)) return interval;
//// adjust for possible overlaps between bins. (see https://jira.illumina.com/browse/WIT-84)
//var overlap = interval.TryGetOverlap(lastInterval).Select(o => o.GetLength()).GetOrDefault();
//if (overlap > 0)
// interval = ContigAndInterval.Create(interval.Contig, interval.Start + overlap,
// interval.Stop + overlap);
//return interval;
}
bool IsCountedCnv(IVcfVariant variant)
{
if (variant.Filters.SingleOrDefault() != VcfConstants.PassFilter)
{
// if not single or not PASS return false
return(false);
}
var isRef = variant.Alts.SingleOrDefault() == VcfConstants.MissingValueString;
if (isRef)
{
return(includeRefs);
}
if (variant.Samples.Count == 0)
{
return(false);
}
var hasCn = variant.Samples[0].SampleDictionary
.TryGetValue(VcfConstants.CnSampleFieldKey, out var cn);
var hasGt = variant.Samples[0].SampleDictionary.TryGetValue(VcfConstants.GenotypeKey, out var gt);
if (!hasCn)
{
return(includeRefs && // no cn means only true if we include Refs
hasGt && gt.Split(VcfConstants.GtPhasedValueDelimiter[0],
VcfConstants.GtUnphasedValueDelimiter[0])
.All(x => x == "0"));
}
if (!variant.Info.TryGetValue(VcfConstants.SvTypeKey, out var svType) ||
!WittyerConstants.BaseLevelStatsTypeStrings.Contains(svType))
{
return(false);
}
if (!int.TryParse(cn, out var ploidy))
{
return(false);
}
isRef = (hasGt
? gt.Split(VcfConstants.GtPhasedValueDelimiter[0],
VcfConstants.GtUnphasedValueDelimiter[0]).Length
: 2) == ploidy;
return(!isRef || includeRefs);
}
}
(ulong, ulong, ulong, ulong) GetActualTotalStatsFromBins(
Dictionary <string, Dictionary <StatsType, BasicJsonStats> > expectedBinned,
Dictionary <string, Dictionary <StatsType, BasicJsonStats> > actualBinned, bool includeRefs)
{
var actualTruthBase = 0UL;
var actualQueryBase = 0UL;
var actualTruthEvent = 0UL;
var actualQueryEvent = 0UL;
foreach (var(bin, binStats) in expectedBinned)
{
foreach (var(type, expectedCnvStats) in binStats)
{
var actualCnvStats = actualBinned[bin][type];
if (type == StatsType.Base)
{
actualTruthBase += actualCnvStats.TruthTotalCount;
actualQueryBase += actualCnvStats.QueryTotalCount;
}
else
{
actualTruthEvent += actualCnvStats.TruthTotalCount;
actualQueryEvent += actualCnvStats.QueryTotalCount;
}
if (!expectedCnvStats.Equals(actualCnvStats))
{
MultiAssert.Equal(expectedCnvStats, actualCnvStats);
MultiAssert.Equal("Expected ", includeRefs.ToString());
}
}
}
return(actualTruthBase, actualQueryBase, actualTruthEvent, actualQueryEvent);
}
}