private WittyerSampleInternal(IVcfSample baseSample, WitDecision wit,
[NotNull] IImmutableList <MatchEnum> what, [NotNull] IImmutableList <FailedReason> why)
{
_baseSample = baseSample;
Wit = wit;
What = what;
Why = why;
}
/// <inheritdoc />
public void Finalize(WitDecision falseDecision, EvaluationMode mode,
GenomeIntervalTree <IContigAndInterval> includedRegions)
{
bool?isIncluded = null;
if (includedRegions != null)
{
isIncluded = includedRegions.TryGetValue(OriginalVariant.Contig, out var tree) &&
tree.Search(CiPosInterval).Any() && // or there's overlap in bed regions
(ReferenceEquals(OriginalVariant, EndOriginalVariant) ||
Equals(OriginalVariant.Contig, EndOriginalVariant.Contig) ||
includedRegions.TryGetValue(EndOriginalVariant.Contig, out tree) &&
tree.Search(CiEndInterval).Any()); // or end overlaps.
}
WittyerVariantInternal.Finalize(this, _overlapInfo, falseDecision, mode, isIncluded);
}
private static bool ParseVariantGetTag([NotNull] string variant, WitDecision targetDecision)
{
var parser = VcfVariantParserSettings.Create(new List <string> {
"sample"
});
var vcfVariant = VcfVariant.TryParse(variant, parser).GetOrThrow();
var sampleDictionary = vcfVariant.Samples.Single().Value.SampleDictionary;
if (vcfVariant.Info.TryGetValue(WittyerConstants.WittyerMetaInfoLineKeys.Who, out var who))
{
if (who.Split(WittyerConstants.SampleValueDel).Length > WittyerConstants.MaxNumberOfAnnotations)
{
return(false);
}
}
return(sampleDictionary
.TryGetValue(WittyerConstants.WittyerMetaInfoLineKeys.Wit).Any(it =>
it != VcfConstants.MissingValueString &&
(it != targetDecision.ToStringDescription() && it != NotAssessedString || sampleDictionary
.TryGetValue(WittyerConstants.WittyerMetaInfoLineKeys.Why)
.Any(val => val != VcfConstants.MissingValueString))));
}
/// <inheritdoc />
public void Finalize(WitDecision falseDecision, EvaluationMode mode,
GenomeIntervalTree <IContigAndInterval> includedRegions)
{
bool?isIncluded = null;
if (includedRegions != null)
{
isIncluded = false;
if (includedRegions.TryGetValue(Contig, out var tree))
{
var startPosition = CiPosInterval.Stop - 1;
var endPosition = CiEndInterval.Start;
if (startPosition >= endPosition)
{
// means cipos or ciend goes past each other
// so any overlap with Start to Stop should mean included.
isIncluded = tree.Search(this).Any();
}
else
{
// ReSharper disable once LoopCanBeConvertedToQuery // prevent closure allocation
foreach (var overlap in tree.Search(startPosition))
{
if (!overlap.Contains(endPosition))
{
continue;
}
isIncluded = true;
break;
}
}
}
}
Finalize(this, _overlapInfo, falseDecision, mode, isIncluded);
}
internal static void Finalize([NotNull] IMutableWittyerSimpleVariant variant,
[NotNull] List <OverlapAnnotation> annotations, WitDecision falseDecision, EvaluationMode mode,
bool?isIncluded)
{
annotations.Sort();
WittyerSampleInternal unwrappedSample;
switch (variant.Sample)
{
case WittyerSampleInternal simple:
unwrappedSample = simple;
break;
case WittyerCopyNumberSample cnSample:
unwrappedSample = cnSample.BaseSample;
break;
case WittyerGenotypedSample gtSample:
unwrappedSample = gtSample.BaseSample;
break;
case WittyerGenotypedCopyNumberSample gtCnSample:
unwrappedSample = gtCnSample.BaseSample.BaseSample;
break;
default:
throw new InvalidDataException(
"Not sure how we get here, you must have created some non-existed wittyer sample type, check with developer!");
}
// expected results:
// isIncluded == null means no bedRegion, so everything is normal.
// isIncluded != null means bedRegion, so if false, override the results as such:
// Wit = NotAssessed.
// Why[0] if Unset = OutsideBedRegion
unwrappedSample.What = ImmutableList <MatchEnum> .Empty;
unwrappedSample.Why = ImmutableList <FailedReason> .Empty;
var isTp = false;
for (var i = 0; i < variant.OverlapInfo.Count; i++)
{
var what = variant.OverlapInfo[i].What;
unwrappedSample.What = unwrappedSample.What.Add(what);
isTp = isTp ||
what == MatchEnum.AlleleAndGenotypeMatch ||
(mode == EvaluationMode.SimpleCounting || mode == EvaluationMode.CrossTypeAndSimpleCounting) &&
what == MatchEnum.AlleleMatch;
var why = variant.OverlapInfo[i].Why;
if (why == FailedReason.Unset)
{
why = i == 0 && isIncluded == false
? FailedReason.OutsideBedRegion
: what == MatchEnum.Unmatched
? FailedReason.NoOverlap
: FailedReason.Other;
}
unwrappedSample.Why = unwrappedSample.Why.Add(why);
}
if (unwrappedSample.What.Count == 0)
{
unwrappedSample.What = EmptyWhat;
}
if (unwrappedSample.Why.Count == 0)
{
unwrappedSample.Why = isIncluded == false ? EmptyOutsideBedWhy : isTp ? EmptyTrueWhy : EmptyFalseWhy;
}
unwrappedSample.Wit = isIncluded == null || isIncluded.Value
? isTp
? WitDecision.TruePositive
: falseDecision
: WitDecision.NotAssessed;
}
public static IWittyerSample Create([NotNull] IVcfSample baseSample, WitDecision wit,
[NotNull] IImmutableList <MatchEnum> what, [NotNull] IImmutableList <FailedReason> why)
=> WittyerSampleInternal.Create(baseSample, wit, what, why);
internal static WittyerSampleInternal Create([NotNull] IVcfSample baseSample, WitDecision wit,
[NotNull] IImmutableList <MatchEnum> what, [NotNull] IImmutableList <FailedReason> why)
=> new WittyerSampleInternal(baseSample, wit, what, why);
