/// <inheritdoc />
public void AddTarget(IMutableWittyerSimpleVariant variant)
{
_baseResult.AddTarget(variant);
switch (variant)
{
case IMutableWittyerBnd bnd:
BpInsTrees.GetOrAdd(variant.VariantType,
_ => GenomeIntervalTree <IMutableWittyerBnd> .Create()).Add(bnd);
break;
case IMutableWittyerVariant cast:
VariantTrees.GetOrAdd(variant.VariantType,
_ => GenomeIntervalTree <IMutableWittyerVariant> .Create()).Add(cast);
break;
default:
throw new ArgumentOutOfRangeException(
$"Unexepected Variant found that was neither {nameof(IWittyerBnd)} nor {nameof(IWittyerVariant)}!");
}
}
public void AddTarget(IMutableWittyerSimpleVariant variant)
{
switch (variant)
{
case IMutableWittyerBnd bnd:
_bndPairs.GetOrAdd(bnd.VariantType, _ => new List <IMutableWittyerBnd>()).Add(bnd);
break;
case IMutableWittyerVariant cast:
_variants.GetOrAdd(cast.VariantType, _ => new List <IMutableWittyerVariant>()).Add(cast);
break;
default:
throw new InvalidCastException(
$"Variant found to not be {nameof(IWittyerBnd)} nor {nameof(IWittyerVariant)}!");
}
AddContig(variant);
Interlocked.Add(ref _numEntries,
variant.VariantType == WittyerType.TranslocationBreakend ||
variant.VariantType == WittyerType.IntraChromosomeBreakend
? 2
: 1);
}
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;
}
