/// <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);
}
/// <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);
}