internal static void DoOverlapping <T>(
[NotNull] IReadOnlyDictionary <WittyerType, GenomeIntervalTree <T> > truthTrees,
[NotNull] T queryVariant, IsAlleleMatch <T> alleleMatchFunc, bool isCrossType, bool isSimpleCounting)
where T : class, IMutableWittyerSimpleVariant
{
if (!truthTrees.TryGetValue(queryVariant.VariantType, out var tree))
{
return; // no match at all, nothing to update
}
var failedReasons = new HashSet <FailedReason>();
foreach (var overlap in tree.Search(queryVariant))
{
failedReasons.Clear();
var(matchEnum, failedReason) = GenerateWhatAndWhy(queryVariant, failedReasons, overlap, alleleMatchFunc, isCrossType);
var wow = overlap.VariantType.HasOverlappingWindows &&
(isSimpleCounting ||
matchEnum == MatchEnum.AlleleAndGenotypeMatch || matchEnum == MatchEnum.LocalAndGenotypeMatch)
? overlap.TryGetOverlap(queryVariant).GetOrDefault()
: null;
var borderDistance = BorderDistance.CreateFromVariant(overlap, queryVariant);
var who = GetNextWhoTag();
var overlapInfo =
OverlapAnnotation.Create(who, matchEnum, wow, borderDistance, failedReason);
overlap.AddToOverlapInfo(overlapInfo);
queryVariant.AddToOverlapInfo(overlapInfo);
uint GetNextWhoTag()
{
var ret = overlap.OriginalVariant.Position;
while (WhoTags.Contains(ret))
{
ret++;
}
WhoTags.Add(ret);
return(ret);
}
}
}
/// <inheritdoc /> public void AddToOverlapInfo(OverlapAnnotation newAnnotation) => _overlapInfo.Add(newAnnotation);
