private OverlapAnnotation(uint who, MatchEnum what, [CanBeNull] IInterval <uint> wow, BorderDistance where,
FailedReason why)
{
Who = who;
What = what;
Wow = wow;
Where = where;
Why = why;
}
public static void WorksWithCi()
{
var query = CreateWittyerVariant(QueryWithCiPos);
var truth = CreateWittyerVariant(TruthWithCiEnd);
var expected = BorderDistance.CreateFromVariant(query, truth);
MultiAssert.Equal(87U, expected.PosBorderLeft);
MultiAssert.Equal(287U, expected.PosBorderRight);
MultiAssert.Equal(686U, expected.EndBorderLeft);
MultiAssert.Equal(986U, expected.EndBorderRight);
MultiAssert.AssertAll();
}
public static void WorksWithBreakend()
{
var query = CreateWittyerBnd(QueryBnd1, QueryBnd2);
var truth = CreateWittyerBnd(TruthBnd1, TruthBnd2);
var expected = BorderDistance.CreateFromVariant(query, truth);
MultiAssert.Equal(85U, expected.PosBorderLeft);
MultiAssert.Equal(117U, expected.PosBorderRight);
MultiAssert.Equal(72U, expected.EndBorderLeft);
MultiAssert.Equal(28U, expected.EndBorderRight);
MultiAssert.AssertAll();
}
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);
}
}
}
public static OverlapAnnotation Create(uint who, MatchEnum what, [CanBeNull] IInterval <uint> wow,
[NotNull] BorderDistance where, FailedReason why)
=> new OverlapAnnotation(who, what, wow, where, why);
