private static GenomeIntervalTree <IContigAndInterval> CreateGenomeIntervalTree(
[NotNull] IEnumerable <IContigAndInterval> contigIntervals)
{
var dictionary = new Dictionary <IContigInfo, MergedIntervalTree <uint> >();
var listOrder = new List <IContigInfo>();
foreach (var contigInterval in contigIntervals)
{
if (!dictionary.TryGetValue(contigInterval.Contig, out var tree))
{
tree = MergedIntervalTree <uint> .Create(null);
listOrder.Add(contigInterval.Contig);
dictionary.Add(contigInterval.Contig, tree);
}
tree.Add(contigInterval);
}
var ret = GenomeIntervalTree <IContigAndInterval> .Create();
foreach (var contig in listOrder)
{
ret.AddRange(dictionary[contig]
.Select(i => i as IContigAndInterval ?? ContigAndInterval.Create(contig, i.Start, i.Stop)));
}
return(ret);
}
internal static TruthForest CreateEmpty(string sampleName)
{
//create empty tree for each supported type. So when we do search it won't be key not found
var dict = new ConcurrentDictionary <WittyerVariantType, GenomeIntervalTree <IWittyerSimpleVariant> >();
foreach (var type in WittyerConstants.SupportedSvType)
{
dict.AddOrUpdate(type, GenomeIntervalTree <IWittyerSimpleVariant> .Create(),
(k, old) => GenomeIntervalTree <IWittyerSimpleVariant> .Create());
}
return(new TruthForest(dict, new List <IVcfVariant>(), sampleName));
}
/// <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 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)}!");
}
}
/// <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 void AddVariantToTrees(IWittyerSimpleVariant variant)
{
var tree = _trees.GetOrAdd(variant.VariantType, GenomeIntervalTree <IWittyerSimpleVariant> .Create());
tree.Add(variant);
}
private IncludeBedFile([NotNull] GenomeIntervalTree <IContigAndInterval> tree,
[NotNull] Lazy <FileInfo> fileSource)
{
IntervalTree = tree;
_fileSource = fileSource;
}
