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)
{
var contig = contigInterval.Contig;
if (!dictionary.TryGetValue(contig, out var tree))
{
tree = MergedIntervalTree <uint> .Create(null);
listOrder.Add(contig);
dictionary.Add(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)));
var other = contig.ToUcscStyle();
if (other.Name == contig.Name)
{
other = contig.ToGrchStyle();
}
if (other.Name != contig.Name)
{
ret.AddRange(dictionary[contig]
.Select(i => ContigAndInterval.Create(other, i.Start, i.Stop)));
}
}
return(ret);
}
internal void AddVariantToTrees(IWittyerSimpleVariant variant)
{
var tree = _trees.GetOrAdd(variant.VariantType, GenomeIntervalTree <IWittyerSimpleVariant> .Create());
tree.Add(variant);
}