/// <summary>
/// Add variants to relevant genomic regions and annotate them if on transcripts
/// </summary>
/// <param name="variants"></param>
public void AddVariantAnnotations(List <Variant> variants)
{
Parallel.ForEach(variants.OrderByDescending(v => v.OneBasedStart).ToList(), v =>
{
if (GenomeForest.Forest.TryGetValue(Chromosome.GetFriendlyChromosomeName(v.ChromosomeID), out var intervalTree))
{
foreach (Interval i in intervalTree.Stab(v.OneBasedStart))
{
lock (i)
{
i.Variants.Add(v);
Transcript t = i as Transcript;
if (t != null)
{
t.AnnotateWithVariant(v);
}
}
}
}
});
PreviouslyAddedVariants = variants;
}
