public void Annotate_Promoter()
{
var variant = GetVariant();
var regulatoryRegion = GetRegulatoryRegion();
const ConsequenceTag expectedConsequence = ConsequenceTag.regulatory_region_variant;
var annotatedRegulatoryRegion = RegulatoryRegionAnnotator.Annotate(variant, regulatoryRegion);
var consequences = annotatedRegulatoryRegion.Consequences.ToList();
Assert.NotNull(annotatedRegulatoryRegion);
Assert.Single(consequences);
Assert.Equal(expectedConsequence, consequences[0]);
}
private void AddRegulatoryRegions(IAnnotatedPosition annotatedPosition)
{
var overlappingRegulatoryRegions = _transcriptCache.GetOverlappingRegulatoryRegions(annotatedPosition.Position);
if (overlappingRegulatoryRegions == null)
{
return;
}
foreach (var annotatedVariant in annotatedPosition.AnnotatedVariants)
{
// In case of insertions, the base(s) are assumed to be inserted at the end position
// if this is an insertion just before the beginning of the regulatory element, this takes care of it
var variant = annotatedVariant.Variant;
var variantEnd = variant.End;
var variantBegin = variant.Type == VariantType.insertion ? variant.End : variant.Start;
// disable regulatory region for SV larger than 50kb
if (variantEnd - variantBegin + 1 > MaxSvLengthForRegulatoryRegionAnnotation)
{
continue;
}
foreach (var regulatoryRegion in overlappingRegulatoryRegions)
{
if (!variant.Overlaps(regulatoryRegion))
{
continue;
}
// if the insertion is at the end, its past the feature and therefore not overlapping
if (variant.Type == VariantType.insertion && variantEnd == regulatoryRegion.End)
{
continue;
}
annotatedVariant.RegulatoryRegions.Add(RegulatoryRegionAnnotator.Annotate(variant, regulatoryRegion));
}
}
}
private static void AddRegulatoryRegions(IAnnotatedVariant[] annotatedVariants, IIntervalForest <IRegulatoryRegion> regulatoryIntervalForest)
{
foreach (var annotatedVariant in annotatedVariants)
{
if (!annotatedVariant.Variant.Behavior.NeedRegulatoryRegions)
{
continue;
}
// In case of insertions, the base(s) are assumed to be inserted at the end position
// if this is an insertion just before the beginning of the regulatory element, this takes care of it
var variant = annotatedVariant.Variant;
int variantBegin = variant.Type == VariantType.insertion ? variant.End : variant.Start;
if (SkipLargeVariants(variantBegin, variant.End))
{
continue;
}
IRegulatoryRegion[] regulatoryRegions =
regulatoryIntervalForest.GetAllOverlappingValues(variant.Chromosome.Index, variantBegin,
variant.End);
if (regulatoryRegions == null)
{
continue;
}
foreach (var regulatoryRegion in regulatoryRegions)
{
// if the insertion is at the end, its past the feature and therefore not overlapping
if (variant.Type == VariantType.insertion && variant.End == regulatoryRegion.End)
{
continue;
}
annotatedVariant.RegulatoryRegions.Add(RegulatoryRegionAnnotator.Annotate(variant, regulatoryRegion));
}
}
}