/// <summary>
/// constructor
/// </summary>
public FeatureVariantEffects(ReferenceAnnotationInterval feature, VariantType vt, int refBegin, int refEnd, bool isSV, VariantType internalCopyNumberType)
{
_isSV = isSV;
_completelyOverlaps = Overlap.Complete(feature.Start, feature.End, refBegin, refEnd);
_overlaps = Overlap.Partial(feature.Start, feature.End, refBegin, refEnd);
_completelyWithin = refBegin >= feature.Start && refEnd <= feature.End;
_lossOrDeletion = vt == VariantType.copy_number_loss || vt == VariantType.deletion || internalCopyNumberType == VariantType.copy_number_loss;
_gainOrDuplication = vt == VariantType.copy_number_gain || vt == VariantType.duplication ||
vt == VariantType.tandem_duplication || internalCopyNumberType == VariantType.copy_number_gain;
_isInsertionDeletion = vt == VariantType.indel;
_isInsertion = vt == VariantType.insertion;
}
