/// <summary> /// determines the regulatory region variant's functional consequence /// </summary> public void DetermineRegulatoryVariantEffects(ReferenceAnnotationInterval feature, VariantType vt, int refBegin, int refEnd, bool isSv, VariantType internalCopyNumberType) { var regulatoryVariantEffects = new FeatureVariantEffects(feature, vt, refBegin, refEnd, isSv, internalCopyNumberType); // RegulatoryRegionAmplification if (regulatoryVariantEffects.Amplification()) { _consequences.Add(ConsequenceType.RegulatoryRegionAmplification); } // RegulatoryRegionAblation if (regulatoryVariantEffects.Ablation()) { _consequences.Add(ConsequenceType.RegulatoryRegionAblation); } // RegulatoryRegionVariant _consequences.Add(ConsequenceType.RegulatoryRegionVariant); }
// ============================================================== // These calls are already mostly cached by FeatureVariantEffects // ============================================================== /// <summary> /// returns true if the variant ablates the transcript [VariationEffect.pm:262 feature_ablation] /// </summary> public bool HasTranscriptAblation() { return(_featureVariantEffects.Ablation()); }