Beispiel #1
0
        /// <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);
        }
Beispiel #2
0
 /// <summary>
 /// returns true if the variant amplifies the transcript [VariationEffect.pm:269 feature_amplification]
 /// </summary>
 public bool HasTranscriptAmplification()
 {
     return(_featureVariantEffects.Amplification());
 }