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