/// <summary>
/// constructor
/// </summary>
public VariantEffect(TranscriptAnnotation ta, Transcript transcript, VariantType internalCopyNumberType = VariantType.unknown)
{
_ta = ta;
_transcript = transcript;
_altAllele = ta.AlternateAllele;
_preCache = new BasicVariantEffects(ta);
_cache = new VariantEffectCache();
_tempCache = new TempVariantEffectCache();
_featureVariantEffects = new FeatureVariantEffects(transcript, _altAllele.NirvanaVariantType,
_altAllele.Start, _altAllele.End, _altAllele.IsStructuralVariant, internalCopyNumberType);
}
/// <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);
}
