public override bool CreateVariantEffect(Variant variant, VariantEffects variantEffects)
{
if (!Intersects(variant))
{
return(false);
}
//for (SpliceSite ss : spliceSites)
// if (ss.intersects(variant)) ss.variantEffect(variant, variantEffects);
// Add intron part
variantEffects.AddEffectType(variant, this, EffectType.INTRON);
return(true);
}
public override bool CreateVariantEffect(Variant variant, VariantEffects variantEffects)
{
if (!Intersects(variant))
{
return(false);
}
if (variant.Includes(this) && variant.VarType == Variant.VariantType.DEL)
{
variantEffects.AddEffectType(variant, this, EffectType.UTR_3_DELETED); // A UTR was removed entirely
return(true);
}
Transcript tr = (Transcript)FindParent(typeof(Transcript));
long distance = utrDistance(variant, tr);
VariantEffect variantEffect = new VariantEffect(variant);
variantEffect.Set(this, EffectType.UTR_3_PRIME, EffectTypeMethods.EffectDictionary[EffectType.UTR_3_PRIME], distance >= 0 ? distance + " bases from CDS" : "");
variantEffect.Distance = distance;
variantEffects.AddEffect(variantEffect);
return(true);
}