public override bool CreateVariantEffect(Variant variant, VariantEffects variantEffects)
{
// Has the whole UTR been deleted?
if (variant.Includes(this) && variant.VarType == Variant.VariantType.DEL)
{
variantEffects.AddEffect(variant, this, EffectType.UTR_5_DELETED, ""); // A UTR was removed entirely
return(true);
}
// Add distance
Transcript tr = (Transcript)FindParent(typeof(Transcript));
long distance = utrDistance(variant, tr);
VariantEffect variantEffect = new VariantEffect(variant);
variantEffect.Set(this, IntervalType, EffectTypeMethods.EffectDictionary[IntervalType], distance >= 0 ? distance + " bases from TSS" : "");
variantEffect.Distance = distance;
variantEffects.AddEffect(variantEffect);
// Start gained?
string gained = startGained(variant);
if (gained != "")
{
variantEffects.AddEffect(variant, this, EffectType.START_GAINED, gained);
}
return(true);
}
/// <summary>
/// Add an effect
/// </summary>
/// <param name="marker"></param>
/// <param name="effectType"></param>
/// <param name="effectImpact"></param>
/// <param name="codonsOld"></param>
/// <param name="codonsNew"></param>
/// <param name="codonNum"></param>
/// <param name="codonIndex"></param>
/// <param name="allowReplace"></param>
/// <returns></returns>
private VariantEffect Effect(Interval marker, EffectType effectType, EffectImpact effectImpact, string codonsOld, string codonsNew, int codonNum, int codonIndex, bool allowReplace)
{
// Create and add variant affect
long cDnaPos = Transcript.BaseNumber2MRnaPos(Variant.OneBasedStart);
VariantEffect varEff = new VariantEffect(Variant, marker, effectType, effectImpact, codonsOld, codonsNew, codonNum, codonIndex, cDnaPos);
VariantEffects.AddEffect(varEff);
// Are there any additional effects? Sometimes a new effect arises from setting codons (e.g. FRAME_SHIFT disrupts a STOP codon)
EffectType addEffType = AdditionalEffect(codonsOld, codonsNew, codonNum, codonIndex);
if (addEffType != EffectType.NONE && addEffType != effectType)
{
if (allowReplace && addEffType.CompareTo(effectType) < 0)
{
// Replace main effect (using default impact)
varEff.SetEffect(addEffType);
}
else
{
// Add effect to list (using default impact)
varEff.AddEffect(addEffType);
}
}
return(varEff);
}
public override bool CreateVariantEffect(Variant variant, VariantEffects variantEffects)
{
if (!Intersects(variant))
{
return(false);
}
Transcript tr = (Transcript)Parent;
bool coding = tr.IsProteinCoding();
// Different analysis for coding or non-coding
bool exonAnnotated = false;
if (!coding || variant.isInterval() || !variant.isVariant())
{
// Non-coding or non-variant? Just annotate as 'exon'
variantEffects.AddEffect(variant, this, EffectType.EXON, "");
exonAnnotated = true;
}
else if (tr.IsCds(variant))
{
// Is it a coding transcript and the variant is within the CDS?
// => We need codon analysis
CodonChange codonChange = CodonChange.Factory(variant, tr, variantEffects);
codonChange.ChangeCodon();
exonAnnotated = true;
}
// Any splice site effect to add?
//for (SpliceSite ss : spliceSites)
// if (ss.intersects(variant)) ss.variantEffect(variant, variantEffects);
return(exonAnnotated);
}
/// <summary>
/// Calculate the effect of this variant
/// </summary>
/// <param name="variant"></param>
/// <param name="variantEffects"></param>
/// <returns></returns>
public virtual bool CreateVariantEffect(Variant variant, VariantEffects variantEffects)
{
if (!Intersects(variant))
{
return(false);
}
variantEffects.AddEffect(variant, this, IntervalType, "");
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);
}