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>
/// CDS length (negative if there is none)
/// </summary>
/// <returns></returns>
public long GetCdsLength()
{
Transcript tr = GetTranscript();
return(tr != null && tr.IsProteinCoding() ?
tr.RetrieveCodingSequence().Count :
-1);
}
protected CodonChangeStructural(Variant variant, Transcript transcript, VariantEffects variantEffects)
: base(variant, transcript, variantEffects)
{
coding = transcript.IsProteinCoding(); // || Config.get().isTreatAllAsProteinCoding();
CountAffectedExons();
}
