/// <summary>
/// Deletion analysis using full transcript information. This is done only when the variant affects more than one exons.
/// </summary>
protected override void Exons()
{
if (exonFull == 0 && exonPartial == 1)
{
// Variant partially affects only one exon?
// => Use the standard (by exon) method
codonChangeSuper();
return;
}
else if (exonFull > 0)
{
// Full exons deleted
ExonLoss();
// Only whole exons deleted? We are done
if (exonPartial == 0)
{
return;
}
}
//---
// A combination of partial and full exons affected
//---
CodonsRefAlt();
EffectType effType;
int lenDiff = cdsAlt.Length - cdsRef.Length;
if (lenDiff % CODON_SIZE != 0)
{
effType = EffectType.FRAME_SHIFT;
}
else if (CodonStartIndex == 0)
{
effType = EffectType.CODON_DELETION;
}
else
{
if (CodonsAlternate == "" || CodonsReference.StartsWith(CodonsAlternate))
{
effType = EffectType.CODON_DELETION;
}
else
{
effType = EffectType.CODON_CHANGE_PLUS_CODON_DELETION;
}
}
// Assign to first exon
foreach (Exon ex in Transcript.Exons)
{
if (Variant.Includes(ex) || Variant.Intersects(ex))
{
Exon = ex;
break;
}
}
// Add variant effect
Effect(Exon, effType, false);
}
