/// <summary>
/// One or more exons fully included (no partial overlap)
/// </summary>
private void exons()
{
Interval cdsMarker = null;
if (Transcript.IsProteinCoding())
{
cdsMarker = Transcript.CdsMarker();
}
foreach (Exon ex in Transcript.Exons)
{
if (Variant.Intersects(ex))
{
EffectImpact impact = EffectImpact.LOW;
// Is the variant affecting a coding part of the exon?
// If so, then this is a HIGH impact effect.
if (cdsMarker != null && Variant.Intersect(ex).Intersects(cdsMarker))
{
impact = EffectImpact.HIGH;
}
// Is the whole exon inverted or just part of it?
EffectType effType = Variant.Includes(ex) ? EffectType.EXON_INVERSION : EffectType.EXON_INVERSION_PARTIAL;
EffectNoCodon(ex, effType, impact);
}
}
}
