/// <summary>
/// Apply a Variant to a marker. Variant is a duplication
/// </summary>
/// <param name="variant"></param>
/// <returns></returns>
protected Interval ApplyDup(Variant variant)
{
Interval m = new Interval(this);
if (variant.OneBasedEnd < m.OneBasedStart)
{
// Duplication before marker start? => Adjust both coordinates
long lenChange = variant.LengthChange();
m.OneBasedStart += lenChange;
m.OneBasedEnd += lenChange;
}
else if (variant.Includes(m))
{
// Duplication includes whole marker? => Adjust both coordinates
long lenChange = variant.LengthChange();
m.OneBasedStart += lenChange;
m.OneBasedEnd += lenChange;
}
else if (m.Includes(variant))
{
// Duplication included in marker? => Adjust end coordinate
m.OneBasedEnd += variant.LengthChange();
}
else if (variant.Intersects(m))
{
// Duplication includes part of marker? => Adjust end
m.OneBasedEnd += variant.IntersectSize(m);
}
else
{
// Duplication after end, no effect on marker coordinates
}
return(m);
}
/// <summary>
/// Does the variant intersect any exons?
/// </summary>
/// <returns></returns>
protected bool IntersectsExons()
{
foreach (Exon ex in Transcript.Exons)
{
if (Variant.Intersects(ex))
{
return(true);
}
}
return(false);
}
/// <summary>
/// How many full / partial exons does the variant affect?
/// </summary>
protected void CountAffectedExons()
{
exonFull = 0;
exonPartial = 0;
foreach (Exon ex in Transcript.Exons)
{
if (Variant.Includes(ex))
{
exonFull++;
}
else if (Variant.Intersects(ex))
{
exonPartial++;
}
}
}
/// <summary>
/// Do something with a variant within this interval
/// </summary>
/// <param name="variant"></param>
public override Interval ApplyVariant(Variant variant)
{
IntervalSequence newIntervalSeq = new IntervalSequence(base.ApplyVariant(variant), new Sequence(Sequence)); // adds the variant to the variant list
if (variant.Intersects(this) && Sequence != null && Sequence.Count != 0)
{
switch (variant.VarType)
{
case Variant.VariantType.SNV:
ApplySnp(variant, newIntervalSeq);
break;
case Variant.VariantType.INS:
ApplyIns(variant, newIntervalSeq);
break;
case Variant.VariantType.DEL:
ApplyDel(variant, newIntervalSeq);
break;
case Variant.VariantType.DUP:
ApplyDup(variant, newIntervalSeq);
break;
case Variant.VariantType.MNV:
ApplyMnp(variant, newIntervalSeq);
break;
case Variant.VariantType.MIXED:
// When applying a MIXED variant, it is decomposed into two
// variants (MNP+InDel) and each of them is applied to the
// marker. So at this point the variants have been fully
// applied and there is no need for further processing.
break;
default:
throw new ArgumentException("Unimplemented method for variant change type " + variant.VarType + "\n\tVariant: " + variant);
}
}
return(newIntervalSeq);
}
/// <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);
}