protected void ApplyMnp(Variant variant, IntervalSequence markerSeq)
{
// Calculate indexes
long idxStart = variant.OneBasedStart - OneBasedStart;
long idxAlt = 0;
// Variant starts before this marker (e.g. motif with sequence)
if (idxStart < 0)
{
idxAlt = -idxStart; // Remove first 'idxStart' bases from ALT sequence
idxStart = 0;
}
long changeSize = variant.IntersectSize(this);
long idxEnd = idxStart + changeSize;
// Apply variant to sequence
ISequence seq = IsStrandPlus() ? Sequence : Sequence.GetReverseComplementedSequence();
StringBuilder seqsb = new StringBuilder();
seqsb.Append(SequenceExtensions.ConvertToString(seq, 0, idxStart));
String seqAlt = variant.SecondAlleleString.Substring((int)idxAlt, (int)changeSize);
seqsb.Append(seqAlt);
seqsb.Append(SequenceExtensions.ConvertToString(seq, idxEnd));
// Update sequence
seq = new Sequence(seq.Alphabet, seqsb.ToString());
markerSeq.Sequence = IsStrandPlus() ? seq : seq.GetReverseComplementedSequence();
}
/// <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);
}