protected void ApplyDup(Variant variant, IntervalSequence markerSeq)
{
// Get sequence in positive strand direction
ISequence seq = IsStrandPlus() ? Sequence : Sequence.GetReverseComplementedSequence();
// Apply duplication to sequence
String dupSeq = SequenceExtensions.ConvertToString(GetSequence(Intersect(variant)));
long idx = variant.OneBasedStart - OneBasedStart - 1;
if (idx >= 0)
{
seq = new Sequence(seq.Alphabet, SequenceExtensions.ConvertToString(seq, 0, idx + 1) + dupSeq + SequenceExtensions.ConvertToString(seq, idx + 1));
}
else
{
seq = new Sequence(seq.Alphabet, dupSeq + SequenceExtensions.ConvertToString(seq));
}
// Update sequence
markerSeq.Sequence = IsStrandPlus() ? seq : seq.GetReverseComplementedSequence();
}
protected void ApplyIns(Variant variant, IntervalSequence markerSeq)
{
// Get sequence in positive strand direction
ISequence seq = IsStrandPlus() ? Sequence : Sequence.GetReverseComplementedSequence();
// Apply change to sequence
String netChange = variant.NetChange(this);
long idx = variant.OneBasedStart - OneBasedStart - 1;
if (idx >= 0)
{
seq = new Sequence(seq.Alphabet, SequenceExtensions.ConvertToString(seq, 0, idx + 1) + netChange + SequenceExtensions.ConvertToString(seq, idx + 1));
}
else
{
seq = new Sequence(seq.Alphabet, netChange + SequenceExtensions.ConvertToString(seq));
}
// Update sequence
markerSeq.Sequence = IsStrandPlus() ? seq : seq.GetReverseComplementedSequence();
}
protected void ApplyDel(Variant variant, IntervalSequence markerSeq)
{
// Get sequence in positive strand direction
ISequence seq = IsStrandPlus() ? Sequence : Sequence.GetReverseComplementedSequence();
// Apply change to sequence
long idxStart = variant.OneBasedStart - OneBasedStart;
long idxEnd = idxStart + variant.Length();
StringBuilder newSeq = new StringBuilder();
if (idxStart >= 0)
{
newSeq.Append(SequenceExtensions.ConvertToString(seq, 0, idxStart));
}
if (idxEnd >= 0 && idxEnd < seq.Count)
{
newSeq.Append(SequenceExtensions.ConvertToString(seq));
}
// Update sequence
seq = new Sequence(seq.Alphabet, newSeq.ToString());
markerSeq.Sequence = IsStrandPlus() ? seq : seq.GetReverseComplementedSequence();
}
/// <summary>
/// Apply a variant to this exon interval and sequence
/// </summary>
/// <param name="variant"></param>
/// <returns></returns>
public override Interval ApplyVariant(Variant variant)
{
IntervalSequence i = base.ApplyVariant(variant) as IntervalSequence;
return(new Exon(i.Parent as Transcript, i.Sequence, i.Source, i.OneBasedStart, i.OneBasedEnd, i.ChromosomeID, i.Strand, i.Variants, FeatureMetadata));
}
