/// <summary>
/// Codon change string (if it's not too long)
/// </summary>
/// <returns></returns>
public string GetCodonChangeMax()
{
if (Variant.Length() > MAX_CODON_SEQUENCE_LEN)
{
return("");
} // Cap length in order not to make VCF files grow too much
if (CodonsRef == "" && CodonsAlt == "")
{
return("");
}
return(CodonsRef + "/" + CodonsAlt);
}
/// <summary>
/// We may have to calculate 'netCdsChange', which is the effect on the CDS.
/// Note: A deletion or a MNP might affect several exons
/// </summary>
/// <returns></returns>
protected override string NetCdsChange()
{
if (Variant.Length() > 1)
{
StringBuilder sb = new StringBuilder();
foreach (Exon exon in Transcript.ExonsSortedStrand)
{
string seq = Variant.NetChange(exon);
sb.Append(exon.IsStrandPlus() ? seq : SequenceExtensions.ConvertToString(new Sequence(Alphabets.AmbiguousDNA, seq).GetReverseComplementedSequence()));
}
return(sb.ToString());
}
return(Variant.NetChange(Transcript.IsStrandPlus()));
}
/// <summary>
/// We may have to calculate 'netCdsChange', which is the effect on the CDS.
/// Note: A deletion or a MNP might affect several exons
/// </summary>
/// <returns></returns>
protected virtual string NetCdsChange()
{
if (!RequireNetCdsChange)
{
return("");
}
if (Variant.Length() > 1)
{
StringBuilder sb = new StringBuilder();
foreach (Exon exon in Transcript.ExonsSortedStrand)
{
sb.Append(Variant.NetChange(exon));
}
return(sb.ToString());
}
return(Variant.NetChange(Transcript.IsStrandMinus()));
}
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();
}