/// <summary>
/// Did we gain a start codon in this 5'UTR interval?
/// </summary>
/// <param name="seqChange"></param>
/// <returns>A new start codon (if gained)</returns>
private string startGained(Variant seqChange)
{
if (!seqChange.isSnv())
{
return("");
} // Only SNPs supported.
// Calculate SNP position relative to UTRs
long pos = seqChange.DistanceBases(get5primeUtrs().OfType <Interval>().ToList(), IsStrandMinus());
// Change base at SNP position
string sequence = getSequence();
char[] chars = sequence.ToCharArray();
char snpBase = seqChange.NetChange(this)[0];
if (IsStrandMinus() && Alphabets.DNA.TryGetComplementSymbol((byte)snpBase, out byte complement))
{
snpBase = (char)complement;
}
chars[pos] = snpBase;
// Do we gain a new start codon?
return(startGained(chars, pos));
}
