/// <summary>
/// Calculate base number in a cds where 'pos' is
/// </summary>
/// <param name="pos"></param>
/// <returns></returns>
protected long CdsBaseNumber(long pos)
{
long cdsbn = Transcript.BaseNumberCds(pos, true);
// Does not intersect the transcript?
if (cdsbn < 0)
{
// 'pos' before transcript start
if (pos <= Transcript.CdsOneBasedStart)
{
if (Transcript.IsStrandPlus())
{
return(0);
}
return(Transcript.RetrieveCodingSequence().Count);
}
// 'pos' is after CDS end
if (Transcript.IsStrandPlus())
{
return(Transcript.RetrieveCodingSequence().Count);
}
return(0);
}
return(cdsbn);
}
private long cdsBaseNumber(long pos, bool usePrevBaseIntron)
{
if (pos < cdsStart)
{
return(Transcript.IsStrandPlus() ? 0 : Transcript.RetrieveCodingSequence().Count - 1);
}
if (pos > cdsEnd)
{
return(Transcript.IsStrandPlus() ? Transcript.RetrieveCodingSequence().Count - 1 : 0);
}
return(Transcript.BaseNumberCds(pos, usePrevBaseIntron));
}
