private void WriteExon(ITranscriptRegion exon, IRequiredFields requiredFields, IGeneralAttributes attribs,
IInterval codingRegion)
{
_writer.WriteExonicRegion(exon, requiredFields, attribs, exon.Id, "exon");
WriteCds(codingRegion, exon, requiredFields, attribs);
WriteUtr(codingRegion, exon, requiredFields, attribs);
}
private void WriteCds(IInterval codingRegion, ITranscriptRegion exon, IRequiredFields requiredFields, IGeneralAttributes attribs)
{
if (!GffUtilities.HasCds(codingRegion, exon))
{
return;
}
var cds = GffUtilities.GetCdsCoordinates(codingRegion, exon);
_writer.WriteExonicRegion(cds, requiredFields, attribs, exon.Id, "CDS");
}
private void Write5PrimeUtr(IInterval codingRegion, ITranscriptRegion exon, IRequiredFields requiredFields,
IGeneralAttributes attribs)
{
int utrEnd = codingRegion.Start - 1;
if (utrEnd > exon.End)
{
utrEnd = exon.End;
}
_writer.WriteExonicRegion(new Interval(exon.Start, utrEnd), requiredFields, attribs, exon.Id, "UTR");
}
private void WriteGene(IGene gene, IRequiredFields requiredFields, string geneId, int internalGeneId)
{
if (_observedGenes.Contains(internalGeneId))
{
return;
}
_observedGenes.Add(internalGeneId);
var gffGene = GetGene(gene, geneId);
_writer.WriteGene(gffGene, requiredFields, internalGeneId);
}
private void WriteUtr(IInterval codingRegion, ITranscriptRegion exon, IRequiredFields requiredFields,
IGeneralAttributes attribs)
{
if (!GffUtilities.HasUtr(codingRegion, exon))
{
return;
}
if (exon.Start < codingRegion.Start)
{
Write5PrimeUtr(codingRegion, exon, requiredFields, attribs);
}
if (exon.End > codingRegion.End)
{
Write3PrimeUtr(codingRegion, exon, requiredFields, attribs);
}
}
private void WriteTranscript(IInterval interval, IRequiredFields requiredFields, IGeneralAttributes attribs) => _writer.WriteTranscript(interval, requiredFields, attribs);