/// <summary>
/// Creates UTRs for transcripts and intergenic regions after reading gene model
/// </summary>
public void CreateIntergenicRegions()
{
foreach (IntervalTree it in GenomeForest.Forest.Values)
{
Gene previousPositiveStrandGene = null;
Gene previousNegativeStrandGene = null;
// Create intergenic regions on each strand
foreach (Gene gene in it.Intervals.OfType <Gene>().OrderBy(g => g.OneBasedStart))
{
Intergenic intergenic = null;
Gene previous = gene.IsStrandPlus() ? previousPositiveStrandGene : previousNegativeStrandGene;
if (previous != null)
{
// if there's a previous gene, create the intergenic region
intergenic = new Intergenic(gene.Chromosome, gene.ChromosomeID, gene.Source, gene.Strand, previous.OneBasedEnd + 1, gene.OneBasedStart - 1, null);
}
// store previous genes on each strand
if (gene.IsStrandPlus())
{
previousPositiveStrandGene = gene;
}
if (gene.IsStrandMinus())
{
previousNegativeStrandGene = gene;
}
// add the intergenic region to the genome forest if it was created
if (intergenic != null && intergenic.Length() > 0)
{
GenomeForest.Add(intergenic);
}
}
}
}
public Intergenic(Intergenic intergenic) : base(intergenic)
{
}
