/// <summary>
/// Junctions the name.
/// </summary>
/// <returns>The name.</returns>
/// <param name="exon1">Exon1.</param>
/// <param name="exon2">Exon2.</param>
public static string JunctionName(Location exon1, Location exon2)
{
if (exon1.Chromosome != exon2.Chromosome || exon1.Strand != exon2.Strand)
{
throw new Exception("Junction crossing chromosomes or strands requested");
}
if (exon1.Overlaps(exon2) || exon2.Overlaps(exon1))
{
throw new Exception("Overlapping exons");
}
if (exon1.Start > exon2.Start)
{
var v = exon1;
exon1 = exon2;
exon2 = v;
}
//if (exon1.Strand == "-")
//{
// return string.Format("{0}:{1}:{2}:{3}", exon1.Chromosome, exon2.End, exon1.Start, exon1.Strand);
//}
//else
//{
return(JunctionName(exon1.Chromosome, Math.Max(exon1.Start, exon1.End), Math.Min(exon2.Start, exon2.End) - 1, exon1.Strand));
}
public static bool Overlaps(Location l1, Location l2)
{
return(l1.Overlaps(l2));
}
