/// <summary>
/// Find the last position before 'pos' within an exon
/// </summary>
/// <param name="pos"></param>
/// <returns></returns>
private long LastExonPositionBefore(long pos)
{
long last = -1;
foreach (Exon ex in Exons.OrderBy(x => x.OneBasedStart))
{
if (pos < ex.OneBasedStart)
{
// Nothing found?
if (last < 0)
{
Console.WriteLine("WARNING: Cannot find last exonic position before " + pos + " for transcript '" + ID + "'");
return(-1);
}
return(last);
}
else if (pos <= ex.OneBasedEnd)
{
return(pos);
}
last = ex.OneBasedEnd;
}
if (last < 0)
{
Console.WriteLine("WARNING: Cannot find last exonic position before " + pos + " for transcript '" + ID + "'");
}
return(pos);
}
/// <summary>
/// Find the first position after 'pos' within an exon
/// </summary>
/// <param name="pos"></param>
/// <returns></returns>
private long FirstExonPositionAfter(long pos)
{
foreach (Exon ex in Exons.OrderBy(x => x.OneBasedStart))
{
if (pos <= ex.OneBasedStart)
{
return(ex.OneBasedStart);
}
if (pos <= ex.OneBasedEnd)
{
return(pos);
}
}
Console.WriteLine("WARNING: Cannot find first exonic position after " + pos + " for transcript '" + ID + "'");
return(-1);
}
