sub addregion 
{
    my ($start,$end) = @_;
    if ($start > $end)
    {
        ($start,$end) = ($end,$start);
    }
    my $done = 0;
    my $k;
    my $tempcoding = 0;

    for ($k=0;$k<@nreg;$k++)
    {
        # calculate sum of bases
        $tempcoding += $nreg[$k][1] - $nreg[$k][0] + 1;

        # new region starts after old region ends
        next if ($nreg[$k][1] < $start);

        # new region ends before old region starts
        if ($end < $nreg[$k][0])
        {
            splice(@nreg,$k,0,[$start,$end]);
            $done = 1;
            last;
        }

        # regions overlap
        $nreg[$k][0] = $start < $nreg[$k][0] ? $start : $nreg[$k][0];
        $nreg[$k][1] = $end > $nreg[$k][1] ? $end : $nreg[$k][1];
        $done = 1;

        # Combine two regions if the new section has brough about an overlap
        while ($k < $#nreg and $nreg[$k][1] > $nreg[$k+1][0])
        {
            $nreg[$k][1] = $nreg[$k+1][1];
            splice(@nreg,$k+1,1);
        }
        last;
    }
    unless ($done)
    {
        push @nreg,[$start,$end];
    }
}