open $fh,"genome_pred_exons.bed";

use List::Util qw( min max );

while(<$fh>)
{
        chomp;
        @lh = split /\t/,$_;
        $ph{$lh[0]."\t".$lh[1]."\t".$lh[2]} .= $lh[3]."\t".$lh[4]."NNNNNN";
}

close($fh);

foreach $k(sort keys %ph)
{
        @c =  sort { $a <=> $b } split ("NNNNNN",$ph{$k});
        @g = ();
        foreach $m(@c)
        {
        	@r = split /\t/,$m;
        	if (@g == 0)
        	{
        		push @g, [$r[0]+0, $r[1]+0];
        		next;
			}
			else
			{
				for ($i = 0;$i <= $#g;$i++)
				{
					if(($r[0] + 0) <= ($g[$i][1] + 1))
					{
						$g[$i][0] = min($g[$i][0]+0, $r[0]+0);
						$g[$i][1] = max($g[$i][1]+0, $r[1]+0);
						last;
					}
					elsif ( $i == $#g )
					{
						push @g, [$r[0]+0, $r[1]+0];
						last;
					}
				} 
        	}
        }
}

print Dumper \@g;