while (<FILE>){
	my @line = split (/\t/,$_); ## tab separated file
	my @tmp = split(/\./,$line[1]); ## chromosome name in field 2, as part of a dot separated string
	$chr{"$tmp[1]"} =  new Set::IntervalTree() unless (defined $chr{"$tmp[1]"});
	$chr{"$tmp[1]"} -> insert($count,$line[2]-1,$line[3]+1); ## fields 3 and 4 contain the coordinates, -1 and +1 to allow search for direct overlaps at start and end
}

##</code><code>##

store (\%chr, "$file.coordinates") or die "Can't store %chr in file.coordinates!\n";

##</code><code>##

    my $hashref;
    %chr = %{$hashref = retrieve("$file.coordinates")};