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 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 direc
+t overlaps at start and end
}

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

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