Dear Cristoforo, When I ran the script I realized that I am too stringent about my selection criteria.

In the second file if $current_line3 >= 3 then the I need to fake around plus/minus 8 of the corresponding position to this line which is ($current_line1). So the condition would be find from file 2 those that $current_line3 >= 3 and it is OK to that ($current_line1)plus minus 8 matches with file 1.

I thought if I put($current_line1)+/- 8 in an array. then say if from file1 $position1 exists in this array it is OK.

If I am not clear please let me know to explain it more.

while(<INPUT2>){
         chomp;
          my @current_line  = split /\t/;
          # eliminate unqualified lines early
          next unless $current_line[2] == 1 && $current_line[3] >= 3;
          #$from = $current_line[1]-8;
          #$to = $current_line[1]+8;
              # for ($from .. $to){
              # push (@range, $_);
              #      }
              #}
        if ($file1{ $current_line[0]}) {
                ($from, $to) = @{ $file1{ $current_line[0] } };
                if ($from <= $current_line[1] && $current_line[1] <= $
+to) {

                print join("\t", $_, "***",$current_line[1]), "\n";


           $true_positives++;
            }
      }
}
[download]