while(){ chomp; my @current_line = split /\t/; # eliminate unqualified lines early next unless $current_line[2] ==1 && $current_line[3] >= 3; if ($file1{ $current_line[0]}) { my ($lo, $hi) = @{ $file1{ $current_line[0] } }; if ($lo <= $current_line[1] && $current_line[1] <= $hi) { print join("\t", $_, "***", $current_line[1]), "\n"; } } } close (INPUT2);