Re^5: Comparing and getting information from two large files and appending it in a new file

To get one line of output for every line in your first input file, there's few changes.

...
my %methrange;
my %methhash;  # this line had been further down in my prev.version, j
+ust move it up
...
    if ( /^\s*Gm10/ ) {
        my ( $bgn, $end, $methcount ) = (split)[3,4,10];
        $methrange{$bgn}{$end}{$_} = undef;
        $methhash{$_}(methcount} = $methcount; # moved up from below
    }
...
            for my $end ( keys %{$methrange{$bgn}} ) {
                if ( $position <= $end ) {
                    for my $match ( keys %{$methrange{$bgn}{$end}} ) {
                        $methhash{$match}{$class}++;  # methcount was 
+moved from here
                    }
                }
            }
 ...
[download]

As for the benchmark, you said that your OP version "took forever". Was "forever" more than an hour and a half? (Did my version yield any improvement at all?) Do you have specific constraints about how much time can be taken up by a single run? If not, I'd say focus more on making sure the output is correct, rather than how long it takes to produce the output.

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