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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 } } } ...
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.

In reply to Re^5: Comparing and getting information from two large files and appending it in a new file by graff
in thread Comparing and getting information from two large files and appending it in a new file by perlkhan77

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