...
my %methrange;
my %methhash;  # this line had been further down in my prev.version, just 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
                    }
                }
            }
 ...