To find a maximum, you can use List::Util.

The following code returns "$chr $begin $end $class" if the class has the maximal total, or 'undefined' instead of the class number if there are more classes having the same maximum. Tweak it to serve your needs:

#!/usr/bin/perl
use warnings;
use strict;
use List::Util qw/max/;

<>; # skip header
for my $line (<>){
    my ($chr, $nr, $begin, $end, @values) = split ' ', $line;

    my %total;
    while (@values) {
        my $class = shift @values;
        my $total = shift @values;
        $total{$class} = $total;
    }
    my $max = max values %total;
    my @maxes = grep $total{$_} == $max, keys %total;
    if (@maxes == 1) {
        print "$chr $begin $end $maxes[0]\n";
    } else {
        print "$chr $begin $end undefined\n";
    }
}
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