for (keys %clone_hash) {
    my $gcnt = (exists $clone_hash{$_}{good}) ? $clone_hash{$_}{good} : 0;
    my $bcnt = (exists $clone_hash{$_}{bad} ) ? $clone_hash{$_}{bad}  : 0;
    print $out "$_\t$gcnt\t$bcnt";
}