untested... 
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";
}

[download]

Update: removed erroneous "exists"

In reply to Re^5: processing key value pairs of a hash by toolic
in thread processing key value pairs of a hash by lomSpace

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