test.boa

s: Sequence = input;
counts: output sum[int] of int;

# iterates over all clusters and if that sequence is rep, then if tax_name is not null emits 1 to the reducer
 foreach(i:int; def(s.cluster[i])){
  if (s.cluster[i].representative){
    foreach(j:int; def(s.annotation[j])){
      if (s.annotation[j].tax_name !="")
    	counts[s.cluster[i].similarity] << 1;
    }
   }
 };