Fix regression in filter_alignments

meteor/counter.py

@@ -158,14 +158,14 @@ def filter_alignments(
             if prev_score == score:
                 # add the genes to the list if it doesn't exist
                 reads[read_id].append(element)
-                genes[read_id].append(int(read_id))
+                genes[read_id].append(int(element.reference_name))
             # case new score is higher
             elif prev_score < score:
                 # set the new score
                 tmp_score[read_id] = score
                 # We keep the new score and forget the previous one
                 reads[read_id] = [element]
-                genes[read_id] = [int(read_id)]
+                genes[read_id] = [int(element.reference_name)]
         return reads, genes
 
     def uniq_from_mult(