diff --git a/src/aln.cpp b/src/aln.cpp index de134dec..6d7cfb1f 100644 --- a/src/aln.cpp +++ b/src/aln.cpp @@ -100,7 +100,7 @@ static inline void align_SE( int min_mapq_diff = best_edit_distance; for (auto &nam : nams) { float score_dropoff = (float) nam.n_hits / n_max.n_hits; - if (tries >= max_tries || best_edit_distance == 0 || score_dropoff < dropoff_threshold) { + if (tries >= max_tries || (max_tries > 1 && best_edit_distance == 0) || score_dropoff < dropoff_threshold) { break; } bool consistent_nam = reverse_nam_if_needed(nam, read, references, k);