BUG: Empty samples (#167)

q2_dada2/_denoise.py

@@ -172,11 +172,13 @@ def _denoise_helper(biom_fp, track_fp, hashed_feature_ids, retain_all_samples,
     # Reintroduce empty samples dropped by dada2.
     table_cols = table.ids(axis='observation')
     table_rows = list(set(df.index) - set(table.ids()))
-    table_to_add = biom.Table(np.zeros((len(table_cols), len(table_rows))),
-                              table_cols, table_rows,
-                              type="OTU table")
-    table = table.concat(table_to_add)
-    # This is necissary (instead of just not reintroducing above)
+
+    # We only want to do this if something was actually dropped
+    if table_rows:
+        table_to_add = biom.Table(np.zeros((len(table_cols), len(table_rows))),
+                                  table_cols, table_rows, type="OTU table")
+        table = table.concat(table_to_add)
+    # This is necessary (instead of just not reintroducing above)
     # dada2 will discard samples which are empty after filtering
     # but will keep samples that are empty after merging
     # so there are potentially samples removed here that were not