tax threshold arg from #1788

sourmash-bio · Apr 27, 2022 · 4e2d43b · 4e2d43b
1 parent 940866d
commit 4e2d43b
Showing 1 changed file with 7 additions and 3 deletions.
diff --git a/src/sourmash/cli/utils.py b/src/sourmash/cli/utils.py
@@ -67,10 +67,14 @@ def range_limited_float_type(arg):
     return f
 
 
-def add_tax_threshold_arg(parser, default=0.1):
+def add_tax_threshold_arg(parser, containment_default=0.1, ani_default=None):
     parser.add_argument(
-        '--containment-threshold', default=default, type=range_limited_float_type,
-        help=f'minimum containment threshold for classification; default={default}'
+        '--containment-threshold', default=containment_default, type=range_limited_float_type,
+        help=f'minimum containment threshold for classification; default={containment_default}',
+    )
+    parser.add_argument(
+        '--ani-threshold', '--aai-threshold', default=ani_default, type=range_limited_float_type,
+        help=f'minimum ANI threshold (nucleotide gather) or AAI threshold (protein gather) for classification; default={ani_default}',
     )