Merge pull request #211 from golobor/master

pairtools dedup: turn mark-dups on by default
open2c · Mar 17, 2024 · b3c2ce3 · b3c2ce3
2 parents 91b40fd + 79afb1e
commit b3c2ce3
Showing 1 changed file with 4 additions and 3 deletions.
diff --git a/pairtools/cli/dedup.py b/pairtools/cli/dedup.py
@@ -139,10 +139,11 @@
 
 ### Output options:
 @click.option(
-    "--mark-dups",
+    "--mark-dups/--no-mark-dups",
+    default=True,
     is_flag=True,
-    help='If specified, duplicate pairs are marked as DD in "pair_type" and '
-    "as a duplicate in the sam entries. [output format option]",
+    help='Specify if duplicate pairs should be marked as DD in "pair_type" and '
+    "as a duplicate in the sam entries. True by default. [output format option]",
 )
 @click.option(
     "--keep-parent-id",