From 79afb1e26dc700826ce1bd1949afbf4b5f7d5836 Mon Sep 17 00:00:00 2001
From: Anton Goloborodko <goloborodko.anton@gmail.com>
Date: Sun, 17 Mar 2024 14:40:48 +0100
Subject: [PATCH] pairtools dedup: markdups is on by default

---
 pairtools/cli/dedup.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/pairtools/cli/dedup.py b/pairtools/cli/dedup.py
index 5ec4f4c..5a2802c 100644
--- a/pairtools/cli/dedup.py
+++ b/pairtools/cli/dedup.py
@@ -140,10 +140,11 @@
 
 ### 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",