From d0538ef046ad25846c1832631e45935f0433af85 Mon Sep 17 00:00:00 2001
From: James Beilsten-Edmands
 <30625594+jbeilstenedmands@users.noreply.github.com>
Date: Tue, 12 Sep 2023 10:32:40 +0100
Subject: [PATCH] Add missing call to generate r-free-flags

---
 src/dials/algorithms/merging/merge.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/dials/algorithms/merging/merge.py b/src/dials/algorithms/merging/merge.py
index 7b201083e3..1757dac567 100644
--- a/src/dials/algorithms/merging/merge.py
+++ b/src/dials/algorithms/merging/merge.py
@@ -502,7 +502,13 @@ def merge_scaled_array_to_mtz_with_report_collection(
         process_merged_data(
             params, mtz_dataset, merged, merged_anomalous, stats_summary
         )
-        mtz = make_merged_mtz_file([mtz_dataset])
+        if params.r_free_flags.reference:
+            r_free_array = r_free_flags_from_reference(params, [mtz_dataset])
+        elif params.r_free_flags.generate:
+            r_free_array = generate_r_free_flags(params, [mtz_dataset])
+        else:
+            r_free_array = None
+        mtz = make_merged_mtz_file([mtz_dataset], r_free_array=r_free_array)
         json_data = collector.create_json()
     return mtz, json_data