From 731b7b758cda5edea1666dbbf577b4b65861a55c Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 3 Dec 2025 12:18:29 +0100
Subject: Writing output local to function

---
 src/gemma.cpp | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'src/gemma.cpp')

diff --git a/src/gemma.cpp b/src/gemma.cpp
index c7f7ab6..f7ebdce 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -2846,7 +2846,7 @@ void GEMMA::BatchRun(PARAM &cPar) {
             cLmm.mdb_calc_gwa(U, eval, UtW, &UtY_col.vector, W,
                               &Y_col.vector, cPar.setGWASnps);
           }
-          else
+          else {
             if (!cPar.file_bfile.empty()) {
               // PLINK analysis
               if (cPar.file_gxe.empty()) {
@@ -2869,8 +2869,9 @@ void GEMMA::BatchRun(PARAM &cPar) {
                                       &Y_col.vector, env);
               }
             }
-          cLmm.WriteFiles(); // write output files
-          cLmm.CopyToParam(cPar);
+            cLmm.WriteFiles(); // write output files
+            cLmm.CopyToParam(cPar);
+          }
         } else {
           debug_msg("fit mvLMM (multiple phenotypes)");
           MVLMM cMvlmm;
-- 
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