From 6ce9ada43491b773bcbb459d6f12d45e2d901ea0 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 8 Dec 2017 10:49:25 +0000
Subject: Legacy mode does not show logl_H1 column in output

---
 src/gemma.cpp | 1 +
 src/lmm.cpp   | 6 ++++--
 2 files changed, 5 insertions(+), 2 deletions(-)

(limited to 'src')

diff --git a/src/gemma.cpp b/src/gemma.cpp
index df8934e..50b13b1 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -1601,6 +1601,7 @@ void GEMMA::Assign(int argc, char **argv, PARAM &cPar) {
       debug_set_strict_mode(true);
     } else if (strcmp(argv[i], "-legacy") == 0) {
       debug_set_legacy_mode(true);
+      warning_msg("you are running in legacy mode - support may drop in future versions of gemma");
     } else {
       cout << "error! unrecognized option: " << argv[i] << endl;
       cPar.error = true;
diff --git a/src/lmm.cpp b/src/lmm.cpp
index ecc8231..91354e1 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -112,7 +112,8 @@ void LMM::WriteFiles() {
       outfile << "se" << "\t";
     }
 
-    outfile << "logl_H1" << "\t";  // we may make this an option
+    if (!is_legacy_mode())
+      outfile << "logl_H1" << "\t";  // we may make this an option
 
     switch(a_mode) {
     case 1:
@@ -144,7 +145,8 @@ void LMM::WriteFiles() {
       outfile << st.se << "\t";
     }
 
-    outfile << st.logl_H1 << "\t";
+    if (!is_legacy_mode())
+      outfile << st.logl_H1 << "\t";
 
     switch(a_mode) {
     case 1:
-- 
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