From 86323ccaf26ad0a3b706a67a0014dd04b9965823 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 5 Oct 2017 11:55:03 +0000
Subject: LMM: skip beta (again) with LRT

---
 src/lmm.cpp                | 14 ++++++++++----
 test/dev_test_suite.sh     |  2 +-
 test/lengthy_test_suite.sh |  1 +
 3 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/lmm.cpp b/src/lmm.cpp
index e2f23a2..1193700 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -107,8 +107,10 @@ void LMM::WriteFiles() {
   }
 
   auto common_header = [&] () {
-    outfile << "beta" << "\t"
-            << "se" << "\t";
+    if (a_mode != 2)
+      outfile << "beta" << "\t";
+
+    outfile << "se" << "\t";
 
     outfile << "logl_H1" << "\t";  // we may make this an option
 
@@ -135,8 +137,12 @@ void LMM::WriteFiles() {
   };
 
   auto sumstats = [&] (SUMSTAT st) {
-    outfile << scientific << setprecision(6) << st.beta << "\t"
-    << st.se << "\t";
+    outfile << scientific << setprecision(6);
+
+    if (a_mode != 2)
+      outfile << st.beta << "\t";
+
+    outfile << st.se << "\t";
 
     outfile << st.logl_H1 << "\t";
 
diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh
index 37f6b28..0fc4423 100755
--- a/test/dev_test_suite.sh
+++ b/test/dev_test_suite.sh
@@ -44,7 +44,7 @@ testBXDLMMLikelihoodRatio() {
     assertEquals 0 $?
 
     outfn=output/$outn.assoc.txt
-    assertEquals "87816" `wc -w < $outfn`
+    assertEquals "80498" `wc -w < $outfn`
     assertEquals "3088458212.93" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
 }
 
diff --git a/test/lengthy_test_suite.sh b/test/lengthy_test_suite.sh
index 327b2b2..231475e 100755
--- a/test/lengthy_test_suite.sh
+++ b/test/lengthy_test_suite.sh
@@ -18,6 +18,7 @@ testPlinkStandardRelatednessMatrixK() {
 }
 
 testPlinkMultivariateLinearMixedModelMultiplePhenotypes_Issue58() {
+    echo "Long running test!"
     # This test passes, but takes over 30 minutes to run!
     # n=2 is original pheno in fam file
     # n=1 is causal1
-- 
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