From df161be507ac0ad1d67a6528ebc664acec89fc9c Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 6 Oct 2017 07:54:01 +0000
Subject: Oops: fixed logic problem after removing Oxford data

---
 src/gemma.cpp | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

(limited to 'src/gemma.cpp')

diff --git a/src/gemma.cpp b/src/gemma.cpp
index 5fbd86c..c890055 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -2736,20 +2736,25 @@ void GEMMA::BatchRun(PARAM &cPar) {
           gsl_vector_view UtY_col = gsl_matrix_column(UtY, 0);
 
           if (!cPar.file_bfile.empty()) {
+            // PLINK analysis
             if (cPar.file_gxe.empty()) {
               cLmm.AnalyzePlink(U, eval, UtW, &UtY_col.vector, W,
                                 &Y_col.vector);
-            } else {
+            }
+            else {
               cLmm.AnalyzePlinkGXE(U, eval, UtW, &UtY_col.vector, W,
                                    &Y_col.vector, env);
             }
           }
-          if (cPar.file_gxe.empty()) {
-            cLmm.AnalyzeBimbam(U, eval, UtW, &UtY_col.vector, W,
-                               &Y_col.vector, cPar.setGWASnps);
-          } else {
-            cLmm.AnalyzeBimbamGXE(U, eval, UtW, &UtY_col.vector, W,
-                                  &Y_col.vector, env);
+          else {
+            // BIMBAM analysis
+            if (cPar.file_gxe.empty()) {
+              cLmm.AnalyzeBimbam(U, eval, UtW, &UtY_col.vector, W,
+                                 &Y_col.vector, cPar.setGWASnps);
+            } else {
+              cLmm.AnalyzeBimbamGXE(U, eval, UtW, &UtY_col.vector, W,
+                                    &Y_col.vector, env);
+            }
           }
 
           cLmm.WriteFiles();
-- 
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