From 11dd6e34a3f58a83bf057cfe3d865d4da0047dd2 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 4 Aug 2021 20:12:22 +0000
Subject: Fixed bug caused by pair_scan not always being set to a default

---
 wqflask/wqflask/marker_regression/run_mapping.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 7a2b9aaa..059b0f31 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -109,6 +109,7 @@ class RunMapping:
             self.mapping_results_path = "{}{}.csv".format(
                 webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename)
 
+        self.pair_scan = False
         self.manhattan_plot = False
         if 'manhattan_plot' in start_vars:
             if start_vars['manhattan_plot'].lower() != "false":
@@ -237,7 +238,6 @@ class RunMapping:
             else:
                 self.method = "em"
             self.model = start_vars['mapmodel_rqtl']
-            self.pair_scan = False
             if 'pair_scan' in start_vars:
                self.pair_scan = True
             if self.permCheck and self.num_perm > 0:
-- 
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