From bf19869b8c721f3097f4d91e484db94c941bc288 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 22 Mar 2022 20:24:24 +0000
Subject: Fix way pair_scan is checked

Previously it would always register as True, due to being in the start_vars
---
 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 cf217a96..35678df9 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -238,7 +238,7 @@ class RunMapping:
                 self.method = "em"
             self.model = start_vars['mapmodel_rqtl']
             self.pair_scan = False
-            if 'pair_scan' in start_vars:
+            if start_vars['pair_scan'] == "true":
                self.pair_scan = True
             if self.permCheck and self.num_perm > 0:
                 self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl(
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