From cfa526cf5cbec3a9c9282955c762c0a60afc03b4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 26 Jul 2021 20:50:31 +0000
Subject: Added check for pair_scan in start_vars

---
 wqflask/wqflask/marker_regression/run_mapping.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index ebad7d36..8b9f89d2 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -126,8 +126,6 @@ class RunMapping:
             self.use_loco = None
         self.suggestive = ""
         self.significant = ""
-        # Initializing this since it is checked in views to determine which template to use
-        self.pair_scan = False
         if 'transform' in start_vars:
             self.transform = start_vars['transform']
         else:
@@ -239,8 +237,9 @@ class RunMapping:
             else:
                 self.method = "em"
             self.model = start_vars['mapmodel_rqtl_geno']
-            # if start_vars['pair_scan'] == "true":
-            #    self.pair_scan = True
+            self.pair_scan = False
+            if 'pair_scan' in start_vars:
+               self.pair_scan = True
             if self.permCheck and self.num_perm > 0:
                 self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl(
                     self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
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