From 879c07bc76aa073b870041f0e111bea7ccba3605 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 10 Feb 2020 14:41:48 -0600
Subject: Fixed issue that was causing rqtl to not work, plus temporarily
 disabled the genome browser for rqtl since it uses centamorgans and I need to
 get that working with the browser

---
 wqflask/wqflask/marker_regression/run_mapping.py        |  4 ++--
 .../static/new/javascript/show_trait_mapping_tools.js   | 17 +++--------------
 wqflask/wqflask/templates/mapping_results.html          |  6 ++++++
 3 files changed, 11 insertions(+), 16 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index ac05c4ad..ba41ffc3 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -623,8 +623,8 @@ def get_chr_lengths(mapping_scale, dataset, qtl_results):
                 this_chr = int(result['chr'])
                 highest_pos = 0
             else:
-                if float(result['ps']) > highest_pos:
-                    highest_pos = float(result['ps'])
+                if float(result['Mb']) > highest_pos:
+                    highest_pos = float(result['Mb'])
 
     return chr_lengths
 
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 3d66a698..b26110d8 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -158,9 +158,9 @@
                             'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 
                             'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples']
 
-  $("#rqtl_geno_compute").on("click", (function(_this) {
+  $(".rqtl_tab, #rqtl_geno_compute").on("click", (function(_this) {
     return function() {
-      if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_compute"){
+      if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_geno_compute"){
         var form_data, url;
         url = "/loading";
         $('input[name=method]').val("rqtl_geno");
@@ -173,18 +173,7 @@
         $('input[name=tool_used]').val("Mapping");
         $('input[name=form_url]').val("/run_mapping");
         $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
-        if ($('input[name=pair_scan]:checked').val() == "true") {
-          run_pair_scan = confirm(runtime_warning_text)
-          if (run_pair_scan == true) {
-            submit_special(url);
-          }
-          else {
-            return false
-          }
-        }
-        else {
-          return submit_special(url);
-        }
+        return submit_special(url);
       } else {
         return true
       }
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 0decbb54..8e0bfddf 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -160,9 +160,11 @@
             <li id="gn1_map_tab">
               <a href="#gn1_map" data-toggle="tab" aria-expanded="true">GN1 Map</a>
             </li>
+            {% if mapping_method == "gemma" or mapping_method == "reaper" %}
             <li id="browser_tab">
                 <a href="#browser_holder" data-toggle="tab" aria-expanded="true">Genome Browser</a>
             </li>
+            {% endif %}
           </ul>
           <div class="tab-content" style="overflow-x: auto;">
             <div class="tab-pane active" id="gn1_map">
@@ -175,6 +177,7 @@
                   {% endif %}
               </div>
             </div>
+            {% if mapping_method == "gemma" or mapping_method == "reaper" %}
             <div class="tab-pane" id="browser_holder" style="height: 600px;">
                 <div id="browser" style="margin-right: 20px; width: 90%;">
                     <div id="controls">
@@ -195,6 +198,7 @@
                     <div id="infoBox"></div>
                 </div>
             </div>
+            {% endif %}
           </div>
         </div>
         <div>
@@ -336,7 +340,9 @@
     </script>
 
     <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
+    {% if mapping_method == "gemma" or mapping_method == "reaper" %}
     <script language="javascript" type="text/javascript" src="/static/new/javascript/init_genome_browser.js"></script>
+    {% endif %}
 
     <script type="text/javascript" charset="utf-8">
         $(document).ready( function () {
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