Updated the way snpbrowser initializes parameters, in preparation for drawing SNP density chart when results exceed a certain value, plus a couple minor fixes

Changed the header bar to put a few items under the "Help" option, since previously the header was too long and would go to a second line when the browser window width was smaller

Changed dataset info link on trait page to same as one on search page

Changed the mapping default to non-LOCO for the time being, until it is faster

9 files changed, 217 insertions, 170 deletions

diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 393b8507..0e999ba2 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -1,8 +1,11 @@
 from __future__ import absolute_import, print_function, division
 
-from flask import Flask, g
+from flask import Flask, g, url_for
+
+from htmlgen import HTMLgen2 as HT
 
 import string
+import piddle as pid
 
 from utility.logger import getLogger
 logger = getLogger(__name__ )
@@ -31,99 +34,110 @@ class SnpBrowser(object):
                 self.table_rows = []
 
     def initialize_parameters(self, start_vars):
-        self.first_run = "true"
-        self.allele_list = []
-        if 'variant' in start_vars: #ZS: Check if not first time loaded (if it has form input)
+        if 'first_run' in start_vars:
             self.first_run = "false"
+        else:
+            self.first_run = "true"
+        self.allele_list = []
+
+        self.variant_type = "SNP"
+        if 'variant' in start_vars:
             self.variant_type = start_vars['variant']
+
+        self.species_name = "Mouse"
+        self.species_id = 1
+        if 'species' in start_vars:
             self.species_name = start_vars['species']
-            if self.species_name.capitalize() == "Mouse":
-                self.species_id = 1
-            elif self.species_name.capitalize() == "Rat":
+            if self.species_name.capitalize() == "Rat":
                 self.species_id = 2
+
+        species_ob = species.TheSpecies(species_name=self.species_name)
+
+        self.chr_list = []
+        for key in species_ob.chromosomes.chromosomes:
+            self.chr_list.append(species_ob.chromosomes.chromosomes[key].name)
+
+        if self.first_run == "true":
+            self.chr = "19"
+            self.start_mb = 30.1
+            self.end_mb = 30.12
+        else:
+            if 'gene_name' in start_vars:
+                if start_vars['gene_name'] != "":
+                    self.gene_name = start_vars['gene_name']
+                else:
+                    self.gene_name = ""
+                    self.chr = start_vars['chr']
+                    try:
+                        self.start_mb = float(start_vars['start_mb'])
+                        self.end_mb = float(start_vars['end_mb'])
+                    except:
+                        self.start_mb = 0.0
+                        self.end_mb = 0.0
             else:
-                self.species_id = 0 #Using this to indicate "All Species"
- 
-            #ZS: Currently this is just assuming mouse for determining the chromosomes. 
-            #    This logic may have to change depending upon what other species are added
-            self.chr_list = []
-            species_ob = species.TheSpecies(species_name="Mouse")
-            for key in species_ob.chromosomes.chromosomes:
-                self.chr_list.append(species_ob.chromosomes.chromosomes[key].name)
-
-            if start_vars['gene_name'] != "":
-                self.gene_name = start_vars['gene_name']
-            else:
-                self.gene_name = ""
-                self.chr = start_vars['chr']
                 try:
+                    self.chr = start_vars['chr']
                     self.start_mb = float(start_vars['start_mb'])
                     self.end_mb = float(start_vars['end_mb'])
                 except:
+                    self.chr = "1"
                     self.start_mb = 0.0
                     self.end_mb = 0.0
 
-            if 'limit_strains' in start_vars:
-                self.limit_strains = "true"
-            else:
+        self.limit_strains = "true"
+        if self.first_run == "false":
+            if 'limit_strains' not in start_vars:
                 self.limit_strains = "false"
+            else:
+                if start_vars['limit_strains'] == "false":
+                    self.limit_strains = "false"
+
+        self.chosen_strains_mouse = ["C57BL/6J",
+                                     "DBA/2J",
+                                     "A/J",
+                                     "129S1/SvImJ",
+                                     "NOD/ShiLtJ",
+                                     "NZO/HlLtJ",
+                                     "WSB/EiJ",
+                                     "PWK/PhJ",
+                                     "CAST/EiJ"]
+        self.chosen_strains_rat = ["BN", "F344"]
+        if 'chosen_strains_mouse' in start_vars:
             self.chosen_strains_mouse = start_vars['chosen_strains_mouse'].split(",")
+        if 'chosen_strains_rat' in start_vars:
             self.chosen_strains_rat = start_vars['chosen_strains_rat'].split(",")
 
-            if self.species_id == 1:
-                self.chosen_strains = self.chosen_strains_mouse
-            elif self.species_id == 2:
-                self.chosen_strains = self.chosen_strains_rat
+        if self.species_id == 1:
+            self.chosen_strains = self.chosen_strains_mouse
+        else:
+            self.chosen_strains = self.chosen_strains_rat
 
+        self.domain = "All"
+        if 'domain' in start_vars:
             self.domain = start_vars['domain']
+        self.function = "All"
+        if 'function' in start_vars:
             self.function = start_vars['function']
+        self.source = "All"
+        if 'source' in start_vars:
             self.source = start_vars['source']
+        self.criteria = ">="
+        if 'criteria' in start_vars:
             self.criteria = start_vars['criteria']
+        self.score = 0.0
+        if 'score' in start_vars:
             self.score = start_vars['score']
 
-            self.redundant = "false"
-            self.diff_alleles = "false"
-            if 'redundant' in start_vars:
-                self.redundant = "true"
-            if 'diff_alleles' in start_vars:
-                self.diff_alleles = "true"
-
-        else: #ZS: Default values
-            self.variant_type = "SNP"
-            self.species_name = "Mouse"
-            species_ob = species.TheSpecies(species_name=self.species_name)
-            self.chr_list = []
-            for key in species_ob.chromosomes.chromosomes:
-                self.chr_list.append(species_ob.chromosomes.chromosomes[key].name)
-
-            self.chr = "19"
-            self.start_mb = 30.1
-            self.end_mb = 30.12
-
-            self.limit_strains = "true"
-
-            self.chosen_strains_mouse = ["C57BL/6J",
-                                         "DBA/2J",
-                                         "A/J",
-                                         "129S1/SvImJ",
-                                         "NOD/ShiLtJ",
-                                         "NZO/HlLtJ",
-                                         "WSB/EiJ",
-                                         "PWK/PhJ",
-                                         "CAST/EiJ"]
-            self.chosen_strains_rat = ["F344"]
-            self.chosen_strains_all = self.chosen_strains_mouse + self.chosen_strains_rat
-
-            self.chosen_strains = self.chosen_strains_mouse
-            
-            self.domain = "All"
-            self.function = "All"
-            self.source = "All"
-            self.criteria = ">="
-            self.score = 0.0
-
-            self.redundant = "false"
-            self.diff_alleles = "true"
+        self.redundant = "false"
+        if self.first_run == "false" and 'redundant' in start_vars:
+            self.redundant = "true"
+        self.diff_alleles = "true"
+        if self.first_run == "false":
+            if 'diff_alleles' not in start_vars:
+                self.diff_alleles = "false"
+            else:
+                if start_vars['diff_alleles'] == "false":
+                    self.diff_alleles = "false"
 
     def get_browser_results(self):
         self.snp_list = None
@@ -567,6 +581,27 @@ class SnpBrowser(object):
 
         return domain_satisfied and function_satisfied and source_satisfied and score_satisfied and different_alleles_satisfied
 
+    def snp_density_map(self, query, results):
+
+        canvas_width = 900
+        canvas_height = 200
+        snp_canvas = pid.PILCanvas(size=(canvas_width, canvas_height))
+        left_offset, right_offset, top_offset, bottom_offset = (30, 30, 40, 50)
+        plot_width = canvas_width - left_offset - right_offset
+        plot_height = canvas_height - top_offset - bottom_offset
+        y_zero = top_offset + plot_height/2
+
+        x_scale = plot_width/(self.end_mb - self.start_mb)
+
+        #draw clickable image map
+        #gifmap = HT.Map
+        n_click = 80.0
+        click_step = plot_width/n_click
+        click_mb_step = (self.end_mb - self.start_mb)/n_click
+
+        #for i in range(n_click):
+        #    href = url_for('snp_browser', first_run="false", chosen_strains_mouse=self.chosen_strains_mouse, chosen_strains_rat=self.chosen_strains_rat, variant=self.variant_type, species=self.species_name, gene_name=self.gene_name, chr=self.chr, start_mb=self.start_mb, end_mb=self.end_mb, limit_strains=self.limit_strains, domain=self.domain, function=self.function, criteria=self.criteria, score=self.score, diff_alleles=self.diff_alleles)
+
 def get_browser_sample_lists(species_id=1):
     strain_lists = {}
     mouse_strain_list = []
diff --git a/wqflask/wqflask/static/new/css/main.css b/wqflask/wqflask/static/new/css/main.css
index 880395a7..097cd997 100644
--- a/wqflask/wqflask/static/new/css/main.css
+++ b/wqflask/wqflask/static/new/css/main.css
@@ -1,11 +1,36 @@
-.security_box {
-    padding-left: 30px;
-    padding-right: 30px;
-}
-
-ol {
-  font-family: Arial;
-  font-weight: bold;
-  font-size: 16px;
-  color: #000082
+@media (max-width: 10px) {
+    .navbar-header {
+        float: none;
+    }
+    .navbar-toggle {
+        display: block;
+    }
+    .navbar-collapse {
+        border-top: 1px solid transparent;
+        box-shadow: inset 0 1px 0 rgba(255,255,255,0.1);
+    }
+    .navbar-collapse.collapse {
+        display: none!important;
+    }
+    .navbar-nav {
+        float: none!important;
+        margin: 7.5px -15px;
+    }
+    .navbar-nav>li {
+        float: none;
+    }
+    .navbar-nav>li>a {
+        padding-top: 10px;
+        padding-bottom: 10px;
+    }
+    .navbar-text {
+        float: none;
+        margin: 15px 0;
+    }
+    .navbar-collapse.collapse.in {
+        display: block!important;
+    }
+    .collapsing {
+        overflow: hidden!important;
+    }
 }
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 1c6791c4..9c806a7f 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -2591,21 +2591,6 @@
             ],
             "Liver mRNA": [
                [
-                  "858",
-                  "EPFLMouseLiverHFDRMA0818",
-                  "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
-               ],
-               [
-                  "852",
-                  "NIA-AgBXD-Liv_HFD-0818",
-                  "NIA Aging BXD HFD Liver Affy Clariom S Gene Level (Aug18) RMA **"
-               ],
-               [
-                  "857",
-                  "EPFLMouseLiverCDHFDRMA0818",
-                  "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
-               ],
-               [
                   "859",
                   "EPFLMouseLiverCDRMA0818",
                   "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
@@ -2626,6 +2611,21 @@
                   "UCLA BXD Liver Affy M430 2.0 (Jan16) RMA"
                ],
                [
+                  "858",
+                  "EPFLMouseLiverHFDRMA0818",
+                  "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
+               ],
+               [
+                  "852",
+                  "NIA-AgBXD-Liv_HFD-0818",
+                  "NIA Aging BXD HFD Liver Affy Clariom S Gene Level (Aug18) RMA **"
+               ],
+               [
+                  "857",
+                  "EPFLMouseLiverCDHFDRMA0818",
+                  "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
+               ],
+               [
                   "430",
                   "EPFLMouseLiverRMA0413",
                   "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
@@ -2641,6 +2641,11 @@
                   "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
                ],
                [
+                  "433",
+                  "EPFLMouseLiverBothExRMA0413",
+                  "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
+               ],
+               [
                   "849",
                   "EPFLMouseLiverCDEx0413",
                   "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
@@ -2651,11 +2656,6 @@
                   "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
                ],
                [
-                  "433",
-                  "EPFLMouseLiverBothExRMA0413",
-                  "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
-               ],
-               [
                   "700",
                   "UTHSC-VGX_MmBXDHepatocytesRMA1014",
                   "UT-VGX Hepatocytes Affy Mouse Gene 1.0 ST Gene Level (Oct14) RMA"
@@ -3672,6 +3672,11 @@
          "Retina-RGC-Rheaume": {
             "Retina Single-cell RNA-Seq": [
                [
+                  "866",
+                  "UConn-RGC-RSeq_log2-0918",
+                  "UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Log2"
+               ],
+               [
                   "865",
                   "UConn-RGC-RSeq_r-0918",
                   "UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Raw"
@@ -3680,11 +3685,6 @@
                   "867",
                   "UConn-RGC-RSeq_s-0918",
                   "UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Siamak"
-               ],
-               [
-                  "866",
-                  "UConn-RGC-RSeq_log2-0918",
-                  "UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Log2"
                ]
             ]
          },
@@ -3712,16 +3712,18 @@
       },
       "rat": {
          "HSNIH-Palmer": {
+            "Infralimbic Cortex mRNA": [
+               [
+                  "861",
+                  "HSNIH-Rat-IL-RSeq-0818",
+                  "HSNIH-Palmer Infralimbic Cortex RNA-Seq (Aug18) rlog"
+               ]
+            ],
             "Lateral Habenula mRNA": [
                [
                   "862",
                   "HSNIH-Rat-LHB-RSeq-0818",
                   "HSNIH-Palmer Lateral Habenula RNA-Seq (Aug18) rlog"
-               ],
-               [
-                  "870",
-                  "HSNIH-Rat-LHB-RSeqlog2-0818",
-                  "HSNIH-Palmer Lateral Habenula RNA-Seq (Aug18) log2"
                ]
             ],
             "Nucleus Accumbens mRNA": [
@@ -3729,11 +3731,13 @@
                   "860",
                   "HSNIH-Rat-Acbc-RSeq-0818",
                   "HSNIH-Palmer Nucleus Accumbens Core RNA-Seq (Aug18) rlog"
-               ],
+               ]
+            ],
+            "Orbitofrontal Cortex mRNA": [
                [
-                  "868",
-                  "HSNIH-Rat-Acbc-RSeqlog2-0818",
-                  "HSNIH-Palmer Nucleus Accumbens Core RNA-Seq (Aug18) log2"
+                  "864",
+                  "HSNIH-Rat-VoLo-RSeq-0818",
+                  "HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) rlog"
                ]
             ],
             "Phenotypes": [
@@ -3743,32 +3747,7 @@
                   "HSNIH-Palmer Phenotypes"
                ]
             ],
-            "Prefrontal Cortex mRNA": [
-               [
-                  "869",
-                  "HSNIH-Rat-IL-RSeqlog2-0818",
-                  "HSNIH-Palmer Infralimbic Cortex RNA-Seq (Aug18) log2"
-               ],
-               [
-                  "872",
-                  "HSNIH-Rat-VoLo-RSeqlog2-0818",
-                  "HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) log2"
-               ],
-               [
-                  "861",
-                  "HSNIH-Rat-IL-RSeq-0818",
-                  "HSNIH-Palmer Infralimbic Cortex RNA-Seq (Aug18) rlog"
-               ],
-               [
-                  "864",
-                  "HSNIH-Rat-VoLo-RSeq-0818",
-                  "HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) rlog"
-               ],
-               [
-                  "871",
-                  "HSNIH-Rat-PL-RSeqlog2-0818",
-                  "HSNIH-Palmer Prelimbic Cortex RNA-Seq (Aug18) log2"
-               ],
+            "Prelimbic Cortex mRNA": [
                [
                   "863",
                   "HSNIH-Rat-PL-RSeq-0818",
@@ -5532,6 +5511,10 @@
                "Phenotypes"
             ],
             [
+               "Infralimbic Cortex mRNA",
+               "Infralimbic Cortex mRNA"
+            ],
+            [
                "Lateral Habenula mRNA",
                "Lateral Habenula mRNA"
             ],
@@ -5540,8 +5523,12 @@
                "Nucleus Accumbens mRNA"
             ],
             [
-               "Prefrontal Cortex mRNA",
-               "Prefrontal Cortex mRNA"
+               "Orbitofrontal Cortex mRNA",
+               "Orbitofrontal Cortex mRNA"
+            ],
+            [
+               "Prelimbic Cortex mRNA",
+               "Prelimbic Cortex mRNA"
             ]
          ],
          "HSNIH-RGSMC": [
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
index d5ce6f84..3f123d6f 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
@@ -94,7 +94,7 @@ $(function() {
   })(this));
   open_window = function(url, name) {
     var options;
-    options = "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900";
+    options = "menubar=yes,toolbar=yes,titlebar=yes,location=yes,resizable=yes,status=yes,scrollbars=yes,directories=yes,width=900";
     return open(url, name, options).focus();
   };
   group_info = function() {
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index a3edd0e6..c1b0cef9 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -829,8 +829,10 @@
         }
     }
 
+    root.chart_range = [range_bottom, range_top]
+
     total_sample_count = 0
-    for (i = 0, i < sample_lists.length; i++) {
+    for (i = 0, i < sample_lists.length; i++;) {
       total_sample_count += get_sample_vals(sample_lists[i]).length
     }
 
@@ -839,7 +841,7 @@
 
       var layout = {
         yaxis: {
-            range: [range_bottom, range_top],
+            range: root.chart_range,
         },
         width: bar_chart_width,
         height: 600,
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 81c04db5..3d03f3b9 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -22,17 +22,22 @@
 <body style="width: 100% !important;">
     <!-- Navbar ================================================== -->
 
-    <div class="navbar navbar-inverse navbar-static-top pull-left" role="navigation" style="width: 100%;">
-
+    <div class="navbar navbar-inverse navbar-static-top pull-left" role="navigation" style="width: 100%; white-space: nowrap;">
+    <!--<div class="navbar navbar-default" style="width: 100%; white-space: nowrap;">-->
             <div class="container-fluid" style="width: 100%;">
                 <!-- Brand and toggle get grouped for better mobile display -->
+                <!---
                 <div class="navbar-header">
-                <a class="navbar-brand" href="/">GeneNetwork</a>
+                  <a class="navbar-brand" href="/">GeneNetwork</a>
                 </div>
+                -->
 
                 <!-- Collect the nav links, forms, and other content for toggling -->
                 <div>
                     <ul class="nav navbar-nav">
+                        <li class="" style="margin-right: 20px;">
+                            <a href="/" style="font-weight: bold;">GeneNetwork</a>
+                        </li>
                         <li class="">
                             <a href="/intro">Intro</a>
                         </li>
@@ -55,22 +60,14 @@
                             <a href="/snp_browser">SNP Browser</a>
                         </li>
                         <li class="">
-                            <a href="/help">Help</a>
-                        </li>
-                        <li class="">
-                            <a href="/news">News</a>
-                        </li>
-                        <li class="">
-                            <a href="/references">References</a>
-                        </li>
-                        <li class="">
-                            <a href="/policies">Policies</a>
-                        </li>
-                        <li class="">
-                            <a href="/links">Links</a>
-                        </li>
-						<li class="">
-                            <a href="/environments">Environments</a>
+                            <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Help <span class="caret"></a>
+                            <ul class="dropdown-menu">
+                              <li><a href="/news">News</a></li>
+                              <li><a href="/references">References</a></li>
+                              <li><a href="/policies">Policies</a></li>
+                              <li><a href="/links">Links</a></li>
+                              <li><a href="/environments">Environments</a></li>
+                            </ul>
                         </li>
                         <li class="">
                             {% if g.user_session.logged_in %}
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 1e6d41c2..c1f8f824 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -46,7 +46,7 @@
     <tr>
         <td>Database</td>
         <td>
-            <a href="http://genenetwork.org/dbdoc/{{ dataset.name }}.html">
+            <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName={{ dataset.name }}">
                 {{ dataset.fullname }}
             </a>
         </td>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index c2c201e1..72b3b00b 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -61,11 +61,11 @@
                             <label style="text-align: right;" class="col-xs-3 control-label">Use LOCO</label>
                             <div style="margin-left:20px;" class="col-xs-6 controls">
                                 <label class="radio-inline">
-                                    <input type="radio" name="use_loco" value="True" checked="">
+                                    <input type="radio" name="use_loco" value="True">
                                     Yes
                                 </label>
                                 <label class="radio-inline">
-                                    <input type="radio" name="use_loco" value="False">
+                                    <input type="radio" name="use_loco" value="False" checked="">
                                     No
                                </label>
                             </div>
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 578bd2fc..3608d0fe 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -11,6 +11,7 @@
 
     <div class="container" style="border-style: double; position: relative; width: 950px; padding-top: 10px; padding-right: 40px;">
       <form id="snp_browser_form" method="get" action="/snp_browser">
+        <input type="hidden" name="first_run" value="{{ first_run }}">
         <input type="hidden" name="chosen_strains_mouse" value="{{ chosen_strains_mouse|join(",") }}">
         <input type="hidden" name="chosen_strains_rat" value="{{ chosen_strains_rat|join(",") }}">
         <div class="col-xs-4" style="padding-left: 0px;">
@@ -18,8 +19,8 @@
             <label for="snp_or_indel" style="text-align: right;" class="col-xs-4 col-form-label"><b>Type:</b></label>
             <div class="col-xs-8">
               <select name="variant">
-                <option value="SNP" selected>SNP</option>
-                <option value="InDel">InDel</option>
+                <option value="SNP" {% if variant_type == "SNP" %}selected{% endif %}>SNP</option>
+                <option value="InDel" {% if variant_type == "InDel" %}selected{% endif %}>InDel</option>
               </select>
             </div>
           </div>