change "rare" threshold to 2.5%; include likely and well-established …

…pathogenic variants on default report regardless of frequency
madprime · Jun 21, 2012 · 6ee5c06 · 6ee5c06
1 parent 8448614
commit 6ee5c06
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Showing 2 changed files with 9 additions and 3 deletions.
diff --git a/public_html/js/datatable_setup.js b/public_html/js/datatable_setup.js
@@ -37,8 +37,14 @@ var datatables_objects = {};
 var variant_table_showall = false;
 var variant_table = false;
 var variant_table_filter = function(){return true;};
-var variant_table_filters = [function(oSettings, aData, iDataIndex) { return !(aData[5]>0.1) && /pathogenic/i.exec(aData[4]); },
-			     function(oSettings, aData, iDataIndex) { return true; }];
+var variant_table_filters =
+    [   function(oSettings, aData, iDataIndex) {
+	    return (!(aData[5]>0.025) || /likely|well-established/i.exec(aData[4])) && /pathogenic/i.exec(aData[4]);
+	},
+	function(oSettings, aData, iDataIndex) {
+	    return true;
+	}
+	];
 
 jQuery(document).ready(function($){
 	$.fn.dataTableExt.afnFiltering.push(function(oSettings, aData, iDataIndex) {

diff --git a/public_html/lib/genome_display.php b/public_html/lib/genome_display.php
@@ -690,7 +690,7 @@ function genome_display($shasum, $oid, $is_admin=false, $options=array()) {
             . "<div id='variant_table_tab_0'>";
 
         $returned_text .= "<div style='float:right; margin-bottom: 3px' id='variant_filter_radio'>
-<input type='radio' name='variant_filter_radio' id='variant_filter_radio0' checked /><label for='variant_filter_radio0'>Show rare (<i>f</i><10%) pathogenic variants</label>
+<input type='radio' name='variant_filter_radio' id='variant_filter_radio0' checked /><label for='variant_filter_radio0'>Show likely pathogenic and rare (&lt;2.5%) pathogenic variants</label>
 <input type='radio' name='variant_filter_radio' id='variant_filter_radio1' /><label for='variant_filter_radio1'>Show all</label>
 </div><br clear=all />";