Include ref allele in genotypes page

Author: bbimber

jbrowse/resources/views/genotypeTable.html

@@ -28,9 +28,10 @@
                 $.each(rows, function(idx, row){
                     var contig = row.contig;
                     var start = row.start;
+                    var refAllele = row.refAllele;
 
                     $.each(row.genotypes, function(idx, gt){
-                        var r = [contig, start, gt.sample];
+                        var r = [contig, start, refAllele, gt.sample];
 
                         var d = demographics[gt.sample] || {};
                         $.each(demographicsFields, function(field, displayName) {
@@ -45,6 +46,7 @@
                 var columns = [
                     {title: 'Contig'},
                     {title: 'Position'},
+                    {title: 'Reference Allele'},
                     {title: 'Sample Name'}
                 ];
 

jbrowse/src/org/labkey/jbrowse/JBrowseController.java

@@ -582,6 +582,7 @@ public ApiResponse execute(GetGenotypesForm form, BindException errors)
                         pos.put("contig", vc.getContig());
                         pos.put("start", vc.getStart());
                         pos.put("end", vc.getEnd());
+                        pos.put("refAllele", vc.getReference().getBaseString());
 
                         JSONArray genotypes = new JSONArray();
                         for (Genotype g : vc.getGenotypes())