Don't use escape in VCFFeature model

GMOD · Nov 18, 2018 · ed42b22 · ed42b22
1 parent 012dc4c
commit ed42b22
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/src/JBrowse/Model/VCFFeature.js b/src/JBrowse/Model/VCFFeature.js
@@ -11,8 +11,8 @@ function (Util) {
             this._id = args.id;
             this.data = this.dataFromVariant(this.variant);
         },
-        
-        get(field) { 
+
+        get(field) {
             return this._get(field) || this._get(field.toLowerCase())
         },
 
@@ -97,7 +97,7 @@ function (Util) {
                 start: start,
                 end: end,
                 seq_id: variant.CHROM,
-                description: Util.escapeHTML( description ),
+                description: description,
                 type: SO_term,
                 reference_allele: ref
             };
@@ -128,7 +128,7 @@ function (Util) {
                     meta: {
                         description: 'VCF ALT field, list of alternate non-reference alleles called on at least one of the samples'
                     },
-                    values: alt.map( Util.escapeHTML )
+                    values: alt
                 };
             }
 
@@ -250,7 +250,7 @@ function (Util) {
 
         _getSOAndDescByExamination: function (ref, alt) {
             if (ref.length == 1 && alt.length == 1) {
-                // use SNV because SO definition of SNP says abundance must be at 
+                // use SNV because SO definition of SNP says abundance must be at
                 // least 1% in population, and can't be sure we meet that
                 return [
                     'SNV',

diff --git a/tests/js_tests/spec/VCF.spec.js b/tests/js_tests/spec/VCF.spec.js
@@ -62,7 +62,7 @@ describe('VCF store', function() {
                           );
          runs(function() {
                   expect(features.length).toEqual( 7 );
-                  expect(features[2].get('alternative_alleles').values).toEqual([ "TC", "&lt;*&gt;" ]);
+                  expect(features[2].get('alternative_alleles').values).toEqual([ "TC", "<*>" ]);
          });
 
 
@@ -122,7 +122,7 @@ describe('VCF store', function() {
                           );
          runs(function() {
                   expect(features.length).toEqual( 37 );
-                  expect(features[0].get('alternative_alleles').values).toEqual([ '&lt;NON_REF&gt;' ]);
+                  expect(features[0].get('alternative_alleles').values).toEqual([ '<NON_REF>' ]);
          });
   });
 
@@ -191,7 +191,7 @@ describe('VCF store', function() {
             start: 1206810422,
             end: 1206810423,
             seq_id: '1',
-            description: 'SNV T -&gt; A',
+            description: 'SNV T -> A',
             type: 'SNV',
             reference_allele: 'T',
             score: 25,