Parse END field

GMOD · Feb 15, 2018 · fedb94c · fedb94c
1 parent ef5cf50
commit fedb94c
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/src/JBrowse/Store/SeqFeature/VCFTabix.js b/src/JBrowse/Store/SeqFeature/VCFTabix.js
@@ -32,8 +32,9 @@ var VCFIndexedFile = declare( TabixIndexedFile, {
     parseLine: function() {
         var i = this.inherited( arguments );
         if( i ) {
+            var ret = i.fields[7].match(/;END=(\d+)/);
             i.start--;
-            i.end = i.start + i.fields[3].length;
+            i.end = ret ? +ret[1] : i.start + i.fields[3].length;
         }
         return i;
     }

diff --git a/src/JBrowse/Store/SeqFeature/VCFTabix/Parser.js b/src/JBrowse/Store/SeqFeature/VCFTabix/Parser.js
@@ -82,9 +82,10 @@ return declare( null, {
         var alt = fields[4];
 
         var SO_term = this._find_SO_term( ref, alt );
+        var ret = (fields[7]||'').match(/;END=(\d+)/);
         var featureData = {
             start:  line.start,
-            end:    line.start+ref.length,
+            end:    ret ? +ret[1] : line.start+ref.length,
             seq_id: line.ref,
             description: this._makeDescriptionString( SO_term, ref, alt ),
             type:   SO_term,