Fix for regularizing names of X, Y, and MT chroms

GMOD · Nov 7, 2018 · eea6ac7 · eea6ac7
1 parent e2f4fa7
commit eea6ac7
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/src/JBrowse/Browser.js b/src/JBrowse/Browser.js
@@ -718,7 +718,8 @@ regularizeReferenceName: function( refname ) {
                      .replace(/^co?n?ti?g/,'ctg')
                      .replace(/^scaff?o?l?d?/,'scaffold')
                      .replace(/^([a-z]*)0+/,'$1')
-                     .replace(/^(\d+)$/, 'chr$1' );
+                     .replace(/^(\d+|x|y)$/, 'chr$1' )
+                     .replace(/^mt$/, 'chrm');
 
     return refname;
 },