fix for writing out VCF filter column

uk/ac/sanger/artemis/components/variant/VCFFilter.java

@@ -751,7 +751,8 @@ public class VCFFilter extends JFrame
           }
         }
 
-        if(record.getFilter().length() == 0)
+        if(  record.getFilter().length() == 0 ||
+            (record.getFilter().length() == 1 && record.getFilter().equals(".")) )
           record.setFilter("PASS");
         return;
       }

uk/ac/sanger/artemis/components/variant/VCFRecord.java

@@ -312,7 +312,9 @@ public class VCFRecord
   
   protected void appendFilter(String filter)
   {
-    if(getFilter().length() == 0 || (getFilter().length() == 1 && getFilter().equals(".")))
+    if(  getFilter().length() == 0 || 
+        (getFilter().length() == 1 && getFilter().equals(".")) ||
+        (getFilter().length() == 3 && getFilter().equals("PASS")))
       this.filter = filter;
     else
       this.filter += ";" + filter;