Must close the writer to flush the cache

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4726 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java

@@ -90,6 +90,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
     }
 
     public void onTraversalDone(Integer result) {
+        writer.close();
         System.out.println(result + " variants were aligned");
     }