Fixed nasty bug where we weren't closing the underlying PositionalOutputStream in IndexingVariantContextWriter

public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IndexingVariantContextWriter.java

@@ -159,4 +159,10 @@ final class PositionalOutputStream extends OutputStream {
     }
 
     public final long getPosition() { return position; }
+
+    @Override
+    public void close() throws IOException {
+        super.close();
+        out.close();
+    }
 }