From 09df584788653878c7be85eb2e3a01da08839f2e Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 14 Jun 2012 09:42:11 -0400
Subject: [PATCH] Fixed nasty bug where we weren't closing the underlying
 PositionalOutputStream in IndexingVariantContextWriter

---
 .../variantcontext/writer/IndexingVariantContextWriter.java | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IndexingVariantContextWriter.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IndexingVariantContextWriter.java
index 4f577fbcf..df0feda8b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IndexingVariantContextWriter.java
+++ b/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();
+    }
 }
\ No newline at end of file