From 52bfe8db8a7e472f2282be89372b0c10021ab10d Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 16 Aug 2012 10:56:07 -0400
Subject: [PATCH] Make sure the storage writer is closed before running
 mergeInfo in multi-threaded output management

-- It's not clear this is cause of GSA-484 but it will help confirm that it's not the cause
---
 .../sting/gatk/io/storage/VariantContextWriterStorage.java    | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
index 72f8581dd..0f5290db7 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
@@ -61,6 +61,7 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
     protected final File file;
     protected OutputStream stream;
     protected final VariantContextWriter writer;
+    boolean closed = false;
 
     /**
      * Constructs an object which will write directly into the output file provided by the stub.
@@ -172,10 +173,13 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
         if(file != null)
             logger.debug("Closing temporary file " + file.getAbsolutePath());
         writer.close();
+        closed = true;
     }
 
     public void mergeInto(VariantContextWriterStorage target) {
         try {
+            if ( ! closed )
+                throw new ReviewedStingException("Writer not closed, but we are merging into the file!");
             final String targetFilePath = target.file != null ? target.file.getAbsolutePath() : "/dev/stdin";
             logger.debug(String.format("Merging %s into %s",file.getAbsolutePath(),targetFilePath));