From 312d97d53bdf5389a94d0a6bf3e296507e1cc636 Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Mon, 26 Jun 2017 13:43:09 -0400
Subject: [PATCH] Close BQSRGatherer's PrintStream when finished

---
 .../broadinstitute/gatk/engine/recalibration/BQSRGatherer.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java
index cb23c02ea..2a83bc383 100644
--- a/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java
+++ b/public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java
@@ -61,8 +61,8 @@ public class BQSRGatherer extends Gatherer  {
             throw new UserException.MissingArgument("output", MISSING_OUTPUT_FILE);
         }
         final GATKReport report = gatherReport(inputs);
-        outputFile.close();
         report.print(outputFile);
+        outputFile.close();
     }
 
     /**