From ba7df054f0be01a3aa02696b0f61136bc5be45c7 Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Sat, 24 Jun 2017 13:40:25 -0400
Subject: [PATCH] Close BQSRGatherer's PrintStream when finished

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

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 2dbe1d50c..cb23c02ea 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
@@ -61,6 +61,7 @@ public class BQSRGatherer extends Gatherer  {
             throw new UserException.MissingArgument("output", MISSING_OUTPUT_FILE);
         }
         final GATKReport report = gatherReport(inputs);
+        outputFile.close();
         report.print(outputFile);
     }