From 856bbd03206e86007aa046f1e0aa721c1d528980 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 23 Sep 2009 19:01:48 +0000
Subject: [PATCH] Let Picard specify the default compression level.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1701 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/io/storage/SAMFileWriterStorage.java          | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
index 0dcd48792..7923b37bf 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
@@ -48,7 +48,10 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
 
     public SAMFileWriterStorage( SAMFileWriterStub stub, File file ) {
         this.file = file;
-        this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getSAMFileHeader(), true, file, stub.getCompressionLevel() );
+        if( stub.getCompressionLevel() != null )
+            this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getSAMFileHeader(), true, file, stub.getCompressionLevel() );
+        else
+            this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getSAMFileHeader(), true, file );
     }
 
     public void addAlignment( SAMRecord read ) {