From ebfbe56b4305a9b75477d6fe50e43f46549fd827 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 23 Sep 2009 18:20:26 +0000
Subject: [PATCH] Make sure compression level always gets pushed into
 SAMFileWriterFactory.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1699 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/io/storage/SAMFileWriterStorage.java            | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

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 9fe56e1a8..0dcd48792 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
@@ -31,7 +31,6 @@ import net.sf.samtools.util.CloseableIterator;
 import java.io.*;
 
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
-import org.broadinstitute.sting.gatk.io.storage.Storage;
 
 /**
  * Provides temporary storage for SAMFileWriters.
@@ -49,7 +48,7 @@ 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 );
+        this.writer = new SAMFileWriterFactory().makeBAMWriter( stub.getSAMFileHeader(), true, file, stub.getCompressionLevel() );
     }
 
     public void addAlignment( SAMRecord read ) {