From 501f6a0e1442329453e944c1bcaae1a2621fab28 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 7 Sep 2010 16:57:51 +0000
Subject: [PATCH] Temporary hack to disable index creation when target BAM is
 /dev/null.  Tim promises me that Picard will put in a real solution next
 week.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4220 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/io/storage/SAMFileWriterStorage.java          | 5 +++++
 1 file changed, 5 insertions(+)

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 dea36e112..a51da7323 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
@@ -58,6 +58,11 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
             factory.setMaxRecordsInRam(stub.getMaxRecordsInRam());
 
         if(stub.getSAMFile() != null) {
+            // HACK: Turn setCreateIndex off if the SAM file is null.  Picard has pledged to fix this
+            //       during the week of 14 Sept 2010.  Eliminate this check when they do.
+            if(stub.getSAMFile().getPath().equals("/dev/null"))
+                factory.setCreateIndex(false);
+            
             if( stub.getCompressionLevel() != null )
                 this.writer = factory.makeBAMWriter( stub.getFileHeader(), stub.isPresorted(), file, stub.getCompressionLevel() );
             else