From e06dfe44c44fb63fb81956e6c13e9efadfdab06d Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 21 Dec 2009 07:01:41 +0000
Subject: [PATCH] Check for null platform (even when the read group isn't null)
 and assign it the default platform if it is

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2420 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/recalibration/RecalDataManager.java  | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
index 8092f8c1a..3bb6ee3f2 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -250,9 +250,13 @@ public class RecalDataManager {
             ((GATKSAMRecord)read).setReadGroup( readGroup );
         }
 
-        if( RAC.FORCE_PLATFORM != null && !readGroup.getPlatform().equals(RAC.FORCE_PLATFORM)) {
+        if( RAC.FORCE_PLATFORM != null && (readGroup.getPlatform() == null || !readGroup.getPlatform().equals(RAC.FORCE_PLATFORM))) {
             readGroup.setPlatform( RAC.FORCE_PLATFORM );
         }
+
+        if ( readGroup.getPlatform() == null ) {
+            readGroup.setPlatform( RAC.DEFAULT_PLATFORM );            
+        }
     }
 
     /**