From 849bd1f45144e2bfa127f7d7cbb1f521a8013045 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 16 Mar 2010 22:01:23 +0000
Subject: [PATCH] Set the eagerDecode flag in such a way that the binary data
 block in the BAM will always be considered dirty.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3014 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../datasources/simpleDataSources/BlockDrivenSAMDataSource.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java
index b575ef6b8..7ee595b21 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java
@@ -411,7 +411,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
          */
         public SAMReaders(Reads sourceInfo) {
             for(File readsFile: sourceInfo.getReadsFiles()) {
-                SAMFileReader2 reader = new SAMFileReader2(readsFile,false);
+                SAMFileReader2 reader = new SAMFileReader2(readsFile,true);
                 reader.setValidationStringency(sourceInfo.getValidationStringency());
 
                 // If no read group is present, hallucinate one.