From 726378be8bc264d9ede025460e3ef55ae6c0469a Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 27 Oct 2009 15:28:05 +0000
Subject: [PATCH] Almost ready to stop doing eagar decoding; waiting on Eric

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1914 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../datasources/simpleDataSources/ReadStreamResource.java     | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReadStreamResource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReadStreamResource.java
index ce91d3a99..1eee99679 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReadStreamResource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReadStreamResource.java
@@ -45,6 +45,8 @@ import java.io.File;
  * @version 0.1
  */
 class ReadStreamResource {
+    final static boolean eagerDecode = true;
+
     /** our log, which we want to capture anything from this class */
     protected static Logger logger = Logger.getLogger(ReadStreamPointer.class);
 
@@ -124,7 +126,7 @@ class ReadStreamResource {
         // right now this is pretty damn heavy, it copies the file list into a reader list every time
         List<SAMFileReader> lst = new ArrayList<SAMFileReader>();
         for (File f : reads.getReadsFiles()) {
-            SAMFileReader reader = new SAMFileReader(f, true);
+            SAMFileReader reader = new SAMFileReader(f, eagerDecode);
             reader.setValidationStringency(reads.getValidationStringency());
 
             final SAMFileHeader header = reader.getFileHeader();