From d9fa04f65cd25bc25294067e2729ef39108fd854 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 17 Mar 2009 22:20:03 +0000
Subject: [PATCH] Fixed logic

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@84 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/playground/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/playground/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
index c3f325c71..64fe01628 100644
--- a/playground/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
+++ b/playground/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
@@ -104,7 +104,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         }
 
         engine.setSafetyChecking(! UNSAFE.toLowerCase().equals("true"));
-        engine.setSortOnFly(! ENABLED_SORT_ON_FLY.toLowerCase().equals("true"));
+        engine.setSortOnFly(ENABLED_SORT_ON_FLY.toLowerCase().equals("true"));
 
         engine.initialize(ENABLED_THREADED_IO.toLowerCase().equals("true"));
         //engine.testReference();