From 7d58544f1729ec4e1e0c75126b00656fdb512a24 Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Tue, 6 Jan 2015 10:32:11 -0500
Subject: [PATCH] Do not use logger, write to stderr, could not get the correct
 logger dependency in pom.xml

---
 public/VectorPairHMM/src/main/c++/Sandbox.java | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/public/VectorPairHMM/src/main/c++/Sandbox.java b/public/VectorPairHMM/src/main/c++/Sandbox.java
index 58234e027..ae8497ea7 100644
--- a/public/VectorPairHMM/src/main/c++/Sandbox.java
+++ b/public/VectorPairHMM/src/main/c++/Sandbox.java
@@ -25,7 +25,6 @@
 
 package org.broadinstitute.gatk.utils.vectorpairhmm;
 
-import org.apache.log4j.Logger;
 import java.util.List;
 import java.util.LinkedList;
 import java.util.Map;
@@ -38,8 +37,6 @@ import java.io.InputStreamReader;
 
 public class Sandbox {
 
-    protected final static Logger logger = Logger.getLogger(Sandbox.class);
-
     private long setupTime = 0;
     private long computeTime = 0;
     //Used to copy references to byteArrays to JNI from reads
@@ -159,7 +156,7 @@ public class Sandbox {
     public native void jniClose();
     public void close()
     {
-        logger.info("Time spent in setup for JNI call : "+(setupTime*1e-9)+" compute time : "+(computeTime*1e-9));
+        System.err.println("Time spent in setup for JNI call : " + (setupTime * 1e-9) + " compute time : " + (computeTime * 1e-9));
         jniClose();
     }
 
@@ -173,7 +170,7 @@ public class Sandbox {
       }
       catch(FileNotFoundException e)
       {
-          logger.error("File "+filename + " cannot be found/read");
+          System.err.println("File "+filename + " cannot be found/read");
           return;
       }
       int idx = 0;