diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java
index 0f59131f5..8e218f950 100755
--- a/public/java/test/org/broadinstitute/sting/BaseTest.java
+++ b/public/java/test/org/broadinstitute/sting/BaseTest.java
@@ -1,20 +1,12 @@
 package org.broadinstitute.sting;
 
-import org.apache.commons.io.FileUtils;
 import org.apache.log4j.*;
 import org.apache.log4j.spi.LoggingEvent;
-import org.apache.xmlbeans.impl.common.IOUtil;
 import org.broadinstitute.sting.commandline.CommandLineUtils;
-import org.broadinstitute.sting.gatk.walkers.diffengine.DiffEngine;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.io.IOUtils;
-import org.testng.Assert;
 
-import javax.swing.*;
 import java.io.*;
-import java.math.BigInteger;
-import java.security.MessageDigest;
-import java.security.NoSuchAlgorithmException;
 import java.util.*;
 
 /**
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala
index d9147a0ed..8b286f090 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala
@@ -24,30 +24,6 @@
 
 package org.broadinstitute.sting.queue.pipeline.examples
 
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
 import org.testng.annotations.Test
 import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 import org.broadinstitute.sting.BaseTest
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala
index 858e1cce6..d50673a1a 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala
@@ -24,54 +24,6 @@
 
 package org.broadinstitute.sting.queue.pipeline.examples
 
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
 import org.testng.annotations.Test
 import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
 import org.broadinstitute.sting.BaseTest