diff --git a/build.xml b/build.xml
index a78c4d738..fe4c7a3f4 100644
--- a/build.xml
+++ b/build.xml
@@ -28,6 +28,7 @@
 
     <property name="build.dir" value="build" />
     <property name="dist.dir" value="dist" />
+    <property name="lib.dir" value="lib" />
     <property name="external.dir" value="external" />
     <property name="public.dir" value="public" />
     <property name="private.dir" value="private" />
@@ -44,11 +45,11 @@
     <property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
     
     <!-- Contracts for Java -->
-    <!-- uncomment out to enable building contracts -->
-    <property name="use.contracts" value="true" /> 
+    <!-- To disable, run with -Duse.contracts=false -->
+    <property name="use.contracts" value="true" />
     <property name="java.contracts" value="${build.dir}/java/contracts" />
-    <property name="cofojaDir" value="settings/repository/com.google/"/>
-    <property name="cofoja.jar" value="${cofojaDir}/cofoja-1.0-20110609.jar"/>
+    <property name="contracts.version" value="1.0-20110609" />
+    <property name="cofoja.jar" value="${lib.dir}/cofoja-${contracts.version}.jar"/>
     
     <!-- where to find the tribble distro -->
     <property name="tribble.dir" value="tribble" />
@@ -101,7 +102,7 @@
     </patternset>
     
     <path id="external.dependencies">
-      <fileset dir="lib">
+      <fileset dir="${lib.dir}">
         <patternset refid="dependency.mask" />
       </fileset>
     </path>
@@ -126,14 +127,14 @@
         <!-- ivy properties -->
         <property name="ivy.install.version" value="2.2.0"/>
         <property name="ivy.home" value="${user.home}/.ant"/>
-        <property name="ivy.jar.dir" value="${ivy.home}/lib"/>
+        <property name="ivy.jar.dir" value="${ivy.home}/${lib.dir}"/>
         <property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/>
         <property name="ivy.settings.dir" value="settings"/>
         <property file="${ivy.settings.dir}/ivysettings.properties"/>
   
-      <mkdir dir="lib"/>
+      <mkdir dir="${lib.dir}"/>
       <mkdir dir="${ivy.jar.dir}"/>
-      <copy file="${cofoja.jar}" toFile="lib/cofoja.jar"/>
+
       <get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
            dest="${ivy.jar.dir}/${ivy.jar.file}"
            usetimestamp="true"/>
@@ -227,6 +228,10 @@
         <equals arg1="${gatk.target}" arg2="private" casesensitive="false" />
       </condition>
 
+      <condition property="include.contracts">
+        <equals arg1="${use.contracts}" arg2="true" />
+      </condition>
+
       <!-- Create the build directory structure used by compile -->
       <mkdir dir="${build.dir}"/>
       <mkdir dir="${java.classes}"/>
@@ -250,7 +255,7 @@
     <target name="init.scala.compile" depends="resolve"
             description="Initializes the scala ant tasks from scala-compiler.jar">
         <path id="scala.classpath">
-            <fileset dir="lib">
+            <fileset dir="${lib.dir}">
                 <include name="scala-compiler-*.jar"/>
                 <include name="scala-library-*.jar"/>
             </fileset>
@@ -285,7 +290,7 @@
             depends="gatk.compile.public.source,gatk.compile.private.source,gatk.compile.external.source" 
             description="compile the GATK source" />
 
-   <target name="gatk.contracts.public" depends="gatk.compile.source">
+   <target name="gatk.contracts.public" depends="gatk.compile.source" if="include.contracts">
         <javac fork="true" memoryMaximumSize="512m" srcdir="${java.public.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
             <classpath>
                 <path refid="external.dependencies" />
@@ -297,7 +302,16 @@
         </javac>   
    </target>
 
-   <target name="gatk.contracts.private" depends="gatk.compile.source" if="include.private">
+    <target name="check.contracts.private" depends="gatk.contracts.public">
+        <condition property="include.contracts.private">
+          <and>
+            <isset property="include.contracts" />
+            <isset property="include.private" />
+          </and>
+        </condition>
+    </target>
+
+   <target name="gatk.contracts.private" depends="check.contracts.private" if="include.contracts.private">
         <javac fork="true" memoryMaximumSize="512m" srcdir="${java.private.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
             <classpath>
                 <path refid="external.dependencies" />
@@ -310,7 +324,7 @@
    </target>
 
     <target name="gatk.contracts" depends="gatk.contracts.public,gatk.contracts.private" 
-            description="create GATK contracts" if="use.contracts" />
+            description="create GATK contracts" if="include.contracts" />
     
     <target name="gatk.compile" depends="tribble,init,resolve,gatk.compile.source,gatk.contracts" />
 
@@ -448,7 +462,7 @@
     <target name="init.jar" depends="sting.compile,extracthelp">
         <mkdir dir="${dist.dir}"/>
         <copy todir="${dist.dir}">
-            <fileset dir="lib" includes="*.jar"/>
+            <fileset dir="${lib.dir}" includes="*.jar"/>
         </copy>
     </target>
 
@@ -460,7 +474,7 @@
               <exclude name="**/utils/variantcontext/**/*.class"/>
             </fileset>
             <fileset dir="${java.classes}" includes="**/commandline/**/*.class"/>
-            <fileset dir="${java.classes}" includes="**/sting/datasources/**/*.class"/>
+            <fileset dir="${java.classes}" includes="**/sting/pipeline/**/*.class"/>
             <fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/>
             <fileset dir="${java.classes}" includes="net/sf/picard/**/*.class"/>
             <fileset dir="${java.classes}" includes="net/sf/samtools/**/*.class"/>
@@ -659,7 +673,7 @@
                 <path refid="external.dependencies" />
                 <pathelement location="${java.classes}"/>
                 <pathelement location="${java.contracts}"/>
-                <pathelement location="lib/testng-5.14.1.jar"/>
+                <pathelement location="${lib.dir}/testng-5.14.1.jar"/>
             </classpath>
             <compilerarg value="-proc:none"/>
 <!-- 
@@ -682,7 +696,7 @@
                 <path refid="scala.dependencies"/>
                 <pathelement location="${scala.test.classes}"/>
                 <pathelement location="${java.test.classes}"/>
-                <pathelement location="lib/testng-5.14.1.jar"/>
+                <pathelement location="${lib.dir}/testng-5.14.1.jar"/>
             </classpath>
         </scalac>
     </target>
@@ -722,9 +736,13 @@
                 <equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
             </condition>
 
+            <condition property="cofoja.jvm.args" value="-javaagent:${cofoja.jar} -Dcom.google.java.contract.log.contract=false" else="">
+                <isset property="include.contracts" />
+            </condition>
+
             <mkdir dir="${report}/@{testtype}"/>
             <echo message="Sting: Running @{testtype} test cases!"/>
-            <taskdef resource="testngtasks" classpath="lib/testng-5.14.1.jar"/>
+            <taskdef resource="testngtasks" classpath="${lib.dir}/testng-5.14.1.jar"/>
             <testng outputDir="${report}/@{testtype}"
                     haltOnFailure="false" failureProperty="test.failure"
                     verbose="2"
@@ -735,9 +753,7 @@
                 <jvmarg value="-Djava.awt.headless=true" />
                 <jvmarg value="-Dpipeline.run=${pipeline.run}" />
                 <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
-                <!-- needs to be if -->
-                <!--jvmarg value="-javaagent:lib/cofoja.jar"/-->
-                <!--jvmarg value="-Dcom.google.java.contract.log.contract=false"/-->
+                <jvmarg line="${cofoja.jvm.args}"/>
 <!--                 <jvmarg value="-Xdebug"/> -->
 <!--                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
                 <classpath>
@@ -764,6 +780,50 @@
         </sequential>
     </macrodef>
 
+    <!-- FAILED-TEST -->
+    <macrodef name="run-failed-test">
+        <attribute name="xmlfailedtestfile" />
+        <sequential>
+            <!-- Get the pipeline run type.  Default to dry.  -->
+            <condition property="pipeline.run" value="dry" else="${pipeline.run}">
+                <equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
+            </condition>
+
+            <condition property="cofoja.jvm.args" value="-javaagent:${cofoja.jar} -Dcom.google.java.contract.log.contract=false" else="">
+                <isset property="include.contracts" />
+            </condition>
+
+            <mkdir dir="${report}/failed_rerun" />
+            <echo message="Sting: Running @{xmlfailedtestfile} test cases!"/>
+            <taskdef resource="testngtasks" classpath="${lib.dir}/testng-5.14.1.jar"/>
+            <testng outputDir="${report}/failed_rerun"
+                    haltOnFailure="false" failureProperty="test.failure"
+                    verbose="2"
+                    workingDir="${basedir}"
+                    useDefaultListeners="false"
+                    listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.StingTextReporter">
+                <jvmarg value="-Xmx${test.maxmemory}" />
+                <jvmarg value="-Djava.awt.headless=true" />
+                <jvmarg value="-Dpipeline.run=${pipeline.run}" />
+                <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
+                <jvmarg line="${cofoja.jvm.args}"/>
+<!--                 <jvmarg value="-Xdebug"/> -->
+<!--                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
+                <classpath>
+                    <path refid="external.dependencies" />
+                    <pathelement location="${java.classes}" />
+                    <pathelement location="${scala.classes}" />
+                    <pathelement location="${java.contracts}" />
+                    <pathelement location="${java.test.classes}" />
+                    <pathelement location="${scala.test.classes}" />
+                </classpath>
+
+                <xmlfileset dir="${basedir}" includes="@{xmlfailedtestfile}" />
+            </testng>
+
+            <fail message="test failed" if="test.failure" />
+        </sequential>
+    </macrodef>
 
     <!-- our three different test conditions: Test, IntegrationTest, PerformanceTest -->
     <target name="test" depends="test.compile,tribble.test" description="Run unit tests">
@@ -798,6 +858,22 @@
         <run-test testtype="${pipetype}"/>
     </target>
 
+    <target name="failed-test" depends="test.compile">
+        <run-failed-test xmlfailedtestfile="${report}/*UnitTest/testng-failed.xml" />
+    </target>
+
+    <target name="failed-integration" depends="test.compile">
+        <run-failed-test xmlfailedtestfile="${report}/*IntegrationTest/testng-failed.xml" />
+    </target>
+
+    <target name="failed-performance" depends="test.compile">
+        <run-failed-test xmlfailedtestfile="${report}/*PerformanceTest/testng-failed.xml" />
+    </target>
+
+    <target name="failed-pipeline" depends="test.compile">
+        <run-failed-test xmlfailedtestfile="${report}/*PipelineTest/testng-failed.xml" />
+    </target>
+
     <!-- ***************************************************************************** -->
     <!-- ***********                     Tribble                             ********* -->
     <!-- ***************************************************************************** -->
@@ -815,7 +891,7 @@
 
     <!-- copy the compiled library -->
     <target name="tribble.compile.copy" description="Copies the compiled tribble library" depends="tribble.compile" if="tribble.compile.exists">
-        <copy todir="lib">
+        <copy todir="${lib.dir}">
             <fileset dir="${tribble.dir}/dist" includes="*.jar"/>
         </copy>
     </target>
@@ -823,7 +899,7 @@
     <!-- copy the precompiled library -->
     <target name="tribble.library.copy" description="Copies the precompiled tribble library" depends="tribble.init" unless="tribble.compile.exists">
         <echo message="Copying the Tribble Library..."/>
-        <copy todir="lib">
+        <copy todir="${lib.dir}">
             <fileset dir="settings/repository/org.broad" includes="tribble*.jar"/>
         </copy>
     </target>
@@ -916,8 +992,8 @@
       <pathconvert property="required.picard.jars" pathsep=":">
         <fileset dir="${basedir}">
 	     <include name="staging" />
-	     <include name="lib/picard-*.*.*.jar" />
-	     <include name="lib/sam-*.jar" />
+	     <include name="${lib.dir}/picard-*.*.*.jar" />
+	     <include name="${lib.dir}/sam-*.jar" />
 	   </fileset>
       </pathconvert>
       <echo message="required.picard.jars=${required.picard.jars}" />
@@ -939,7 +1015,7 @@
     <!-- Find bug tasks                                                                   -->
     <!-- ******************************************************************************** -->
     <path id="findbugs.classpath">
-      <fileset dir="lib" erroronmissingdir="true" includes="*.jar"/>
+      <fileset dir="${lib.dir}" erroronmissingdir="true" includes="*.jar"/>
     </path>
     <target         name="findbugs" depends="dist">
         <antcall    target  ="resolve">
@@ -964,7 +1040,8 @@
     <target name="clean" description="clean up" depends="tribble.clean,clean.javadoc">
         <delete dir="out"/>
         <delete dir="${build.dir}"/>
-        <delete dir="lib"/>
+        <delete dir="${lib.dir}"/>
+        <delete dir="dump"/>
         <delete dir="staging"/>
         <delete dir="${dist.dir}"/>
         <delete dir="pipelinetests"/>
diff --git a/ivy.xml b/ivy.xml
index 10e4ee570..3f3d1c97f 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -63,6 +63,10 @@
     <dependency org="net.sourceforge.findbugs" name="jsr305" rev="1.3.2" conf="test"/>
     <dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test" />
 
+    <!-- Contracts for Java and dependencies -->
+    <dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-20110609" />
+    <dependency org="asm" name="asm-all" rev="3.3.1" />
+
     <!-- POI, for reading pipeline files -->
     <dependency org="org.apache.poi" name="poi" rev="3.8-beta3" />
     <dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3" />
diff --git a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
index f8e298d88..b9e380295 100755
--- a/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
+++ b/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java
@@ -25,20 +25,21 @@
 
 package org.broadinstitute.sting.analyzecovariates;
 
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.gatk.walkers.recalibration.*;
+import org.broadinstitute.sting.gatk.walkers.recalibration.Covariate;
+import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatum;
+import org.broadinstitute.sting.gatk.walkers.recalibration.RecalibrationArgumentCollection;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.commandline.CommandLineProgram;
-import org.broadinstitute.sting.commandline.Argument;
 
+import java.io.*;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.List;
 import java.util.Map;
 import java.util.regex.Pattern;
-import java.io.*;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/commandline/Argument.java b/public/java/src/org/broadinstitute/sting/commandline/Argument.java
index b2ee9d1fc..33592287d 100755
--- a/public/java/src/org/broadinstitute/sting/commandline/Argument.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/Argument.java
@@ -25,12 +25,7 @@
 
 package org.broadinstitute.sting.commandline;
 
-import java.lang.annotation.Documented;
-import java.lang.annotation.ElementType;
-import java.lang.annotation.Inherited;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
+import java.lang.annotation.*;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
index c36a8e04f..b47677b08 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
@@ -27,10 +27,10 @@ package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.List;
-import java.util.Collections;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Iterator;
+import java.util.List;
 
 /**
  * A group of argument definitions.
diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
index 39e698ca3..9f92df6e0 100755
--- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
@@ -27,10 +27,10 @@ package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.Set;
-import java.util.HashSet;
 import java.util.Collection;
+import java.util.HashSet;
 import java.util.Iterator;
+import java.util.Set;
 
 /**
  * A collection of argument definitions.
diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
index 6c50e1784..9c33e084d 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
@@ -25,12 +25,12 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.walkers.Multiplex;
 import org.broadinstitute.sting.gatk.walkers.Multiplexer;
-import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.lang.annotation.Annotation;
diff --git a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java b/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
index d404a2b6e..aba4fc109 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java
@@ -25,14 +25,20 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.apache.log4j.*;
+import org.apache.log4j.FileAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.PatternLayout;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.help.ApplicationDetails;
 import org.broadinstitute.sting.utils.help.HelpFormatter;
 
 import java.io.IOException;
-import java.util.*;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.EnumSet;
+import java.util.Locale;
 
 public abstract class CommandLineProgram {
 
diff --git a/public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java b/public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
index 99608f167..bd2006388 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
@@ -25,11 +25,17 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.apache.log4j.*;
+import org.apache.log4j.Appender;
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Logger;
+import org.apache.log4j.PatternLayout;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.*;
 import java.lang.annotation.Annotation;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.LinkedHashMap;
+import java.util.Map;
 
 /**
  * Static utility methods for working with command-line arguments.
diff --git a/public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java b/public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java
index 8029db7b3..4e6c3a16f 100644
--- a/public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java
@@ -26,8 +26,6 @@ package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.Utils;
 
-import java.util.Collection;
-
 /**
  * Specifies that a value was missing when attempting to populate an argument.
  */
diff --git a/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java b/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
index 717c5c522..8423bb2f2 100755
--- a/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
@@ -25,16 +25,16 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.ApplicationDetails;
 import org.broadinstitute.sting.utils.help.HelpFormatter;
-import org.apache.log4j.Logger;
 
-import java.lang.reflect.*;
+import java.lang.reflect.Field;
 import java.util.*;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java b/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java
index d1cda3ed9..a070cb5a1 100755
--- a/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java
+++ b/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java
@@ -27,10 +27,8 @@ package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.Utils;
 
-import java.util.regex.Pattern;
 import java.util.regex.Matcher;
-import java.util.List;
-import java.util.ArrayList;
+import java.util.regex.Pattern;
 
 /**
  * Holds a pattern, along with how to get to the argument definitions that could match that pattern.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
index fd7e749c3..a080ab439 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
@@ -25,30 +25,21 @@
 
 package org.broadinstitute.sting.gatk;
 
-import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
-import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
+import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
-import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
-import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
-import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.util.*;
-
-import net.sf.picard.filter.SamRecordFilter;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.ListFileUtils;
-import org.broadinstitute.sting.utils.text.XReadLines;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
 
 /**
  * @author aaron
diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
index 7982f61e2..da2be74bf 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
@@ -26,13 +26,15 @@
 package org.broadinstitute.sting.gatk;
 
 import org.broad.tribble.TribbleException;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.ArgumentCollection;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.walkers.Attribution;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.text.TextFormattingUtils;
-import org.broadinstitute.sting.utils.help.ApplicationDetails;
-import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.ApplicationDetails;
+import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index f8527c33b..918bc1251 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -28,24 +28,14 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.samtools.*;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.ArgumentException;
-import org.broadinstitute.sting.commandline.ArgumentSource;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.commandline.CommandLineUtils;
-import org.broadinstitute.sting.commandline.ParsingEngine;
-import org.broadinstitute.sting.commandline.Tags;
+import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.gatk.datasources.reads.Shard;
+import org.broadinstitute.sting.gatk.datasources.reads.*;
 import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
-import org.broadinstitute.sting.gatk.datasources.reads.MonolithicShardStrategy;
-import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
-import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategyFactory;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
 import org.broadinstitute.sting.gatk.executive.MicroScheduler;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
@@ -65,6 +55,7 @@ import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java b/public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
index 27a86ab3f..7cb615f7f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
@@ -25,13 +25,12 @@
 package org.broadinstitute.sting.gatk;
 
 import net.sf.picard.filter.SamRecordFilter;
-
-import java.util.Map;
-import java.util.HashMap;
-import java.util.Collections;
-
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
 /**
  * Holds a bunch of basic information about the traversal.
  */
diff --git a/public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java b/public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java
index 1a361029a..93fa2d146 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileReader;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
index 9553f651e..cf190835e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
@@ -25,19 +25,18 @@
 
 package org.broadinstitute.sting.gatk;
 
-import net.sf.picard.filter.SamRecordFilter;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.text.TextFormattingUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.help.DescriptionTaglet;
 import org.broadinstitute.sting.utils.help.DisplayNameTaglet;
 import org.broadinstitute.sting.utils.help.SummaryTaglet;
-import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index 93638f21d..ee2e85025 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -26,17 +26,16 @@
 package org.broadinstitute.sting.gatk.arguments;
 
 import net.sf.samtools.SAMFileReader;
-import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
-import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.gatk.DownsampleType;
 import org.broadinstitute.sting.gatk.DownsamplingMethod;
-import org.broadinstitute.sting.utils.interval.IntervalSetRule;
+import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
 import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
+import org.broadinstitute.sting.utils.interval.IntervalSetRule;
 import org.simpleframework.xml.*;
 import org.simpleframework.xml.core.Persister;
 import org.simpleframework.xml.stream.Format;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
index 337c2664c..17e4a0743 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
@@ -26,13 +26,13 @@
 package org.broadinstitute.sting.gatk.contexts;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.HasGenomeLocation;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
-import java.util.*;
+import java.util.List;
 
 /**
  * Useful class for forwarding on locusContext data from this iterator
diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java
index 6a0d30837..1f9a7d705 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java
@@ -27,8 +27,8 @@ package org.broadinstitute.sting.gatk.contexts;
 
 import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
index 760b3a7bc..376064cdb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
@@ -25,11 +25,12 @@
 
 package org.broadinstitute.sting.gatk.contexts;
 
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.BaseUtils;
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Requires;
 import net.sf.samtools.util.StringUtil;
-import com.google.java.contract.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 /**
  * The section of the reference that overlaps with the given
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
index b36c59a2c..e92599494 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
@@ -1,16 +1,14 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
+
+import java.util.Collections;
 import java.util.List;
 import java.util.NoSuchElementException;
-import java.util.ArrayList;
-import java.util.Collections;
-
-import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 /**
  * User: hanna
  * Date: May 13, 2009
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
index 330a9e4f7..ff312bcac 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
@@ -1,13 +1,12 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
+import net.sf.picard.reference.ReferenceSequence;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.Window;
-import org.broadinstitute.sting.gatk.walkers.Reference;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import net.sf.picard.reference.ReferenceSequence;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 /*
  * Copyright (c) 2009 The Broad Institute
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java
index 72b962522..55304da34 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java
@@ -1,16 +1,15 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.iterators.LocusIterator;
-import org.broadinstitute.sting.gatk.ReadProperties;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.Collection;
 
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-
 /**
  * Presents data sharded by locus to the traversal engine.
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
index b467a2ab5..f9ed0cb74 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
-import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.DownsampleType;
+import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.iterators.LocusIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
index a91e169c1..223659a46 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
@@ -5,10 +5,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
-import java.util.List;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.List;
 /**
  * User: hanna
  * Date: May 21, 2009
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
index d2c097f5d..3d62faf49 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
@@ -1,9 +1,8 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.utils.GenomeLoc;
 /*
  * Copyright (c) 2009 The Broad Institute
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java
index 5a672b09f..7843e7518 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java
@@ -1,14 +1,13 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.Collection;
 
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-
 /**
  * Present data sharded by read to a traversal engine.
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java
index 0c4b78a7c..e809092d4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java
@@ -1,11 +1,10 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 
-import java.util.Collection;
 import java.util.Arrays;
-
-import net.sf.samtools.SAMRecord;
+import java.util.Collection;
 /**
  * User: hanna
  * Date: May 22, 2009
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
index d6c938f36..efb92235f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
@@ -1,16 +1,16 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
-import org.broadinstitute.sting.utils.*;
-
-import java.util.Collections;
-import java.util.Collection;
-import java.util.Arrays;
-
-import net.sf.samtools.SAMSequenceRecord;
-import net.sf.samtools.SAMRecord;
-import net.sf.picard.reference.ReferenceSequence;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.picard.reference.ReferenceSequence;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMSequenceRecord;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
 /**
  * User: hanna
  * Date: May 22, 2009
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
index feed2ab85..39c632539 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
@@ -25,9 +25,9 @@
 
 package org.broadinstitute.sting.gatk.datasources.providers;
 
-import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.utils.GenomeLoc;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
index a0ea32f9b..803bd885b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
@@ -1,15 +1,14 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.ArrayList;
-import java.util.List;
 import java.util.Collection;
-
-import net.sf.picard.reference.IndexedFastaSequenceFile;
+import java.util.List;
 /**
  * User: hanna
  * Date: May 8, 2009
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java
index a9e04e357..de938e845 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java
@@ -24,9 +24,6 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import net.sf.samtools.SAMFileReader;
-import net.sf.samtools.SAMRecord;
-import org.apache.commons.lang.ArrayUtils;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 
 import java.io.File;
@@ -35,9 +32,7 @@ import java.io.IOException;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.nio.channels.FileChannel;
-import java.util.ArrayList;
 import java.util.Iterator;
-import java.util.List;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
index 34693d501..521bcd5a3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
@@ -39,12 +39,7 @@ import java.io.RandomAccessFile;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.nio.channels.FileChannel;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 /**
  * Writes schedules for a single BAM file to a target output file.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
index 266232c0f..467aebac5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
@@ -26,20 +26,10 @@ package org.broadinstitute.sting.gatk.datasources.reads;
 
 import net.sf.picard.util.PeekableIterator;
 import net.sf.samtools.GATKBAMFileSpan;
-import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.NoSuchElementException;
+import java.util.*;
 
 /**
  * Assign intervals to the most appropriate blocks, keeping as little as possible in memory at once.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
index c014c1995..e4141f61c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
@@ -29,19 +29,11 @@ import net.sf.samtools.GATKBAMFileSpan;
 import net.sf.samtools.SAMFileSpan;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.SortedMap;
-import java.util.TreeMap;
+import java.util.*;
 
 /**
  * Represents a small section of a BAM file, and every associated interval.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
index 8ebb8b1a8..5d0c38b78 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
@@ -23,24 +23,18 @@
  */
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import net.sf.samtools.Bin;
-
-import net.sf.samtools.GATKBAMFileSpan;
-import net.sf.samtools.GATKBin;
-import net.sf.samtools.GATKChunk;
-import net.sf.samtools.LinearIndex;
-import net.sf.samtools.SAMException;
-import net.sf.samtools.util.RuntimeIOException;
+import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
-import java.lang.ref.SoftReference;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.nio.channels.FileChannel;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 
 /**
  * A basic interface for querying BAM indices.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java
index f9b998a60..daf1b77e3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java
@@ -24,11 +24,7 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import net.sf.samtools.Bin;
-import net.sf.samtools.GATKBAMFileSpan;
-import net.sf.samtools.GATKBin;
-import net.sf.samtools.GATKChunk;
-import net.sf.samtools.LinearIndex;
+import net.sf.samtools.*;
 
 import java.util.ArrayList;
 import java.util.Collections;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
index fc3f76ab7..4ddf28dce 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
@@ -35,16 +35,7 @@ import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.NoSuchElementException;
-import java.util.PriorityQueue;
-import java.util.Queue;
+import java.util.*;
 
 /**
  * Shard intervals based on position within the BAM file.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java
index 26af890b4..19d33aa6b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.reads;
 
+import net.sf.samtools.SAMFileSpan;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;
@@ -7,8 +8,6 @@ import org.broadinstitute.sting.utils.Utils;
 import java.util.List;
 import java.util.Map;
 
-import net.sf.samtools.SAMFileSpan;
-
 /**
  * Handles locus shards of BAM information.
  * @author aaron
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java
index 950d67428..a5ca07853 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java
@@ -24,17 +24,18 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import net.sf.samtools.GATKBAMFileSpan;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileSpan;
+import net.sf.samtools.SAMSequenceRecord;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 
-import java.util.*;
-
-import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMSequenceRecord;
-import net.sf.samtools.SAMFileSpan;
-import net.sf.picard.reference.IndexedFastaSequenceFile;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
 
 /**
  * A sharding strategy for loci based on reading of the index.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java
index 7579c22f6..278eeb898 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.datasources.reads;
 
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.util.List;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java
index 10228ecd7..28b737f28 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java
@@ -4,8 +4,8 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.Iterator;
-import java.util.NoSuchElementException;
 import java.util.List;
+import java.util.NoSuchElementException;
 
 /**
  * Create a giant shard representing all the data in the input BAM(s).
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
index 9aecd7779..4d9c9092d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
@@ -1,15 +1,17 @@
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter;
-
-import java.util.*;
-
 import net.sf.samtools.SAMFileSpan;
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter;
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
 /**
  *
  * User: aaron
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java
index da70a615b..c2235ec73 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java
@@ -25,12 +25,11 @@
 package org.broadinstitute.sting.gatk.datasources.reads;
 
 import net.sf.samtools.SAMFileSpan;
-
-import java.util.*;
-
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 
+import java.util.*;
+
 /**
  * The sharding strategy for reads using a simple counting mechanism.  Each read shard
  * has a specific number of reads (default to 10K) which is configured in the constructor.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
index c2aa5f18e..6064806f3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
@@ -24,21 +24,19 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.picard.sam.MergingSamRecordIterator;
+import net.sf.picard.sam.SamFileHeaderMerger;
 import net.sf.samtools.*;
 import net.sf.samtools.util.CloseableIterator;
-import net.sf.picard.filter.SamRecordFilter;
-import net.sf.picard.sam.SamFileHeaderMerger;
-import net.sf.picard.sam.MergingSamRecordIterator;
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.DownsamplingMethod;
-import org.broadinstitute.sting.gatk.filters.ReadFilter;
-import org.broadinstitute.sting.gatk.iterators.*;
-import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.ReadMetrics;
+import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator;
+import org.broadinstitute.sting.gatk.filters.ReadFilter;
+import org.broadinstitute.sting.gatk.iterators.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.baq.BAQ;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java
index 418f5d3ee..f8d941784 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java
@@ -2,17 +2,13 @@ package org.broadinstitute.sting.gatk.datasources.reads;
 
 import net.sf.samtools.SAMFileSpan;
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.gatk.ReadMetrics;
 import org.broadinstitute.sting.gatk.ReadProperties;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.HasGenomeLocation;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.io.Serializable;
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java
index fa733ce12..780b41ef7 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java
@@ -1,10 +1,10 @@
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.samtools.SAMSequenceDictionary;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 /**
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java
index ae0f1cf43..07c13a76e 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java
@@ -25,17 +25,17 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads.utilities;
 
-import org.broadinstitute.sting.commandline.CommandLineProgram;
+import net.sf.samtools.BAMIndex;
+import net.sf.samtools.SAMFileReader;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.instrumentation.Sizeof;
 
 import java.io.File;
 import java.lang.reflect.Field;
-import java.util.Map;
 import java.util.List;
-
-import net.sf.samtools.*;
+import java.util.Map;
 
 /**
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java
index f03e2a44f..54de04379 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java
@@ -24,12 +24,12 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads.utilities;
 
-import org.broadinstitute.sting.commandline.CommandLineProgram;
-import org.broadinstitute.sting.commandline.Argument;
-import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMFileReader;
-import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMFileWriterFactory;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
 
 import java.io.File;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java
index df7dccaa9..773541d11 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java
@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads.utilities;
 
-import net.sf.samtools.SAMFileReader;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java
index c2d64ddd8..ef69a8e5f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java
@@ -25,16 +25,15 @@
 
 package org.broadinstitute.sting.gatk.datasources.reference;
 
-import net.sf.picard.reference.ReferenceSequenceFileFactory;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import net.sf.picard.reference.FastaSequenceIndexBuilder;
-import net.sf.picard.sam.CreateSequenceDictionary;
-import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.picard.reference.FastaSequenceIndex;
+import net.sf.picard.reference.FastaSequenceIndexBuilder;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.picard.sam.CreateSequenceDictionary;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.file.FSLockWithShared;
 import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 
 import java.io.File;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java
index 934f4f997..21f58d480 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java
@@ -28,11 +28,7 @@ import net.sf.samtools.SAMSequenceDictionary;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 /**
  * A pool of open resources, all of which can create a closeable iterator.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java
index 0a5981a1b..067bf3f72 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java
@@ -3,11 +3,10 @@ package org.broadinstitute.sting.gatk.datasources.sample;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.yaml.snakeyaml.TypeDescription;
 import org.yaml.snakeyaml.Yaml;
 import org.yaml.snakeyaml.constructor.Constructor;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java b/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java
index a1419ba70..5dbd90405 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java
@@ -1,15 +1,20 @@
 
 package org.broadinstitute.sting.gatk.examples;
 
-import net.sf.samtools.*;
-import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.contexts.*;
-import org.broadinstitute.sting.utils.pileup.*;
+import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
-import java.util.*;
 import java.io.PrintStream;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
 
 /**
  * Computes the coverage per sample.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
index b96d0ffbf..26205a203 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
@@ -25,6 +25,8 @@
 
 package org.broadinstitute.sting.gatk.examples;
 
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -32,8 +34,6 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidSNPGenotypePriors;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.io.PrintStream;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java b/public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
index 3e335733d..b23782563 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
@@ -25,18 +25,18 @@
 
 package org.broadinstitute.sting.gatk.executive;
 
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
-import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
+import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
+import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.ArrayList;
-import java.util.List;
 import java.util.Iterator;
+import java.util.List;
 /**
  * Manages the
  */
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
index 8a27e008c..59fb4aa9e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
@@ -1,27 +1,27 @@
 package org.broadinstitute.sting.gatk.executive;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.io.*;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.io.OutputTracker;
+import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
+import org.broadinstitute.sting.gatk.walkers.TreeReducible;
+import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
 
-import java.util.Queue;
-import java.util.LinkedList;
 import java.util.Collection;
-import java.util.concurrent.Executors;
+import java.util.LinkedList;
+import java.util.Queue;
 import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
 import java.util.concurrent.FutureTask;
 
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-
 /**
  * A microscheduler that schedules shards according to a tree-like structure.
  * Requires a special walker tagged with a 'TreeReducible' interface.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
index 4cb571c45..9466fdf75 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
@@ -1,22 +1,21 @@
 package org.broadinstitute.sting.gatk.executive;
 
-import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
+import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.io.DirectOutputTracker;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.Walker;
 
 import java.util.Collection;
 
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-
 
 /** A micro-scheduling manager for single-threaded execution of a traversal. */
 public class LinearMicroScheduler extends MicroScheduler {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
index cfe0f8187..23e5769f1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
@@ -25,26 +25,18 @@
 
 package org.broadinstitute.sting.gatk.executive;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.datasources.reads.ShardStrategy;
+import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.gatk.io.OutputTracker;
+import org.broadinstitute.sting.gatk.iterators.NullSAMIterator;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.gatk.traversals.*;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.io.OutputTracker;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.gatk.iterators.NullSAMIterator;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.ReadMetrics;
-
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.PrintStream;
-import java.lang.management.ManagementFactory;
-import java.util.*;
-
-import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.threading.*;
@@ -52,6 +44,11 @@ import org.broadinstitute.sting.utils.threading.*;
 import javax.management.JMException;
 import javax.management.MBeanServer;
 import javax.management.ObjectName;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.PrintStream;
+import java.lang.management.ManagementFactory;
+import java.util.Collection;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java b/public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java
index 76e0c1c8a..7be37a616 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java
@@ -1,10 +1,9 @@
 package org.broadinstitute.sting.gatk.executive;
 
 import org.broadinstitute.sting.gatk.io.storage.Storage;
-import org.broadinstitute.sting.gatk.io.OutputTracker;
 
-import java.util.Collection;
 import java.util.ArrayList;
+import java.util.Collection;
 
 /**
  * User: hanna
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java b/public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java
index 151a1ba26..7aac70b47 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.executive;
 
-import java.util.Queue;
-import java.util.List;
 import java.util.ArrayList;
 import java.util.LinkedList;
+import java.util.List;
+import java.util.Queue;
 import java.util.concurrent.Future;
 /**
  * User: hanna
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
index b78a4edc9..6136bd68d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.executive;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
+import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
 import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
-import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.concurrent.Callable;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java b/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
index 8fb4adb5d..d36a3b576 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
@@ -4,8 +4,8 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.concurrent.Callable;
-import java.util.concurrent.Future;
 import java.util.concurrent.ExecutionException;
+import java.util.concurrent.Future;
 /**
  * User: hanna
  * Date: Apr 29, 2009
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java b/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
index 5c341bb02..cfbce58ee 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
@@ -1,17 +1,20 @@
 package org.broadinstitute.sting.gatk.executive;
 
-import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.gatk.iterators.*;
+import net.sf.picard.util.PeekableIterator;
 import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-
-import java.util.*;
-
-import net.sf.picard.util.PeekableIterator;
+import org.broadinstitute.sting.gatk.datasources.reads.Shard;
+import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
+import org.broadinstitute.sting.gatk.iterators.LocusIterator;
+import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
+import java.util.Iterator;
+import java.util.List;
+import java.util.NoSuchElementException;
+
 /**
  * Buffer shards of data which may or may not contain multiple loci into
  * iterators of all data which cover an interval.  Its existence is an homage
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java
index b8a3ee977..0987c5d74 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java
@@ -24,8 +24,10 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
-import net.sf.samtools.*;
+import net.sf.samtools.Cigar;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import net.sf.samtools.SAMRecord;
 
 /**
  * Filter out reads with wonky cigar strings.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java
index 3b988c8fb..8596e18eb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java
@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java b/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
index 84390c173..03fc2063b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
@@ -23,17 +23,16 @@
  */
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.samtools.util.CloserUtil;
-
-import java.util.Iterator;
-import java.util.NoSuchElementException;
-import java.util.Collection;
-
+import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.CloseableIterator;
-import net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.util.CloserUtil;
 import org.broadinstitute.sting.gatk.ReadMetrics;
 
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+
 /**
  * Filtering Iterator which takes a filter and an iterator and iterates
  * through only those records which are not rejected by the filter.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java
index fb3c38582..589910fc7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /*
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java
index b7806524a..cd77a9e7e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckReadFilter.java
@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java b/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
index cda08fb66..67f82235d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
@@ -25,11 +25,8 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 
-import net.sf.picard.filter.SamRecordFilter;
-
 import java.util.Collection;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
index 4deeb09ee..74deace9a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
@@ -24,8 +24,8 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMSequenceRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java
index bcd473b15..75369b306 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java
@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java
old mode 100755
new mode 100644
similarity index 50%
rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java
rename to public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java
index 7e1d86105..1afec36d1
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java
@@ -1,6 +1,5 @@
 /*
- * Copyright (c) 2010, The Broad Institute
- *
+ * Copyright (c) 2009 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
@@ -12,6 +11,7 @@
  *
  * 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
@@ -22,25 +22,21 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.walkers.variantutils;
+package org.broadinstitute.sting.gatk.filters;
 
-import org.broadinstitute.sting.WalkerTest;
-import org.testng.annotations.Test;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.QualityUtils;
 
-import java.io.File;
-import java.util.Arrays;
+/**
+ * Filter out mapping quality zero reads.
+ *
+ * @author ebanks
+ * @version 0.1
+ */
 
-public class BatchMergeIntegrationTest extends WalkerTest {
-    @Test
-    public void testBatchMerge1() {
-        String bam = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.bam";
-        String alleles = validationDataLocation +  "batch.merge.alleles.vcf";
-        WalkerTestSpec spec = new WalkerTestSpec(
-                "-T UnifiedGenotyper -NO_HEADER -BTI alleles -stand_call_conf 0.0 -glm BOTH -G none -nsl -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -o %s -R " + b37KGReference
-                        + " -B:alleles,VCF " + alleles
-                        + " -I " + bam,
-                1,
-                Arrays.asList("f4ed8f4ef2cba96823c06e90e9d0de35"));
-        executeTest("testBatchMerge UG genotype given alleles:" + new File(bam).getName() + " with " + new File(alleles).getName(), spec);
+public class MappingQualityUnavailableReadFilter extends ReadFilter {
+    public boolean filterOut(SAMRecord rec) {
+        return (rec.getMappingQuality() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE);
     }
-}
\ No newline at end of file
+}
+
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ZeroMappingQualityReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityZeroReadFilter.java
similarity index 90%
rename from public/java/src/org/broadinstitute/sting/gatk/filters/ZeroMappingQualityReadFilter.java
rename to public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityZeroReadFilter.java
index 7e6fc5e82..e49d4117c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/ZeroMappingQualityReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityZeroReadFilter.java
@@ -24,17 +24,16 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /**
- * Filter out zero mapping quality reads.
+ * Filter out mapping quality zero reads.
  *
  * @author hanna
  * @version 0.1
  */
 
-public class ZeroMappingQualityReadFilter extends ReadFilter {
+public class MappingQualityZeroReadFilter extends ReadFilter {
     public boolean filterOut(SAMRecord rec) {
         return (rec.getMappingQuality() == 0);
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java
index 584783d34..7bcee033f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java
index 8a2fd5af3..cd31da61a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java
@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java
index d5d40ec38..490a55040 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java
@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java
index fc21538e8..29738e499 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /*
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java
index cfbba0383..31c2144ce 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentReadFilter.java
@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
index dcddebd55..8ad91ac1c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java
@@ -25,9 +25,7 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
-
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java
index 691fd95f0..30b2f828d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java
@@ -25,11 +25,9 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
-
-import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 /**
  * Filter out PL matching reads.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java
index 4ef88402d..81044b888 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java
@@ -1,14 +1,12 @@
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
-
-import java.util.Set;
-import java.util.HashSet;
-
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
+import java.util.HashSet;
+import java.util.Set;
+
 /**
  * Created by IntelliJ IDEA.
  * User: asivache
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
index 1d74ee20e..227637761 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.filters;
 
 import net.sf.picard.filter.SamRecordFilter;
-import net.sf.samtools.SAMFileHeader;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
index 69ebc8b04..0e5e8800c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
@@ -25,17 +25,16 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import java.util.*;
-import java.util.Map.Entry;
-import java.io.File;
-import java.io.FileNotFoundException;
-
-import net.sf.picard.filter.SamRecordFilter;
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.*;
+import java.util.Map.Entry;
+
 /**
  * Removes records matching the read group tag and exact match string.
  * For example, this filter value:
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java
index 1b2a77f45..16eeed3cc 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java
@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
index 682b22b1f..99d6bc154 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
@@ -25,9 +25,8 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java
index 05b472036..2f93cbcae 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java
@@ -25,9 +25,8 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
-import net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java
index ac4f4853a..e7ee345d2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java
@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java b/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java
index 865528688..658a28fbd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java
@@ -25,9 +25,9 @@
 
 package org.broadinstitute.sting.gatk.io;
 
-import org.broadinstitute.sting.gatk.io.stubs.Stub;
-import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
 import org.broadinstitute.sting.gatk.io.storage.Storage;
+import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
+import org.broadinstitute.sting.gatk.io.stubs.Stub;
 
 /**
  * Maps creation of storage directly to output streams in parent.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java b/public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
index b68013aa4..f39ba2d8d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
@@ -26,20 +26,20 @@
 package org.broadinstitute.sting.gatk.io;
 
 import net.sf.samtools.SAMFileReader;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.commandline.ArgumentSource;
-import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
-import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.gatk.io.storage.Storage;
+import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
 import org.broadinstitute.sting.gatk.io.stubs.Stub;
-import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
-import org.broadinstitute.sting.gatk.io.storage.Storage;
+import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
 
-import java.io.*;
+import java.io.OutputStream;
 import java.lang.reflect.Field;
-import java.util.Map;
 import java.util.HashMap;
+import java.util.Map;
 
 /**
  * Manages the output and err streams that are created specifically for walker
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java b/public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java
index 8701ecf3c..a9a74925d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.io;
 
-import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileWriter;
 
 /**
  * A writer that will allow unsorted BAM files to be written
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java b/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java
index 36960246a..999deddd1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java
@@ -25,15 +25,16 @@
 
 package org.broadinstitute.sting.gatk.io;
 
-import org.broadinstitute.sting.gatk.io.stubs.Stub;
-import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
-import org.broadinstitute.sting.gatk.io.storage.Storage;
 import org.broadinstitute.sting.gatk.executive.OutputMergeTask;
+import org.broadinstitute.sting.gatk.io.storage.Storage;
+import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
+import org.broadinstitute.sting.gatk.io.stubs.Stub;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.util.*;
 import java.io.File;
 import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  * An output tracker that can either track its output per-thread or directly,
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
index 4dc976289..56c9c0465 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
@@ -25,14 +25,14 @@
 
 package org.broadinstitute.sting.gatk.io.storage;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.*;
+import java.nio.channels.Channels;
 import java.nio.channels.FileChannel;
 import java.nio.channels.WritableByteChannel;
-import java.nio.channels.Channels;
 
 public class OutputStreamStorage extends OutputStream implements Storage<OutputStream> {
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
index 610db1d76..cb8786be1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
@@ -27,17 +27,16 @@ package org.broadinstitute.sting.gatk.io.storage;
 
 import net.sf.samtools.*;
 import net.sf.samtools.util.CloseableIterator;
-
-import java.io.*;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
-
 import net.sf.samtools.util.RuntimeIOException;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.SimplifyingSAMFileWriter;
 
+import java.io.File;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+
 /**
  * Provides temporary storage for SAMFileWriters.
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
index ee5c56524..66907dd6b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
@@ -25,9 +25,9 @@
 
 package org.broadinstitute.sting.gatk.io.storage;
 
-import org.broadinstitute.sting.gatk.io.stubs.Stub;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
+import org.broadinstitute.sting.gatk.io.stubs.Stub;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
index 74176ec35..1da03e9c2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
@@ -1,16 +1,21 @@
 package org.broadinstitute.sting.gatk.io.storage;
 
+import net.sf.samtools.util.BlockCompressedOutputStream;
 import org.apache.log4j.Logger;
 import org.broad.tribble.source.BasicFeatureSource;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
-
-import java.io.*;
-
-import net.sf.samtools.util.BlockCompressedOutputStream;
+import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.PrintStream;
 
 /**
  * Provides temporary and permanent storage for genotypes in VCF format.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
index 00e78f391..8bc97c886 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
@@ -30,8 +30,8 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.io.OutputStream;
 import java.io.File;
+import java.io.OutputStream;
 import java.lang.reflect.Constructor;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java
index 5cf84c5a2..27bcb8a1c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java
@@ -27,9 +27,9 @@ package org.broadinstitute.sting.gatk.io.stubs;
 
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 
-import java.io.OutputStream;
-import java.io.IOException;
 import java.io.File;
+import java.io.IOException;
+import java.io.OutputStream;
 
 /**
  * A stub for routing and management of anything backed by an OutputStream.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java
index d847015ed..f124c2302 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java
@@ -24,14 +24,14 @@
 
 package org.broadinstitute.sting.gatk.io.stubs;
 
-import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
-import org.broadinstitute.sting.commandline.ArgumentSource;
+import net.sf.samtools.SAMFileReader;
 import org.broadinstitute.sting.commandline.ArgumentMatches;
+import org.broadinstitute.sting.commandline.ArgumentSource;
+import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
 import org.broadinstitute.sting.commandline.ParsingEngine;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import net.sf.samtools.SAMFileReader;
 
 import java.io.File;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
index a9a272220..38640eda0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
@@ -25,18 +25,17 @@
 
 package org.broadinstitute.sting.gatk.io.stubs;
 
+import net.sf.samtools.SAMFileWriter;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
-import net.sf.samtools.SAMFileWriter;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.lang.annotation.Annotation;
-import java.util.List;
-import java.util.Arrays;
 import java.io.File;
 import java.io.OutputStream;
+import java.lang.annotation.Annotation;
+import java.util.Arrays;
+import java.util.List;
 
 /**
  * Insert a SAMFileWriterStub  instead of a full-fledged concrete OutputStream implementations.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
index f5c1e0efc..d8e59a3dd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
@@ -25,20 +25,19 @@
 
 package org.broadinstitute.sting.gatk.io.stubs;
 
+import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMFileHeader;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.io.OutputTracker;
+import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
+import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
 import java.io.OutputStream;
 
-import org.broadinstitute.sting.gatk.io.OutputTracker;
-import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.baq.BAQ;
-
 /**
  * A stub for routing and management of SAM file reading and writing.
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
index 7521e754d..615841f02 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
@@ -25,14 +25,17 @@
 
 package org.broadinstitute.sting.gatk.io.stubs;
 
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 import java.io.OutputStream;
-import java.util.*;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
 
 /**
  * Injects new command-line arguments into the system providing support for the genotype writer.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
index 1a79d2785..bb84f9457 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java
@@ -25,19 +25,19 @@
 
 package org.broadinstitute.sting.gatk.io.stubs;
 
-import java.io.File;
-import java.io.PrintStream;
-import java.io.OutputStream;
-import java.util.Collection;
-
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.gatk.CommandLineExecutable;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.io.File;
+import java.io.OutputStream;
+import java.io.PrintStream;
+import java.util.Collection;
 
 /**
  * A stub for routing and management of genotype reading and writing.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java
index b5643f834..478675f9d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java
@@ -1,13 +1,11 @@
 package org.broadinstitute.sting.gatk.iterators;
 
+import net.sf.picard.sam.MergingSamRecordIterator;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMRecord;
-import net.sf.picard.sam.MergingSamRecordIterator;
 
 import java.util.Iterator;
 
-import org.broadinstitute.sting.gatk.ReadProperties;
-
 /*
  * Copyright (c) 2009 The Broad Institute
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java
index f3a060be1..7eaf4be41 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java
@@ -26,12 +26,11 @@ package org.broadinstitute.sting.gatk.iterators;
 
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.CloseableIterator;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.Queue;
 import java.util.LinkedList;
 import java.util.NoSuchElementException;
-
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import java.util.Queue;
 
 /**
  * Buffers access to a large stream of reads, replenishing the buffer only when the reads  
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/DownsampleIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/DownsampleIterator.java
index 1342f11fd..835748ff0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/DownsampleIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/DownsampleIterator.java
@@ -1,11 +1,10 @@
 package org.broadinstitute.sting.gatk.iterators;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 
 import java.util.Iterator;
 
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-
 
 public class DownsampleIterator implements StingSAMIterator {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java
index aa376a12a..240564d34 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java
@@ -3,8 +3,8 @@ package org.broadinstitute.sting.gatk.iterators;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
-import java.util.NoSuchElementException;
 import java.util.Iterator;
+import java.util.NoSuchElementException;
 /**
  * User: hanna
  * Date: May 12, 2009
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java
index 30c1cf512..e177984ca 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java
@@ -1,11 +1,10 @@
 package org.broadinstitute.sting.gatk.iterators;
 
 import net.sf.samtools.util.CloseableIterator;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 
 import java.util.Iterator;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-
 /**
  * Iterator that traverses a SAM File, accumulating information on a per-locus basis
  */
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
index 4e58813f5..e13c5a764 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
@@ -25,19 +25,27 @@
 
 package org.broadinstitute.sting.gatk.iterators;
 
-import net.sf.samtools.*;
 import net.sf.picard.util.PeekableIterator;
+import net.sf.samtools.Cigar;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.ReadProperties;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.DownsamplingMethod;
 import org.broadinstitute.sting.gatk.DownsampleType;
+import org.broadinstitute.sting.gatk.DownsamplingMethod;
+import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.ReservoirDownsampler;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.pileup.*;
+import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileupImpl;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java
index ff458467f..21b71c9e6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.iterators;
 
-import org.broadinstitute.sting.gatk.ReadProperties;
 import net.sf.samtools.SAMRecord;
 
 import java.util.Iterator;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java
index c2d3976ea..cc499b247 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java
@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.gatk.iterators;
 
-import org.broadinstitute.sting.gatk.ReadProperties;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.CloseableIterator;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java
index 239392eec..2f30d12a8 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java
@@ -1,13 +1,8 @@
 package org.broadinstitute.sting.gatk.iterators;
 
 import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMTag;
-import net.sf.samtools.SAMReadGroupRecord;
-import org.broadinstitute.sting.gatk.ReadProperties;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.apache.log4j.Logger;
-
-import java.util.List;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 /**
  * An iterator which does post-processing of a read, including potentially wrapping
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java
index d294993d4..1b248d097 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java
@@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.iterators;
 
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.CloseableIterator;
-import org.broadinstitute.sting.gatk.ReadProperties;
 /**
  *
  * User: aaron
diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
index a51ca9292..69c0b3e0a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
@@ -26,19 +26,16 @@ package org.broadinstitute.sting.gatk.phonehome;
 
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.CommandLineUtils;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.jets3t.service.S3Service;
 import org.jets3t.service.S3ServiceException;
 import org.jets3t.service.impl.rest.httpclient.RestS3Service;
-import org.jets3t.service.model.S3Bucket;
 import org.jets3t.service.model.S3Object;
 import org.jets3t.service.security.AWSCredentials;
 import org.simpleframework.xml.Element;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java
index fa0c323b5..ce924fd87 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java
@@ -25,17 +25,17 @@
 
 package org.broadinstitute.sting.gatk.refdata;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.lang.reflect.Constructor;
 import java.util.Iterator;
 import java.util.regex.Pattern;
-import java.io.FileNotFoundException;
-import java.io.File;
-import java.lang.reflect.Constructor;
 
 /**
  * This is a low-level iterator designed to provide system-wide generic support for reading record-oriented data
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
index cff97e4ee..59b273d38 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
@@ -2,9 +2,9 @@ package org.broadinstitute.sting.gatk.refdata;
 
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.HasGenomeLocation;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
index 43bf6f8e0..d03b122e2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.refdata;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java
index b3cb22a03..b7437e6e8 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java
@@ -6,9 +6,9 @@ import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.Iterator;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index c7c0468e7..1d622e2c7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -3,17 +3,13 @@ package org.broadinstitute.sting.gatk.refdata;
 import org.broad.tribble.Feature;
 import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broad.tribble.gelitext.GeliTextFeature;
-import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.MutableGenotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.*;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
index 59cd14a22..6bba754be 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableCodec.java
@@ -25,12 +25,6 @@
 
 package org.broadinstitute.sting.gatk.refdata.features.annotator;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.StringTokenizer;
-
 import org.apache.log4j.Logger;
 import org.broad.tribble.Feature;
 import org.broad.tribble.exception.CodecLineParsingException;
@@ -41,6 +35,12 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.StringTokenizer;
+
 public class AnnotatorInputTableCodec implements ReferenceDependentFeatureCodec<AnnotatorInputTableFeature> {
 
     private static Logger logger = Logger.getLogger(AnnotatorInputTableCodec.class);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java
index d97e378fb..d12badd28 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java
@@ -25,13 +25,13 @@
 
 package org.broadinstitute.sting.gatk.refdata.features.annotator;
 
+import org.broad.tribble.Feature;
+
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
 
-import org.broad.tribble.Feature;
-
 /**
  * This class represents a single record in an AnnotatorInputTable.
  */
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java
index 7f97451cf..5e536d4c1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleCodec.java
@@ -26,19 +26,19 @@ package org.broadinstitute.sting.gatk.refdata.features.beagle;
 
 
 import org.broad.tribble.Feature;
+import org.broad.tribble.exception.CodecLineParsingException;
 import org.broad.tribble.readers.AsciiLineReader;
 import org.broad.tribble.readers.LineReader;
+import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.regex.Matcher;
 import java.util.regex.Pattern;
-import org.broad.tribble.exception.CodecLineParsingException;
-import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 
 public class BeagleCodec implements ReferenceDependentFeatureCodec<BeagleFeature> {
     private String[] header;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java
index c7bf86569..e6832754d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/beagle/BeagleFeature.java
@@ -25,14 +25,11 @@
 package org.broadinstitute.sting.gatk.refdata.features.beagle;
 
 import org.broad.tribble.Feature;
-
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 import java.util.ArrayList;
 import java.util.Map;
 
-import net.sf.samtools.util.StringUtil;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-
 public class BeagleFeature implements Feature {
 
     private String chr;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
index 4648efd1e..d12114f9a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
@@ -4,9 +4,8 @@ import org.broad.tribble.Feature;
 import org.broadinstitute.sting.gatk.refdata.Transcript;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java
index 00b7c45d9..43e2c3ff5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupCodec.java
@@ -25,15 +25,15 @@
 
 package org.broadinstitute.sting.gatk.refdata.features.sampileup;
 
-import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.Feature;
+import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.exception.CodecLineParsingException;
 import org.broad.tribble.readers.LineReader;
 import org.broad.tribble.util.ParsingUtils;
 
 import java.util.ArrayList;
-import java.util.regex.Pattern;
 import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import static org.broadinstitute.sting.gatk.refdata.features.sampileup.SAMPileupFeature.VariantType;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java
index a794c2704..378f26934 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/sampileup/SAMPileupFeature.java
@@ -25,12 +25,11 @@
 
 package org.broadinstitute.sting.gatk.refdata.features.sampileup;
 
+import net.sf.samtools.util.StringUtil;
 import org.broad.tribble.Feature;
 
 import java.util.List;
 
-import net.sf.samtools.util.StringUtil;
-
 /**
  * A tribble feature representing a SAM pileup.
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java
index 15f559d46..039b8adde 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/samread/SAMReadCodec.java
@@ -24,14 +24,14 @@
 
 package org.broadinstitute.sting.gatk.refdata.features.samread;
 
+import net.sf.samtools.Cigar;
+import net.sf.samtools.TextCigarCodec;
+import net.sf.samtools.util.StringUtil;
 import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.exception.CodecLineParsingException;
 import org.broad.tribble.readers.LineReader;
 import org.broad.tribble.util.ParsingUtils;
-import net.sf.samtools.util.StringUtil;
-import net.sf.samtools.TextCigarCodec;
-import net.sf.samtools.Cigar;
 
 /**
  * Decodes a simple SAM text string.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java
index b831606a3..745ccdd9f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/BedTableCodec.java
@@ -1,13 +1,8 @@
 package org.broadinstitute.sting.gatk.refdata.features.table;
 
 import org.broad.tribble.Feature;
-import org.broad.tribble.readers.LineReader;
 import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.io.IOException;
-import java.util.ArrayList;
 import java.util.Arrays;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
old mode 100644
new mode 100755
index 6f0a712bf..ab1ac59d8
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java
@@ -1,16 +1,14 @@
 package org.broadinstitute.sting.gatk.refdata.features.table;
 
 import org.broad.tribble.Feature;
-import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.readers.LineReader;
 import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.interval.IntervalUtils;
 
 import java.io.IOException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
 
 /**
  * implementation of a simple table (tab or comma delimited format) input files
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java
old mode 100644
new mode 100755
index 6ff0384a0..ca73ee960
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.refdata.features.table;
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
-import java.util.*;
+import java.util.List;
 
 /**
  * A feature representing a single row out of a text table
@@ -55,10 +55,14 @@ public class TableFeature implements Feature {
     }
 
     public List<String> getAllValues() {
-        return getValuesTo(values.size()-1);
+        return getValuesTo(values.size());
     }
 
     public List<String> getValuesTo(int columnPosition) {
         return values.subList(0,columnPosition);
     }
+
+    public List<String> getHeader() {
+        return keys;
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java
index 5bb65f9a2..085d6b5b3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java
@@ -10,7 +10,6 @@ import org.broad.tribble.util.LittleEndianOutputStream;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/QueryableTrack.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/QueryableTrack.java
index 19050ae11..731df997d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/QueryableTrack.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/QueryableTrack.java
@@ -28,7 +28,6 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.io.IOException;
-import java.util.Iterator;
 
 /**
  * @author aaron
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
index 3b9f8243f..ba1ca674e 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
@@ -35,8 +35,6 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
 import java.io.IOException;
-import java.lang.reflect.Type;
-import java.util.Iterator;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
index c2057ad5e..19c91be1b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
@@ -42,15 +42,17 @@ import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.SequenceDictionaryUtils;
-import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.file.FSLockWithShared;
 import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException;
 import org.broadinstitute.sting.utils.instrumentation.Sizeof;
 
-import java.io.*;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
 import java.util.*;
 
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java
index 462bf98df..104ba87b5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java
@@ -28,8 +28,6 @@ import org.broad.tribble.Feature;
 import org.broad.tribble.iterators.CloseableTribbleIterator;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
-import java.util.Iterator;
-
 
 /**
  * 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java
index 1553402a5..59e8471a3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java
@@ -28,8 +28,6 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.HasGenomeLocation;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java
index 83aa5f056..96086598a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java
@@ -2,12 +2,8 @@ package org.broadinstitute.sting.gatk.refdata.utils;
 
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.util.CloseableIterator;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
-import java.util.Iterator;
-import java.util.List;
-
 /**
  * @author aaron
  *         <p/>
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/StringToGenomeLocIteratorAdapter.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/StringToGenomeLocIteratorAdapter.java
index 101784d97..fc7f7c58f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/StringToGenomeLocIteratorAdapter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/StringToGenomeLocIteratorAdapter.java
@@ -25,10 +25,10 @@
 
 package org.broadinstitute.sting.gatk.refdata.utils;
 
+import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.bed.BedParser;
-import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 
 import java.util.Iterator;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java
index 75e7c1a32..3201769e0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java
@@ -3,8 +3,8 @@ package org.broadinstitute.sting.gatk.refdata.utils.helpers;
 import net.sf.samtools.util.SequenceUtil;
 import org.broad.tribble.annotation.Strand;
 import org.broad.tribble.dbsnp.DbSNPFeature;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Arrays;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
index e1085c6b2..89a179d0e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
@@ -25,11 +25,11 @@
 package org.broadinstitute.sting.gatk.traversals;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.ReadMetrics;
 import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.ReadMetrics;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -38,7 +38,10 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.PrintStream;
-import java.util.*;
+import java.util.Arrays;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
 
 public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,ProviderType extends ShardDataProvider> {
     // Time in milliseconds since we initialized this engine
diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
index 89ff688a7..1ba48ca5f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
@@ -28,12 +28,11 @@ package org.broadinstitute.sting.gatk.traversals;
 import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
 import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
+import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.gatk.walkers.DuplicateWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
index 240176f2f..232989fb0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
@@ -10,7 +10,6 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java
index f15a20cd3..196d54036 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java
@@ -1,16 +1,18 @@
 package org.broadinstitute.sting.gatk.traversals;
 
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.ReadPairWalker;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMRecordCoordinateComparator;
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
-import org.apache.log4j.Logger;
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMRecordCoordinateComparator;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.ReadPairWalker;
+import org.broadinstitute.sting.gatk.walkers.Requires;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
 
 /**
  * Traverse over a collection of read pairs, assuming that a given shard will contain all pairs.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
index 670676b48..06e4539c4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
@@ -2,14 +2,16 @@ package org.broadinstitute.sting.gatk.traversals;
 
 import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.gatk.WalkerManager;
 import org.broadinstitute.sting.gatk.ReadMetrics;
+import org.broadinstitute.sting.gatk.WalkerManager;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.datasources.providers.*;
+import org.broadinstitute.sting.gatk.datasources.providers.ReadBasedReferenceOrderedView;
+import org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView;
+import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
+import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 /*
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java
index a29e51189..2541921e9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java
@@ -1,11 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
-import java.lang.annotation.Documented;
-import java.lang.annotation.Inherited;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
-import java.lang.annotation.ElementType;
+import java.lang.annotation.*;
 /**
  * User: hanna
  * Date: May 19, 2009
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java
index 99dd46cbe..03097887d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java
@@ -1,11 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
-import java.lang.annotation.Documented;
-import java.lang.annotation.Inherited;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
-import java.lang.annotation.ElementType;
+import java.lang.annotation.*;
 
 /**
  * User: hanna
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java
index 25455b587..8fa6a4c1b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java
@@ -1,11 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
-import java.lang.annotation.Documented;
-import java.lang.annotation.Inherited;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
-import java.lang.annotation.ElementType;
+import java.lang.annotation.*;
 /**
  * User: hanna
  * Date: May 14, 2009
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
index 1a3f87a7a..ca4e3f5e3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
@@ -25,29 +25,29 @@
 
 package org.broadinstitute.sting.gatk.walkers;
 
-import net.sf.samtools.*;
-import net.sf.picard.reference.ReferenceSequenceFileFactory;
-import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.ReferenceSequence;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.picard.reference.ReferenceSequenceFileFactory;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.util.StringUtil;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.clipreads.ClippingOp;
 import org.broadinstitute.sting.utils.clipreads.ClippingRepresentation;
 import org.broadinstitute.sting.utils.clipreads.ReadClipper;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 
-import java.util.*;
-import java.util.regex.Pattern;
-import java.util.regex.Matcher;
 import java.io.File;
 import java.io.PrintStream;
-
-import net.sf.samtools.util.StringUtil;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
+import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 /**
  * This ReadWalker provides simple, yet powerful read clipping capabilities.  It allows the user to clip bases in reads
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java
index 1fc606f07..4bfedb672 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java
@@ -1,16 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers;
 
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
 import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentReadFilter;
+import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.util.List;
 import java.util.Set;
-import java.util.Arrays;
-
-import net.sf.samtools.SAMRecord;
-import net.sf.picard.filter.SamRecordFilter;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java
index a272150c7..56287df31 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java
@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
 import net.sf.samtools.SAMFileWriter;
-import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java
index 13a55eaac..fcfcb81b5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 
+import java.io.PrintStream;
 import java.text.DecimalFormat;
 import java.text.NumberFormat;
-import java.io.PrintStream;
 
 
 /*
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/GCContentByIntervalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/GCContentByIntervalWalker.java
index c0f469973..68bea4dba 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/GCContentByIntervalWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/GCContentByIntervalWalker.java
@@ -28,13 +28,12 @@ import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 
 import java.io.PrintStream;
-import java.util.*;
+import java.util.List;
 
 /**
  * Walks along reference and calculates the GC content for each interval.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
index fc4b403c5..b0b2687f4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
@@ -1,9 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers;
 
-import org.broadinstitute.sting.gatk.filters.*;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.filters.DuplicateReadFilter;
+import org.broadinstitute.sting.gatk.filters.FailsVendorQualityCheckReadFilter;
+import org.broadinstitute.sting.gatk.filters.NotPrimaryAlignmentReadFilter;
+import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
index 84d868c1a..508d1f6ee 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
@@ -26,22 +26,22 @@
 package org.broadinstitute.sting.gatk.walkers;
 
 import org.broad.tribble.dbsnp.DbSNPFeature;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
-import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
+import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.List;
-import java.io.PrintStream;
 
 /**
  * Prints the alignment in the pileup format. In the pileup format, each line represents a genomic position,
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java
index 9ac3fc0e6..158992a22 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java
@@ -25,15 +25,15 @@
 
 package org.broadinstitute.sting.gatk.walkers;
 
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.commandline.Output;
 
-import java.util.Iterator;
 import java.io.PrintStream;
+import java.util.Iterator;
 
 /**
  * Prints out all of the RODs in the input data set. Data is rendered using the toString() method
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
index 07938d322..a189c00b5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
@@ -28,14 +28,12 @@ package org.broadinstitute.sting.gatk.walkers;
 import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.utils.baq.BAQ;
 
-import java.io.PrintStream;
-
 /**
  * Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear
  * in the input file.  It can dynamically merge the contents of multiple input BAM files, resulting
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
index a5486fd9a..db2038aa3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java
index 6c1e64c4e..e9a381a85 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java
@@ -1,11 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
-import java.lang.annotation.Documented;
-import java.lang.annotation.Inherited;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
-import java.lang.annotation.ElementType;
+import java.lang.annotation.*;
 /**
  * User: hanna
  * Date: May 19, 2009
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java
index 014acff9c..486d233b7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java
@@ -25,14 +25,20 @@
 
 package org.broadinstitute.sting.gatk.walkers;
 
-import net.sf.samtools.*;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 /**
  * Divides the input data set into separate BAM files, one for each sample in the input data set.  The split
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
index f0ba8bb46..384742302 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
@@ -25,14 +25,14 @@
 
 package org.broadinstitute.sting.gatk.walkers;
 
-import java.util.List;
-
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.filters.MalformedReadFilter;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.apache.log4j.Logger;
+
+import java.util.List;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java
index 0e4d40675..4d46607e5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java
@@ -1,10 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
-import java.lang.annotation.Documented;
-import java.lang.annotation.ElementType;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
+import java.lang.annotation.*;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java
index 0b718071d..9827fdf09 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java
@@ -25,7 +25,10 @@
 
 package org.broadinstitute.sting.gatk.walkers;
 
-import java.lang.annotation.*;
+import java.lang.annotation.Documented;
+import java.lang.annotation.Inherited;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
 
 /**
  * Describes the size of the window into the genome.  Has differing semantics based on
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
index b02dcd8e2..3144098a8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
@@ -25,21 +25,21 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class AlleleBalance implements InfoFieldAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
index 0be737897..a99f87a70 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
@@ -1,12 +1,16 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
+import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.gatk.contexts.*;
-import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
@@ -62,5 +66,5 @@ public class AlleleBalanceBySample implements GenotypeAnnotation, ExperimentalAn
 
     public List<String> getKeyNames() { return Arrays.asList("AB"); }
 
-    public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), -1, VCFHeaderLineType.Float, "Allele balance for each het genotype")); }
+    public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Allele balance for each het genotype")); }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java
index 51b5381dc..6c14e7445 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AnnotationByDepth.java
@@ -1,8 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+
 import java.util.Map;
 
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
index 244627154..66416ce11 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
@@ -31,19 +31,19 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class BaseCounts implements InfoFieldAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
index ff916bedd..2a5c996f7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
@@ -1,16 +1,16 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
-import java.util.Arrays;
 
 
 public class BaseQualityRankSumTest extends RankSumTest {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
index 143722d7c..74f7f9d80 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
@@ -25,24 +25,29 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 
 public class ChromosomeCounts implements InfoFieldAnnotation, StandardAnnotation {
 
     private String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };
-    private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, -1, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"),
-            new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, -1, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
+    private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"),
+            new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
             new VCFInfoHeaderLine(VCFConstants.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes") };
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
index e56825dbe..c384e0d09 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
@@ -1,18 +1,19 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class DepthOfCoverage implements InfoFieldAnnotation, StandardAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
index 754d28dfd..e3e8bc258 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
@@ -1,20 +1,20 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCompoundHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
@@ -142,5 +142,5 @@ public class DepthPerAlleleBySample implements GenotypeAnnotation, StandardAnnot
  //   public String getIndelBases()
     public List<String> getKeyNames() { return Arrays.asList("AD"); }
 
-    public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), VCFCompoundHeaderLine.UNBOUNDED, VCFHeaderLineType.Integer, "Allelic depths for the ref and alt alleles in the order listed")); }
+    public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Allelic depths for the ref and alt alleles in the order listed")); }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
index 2115526a6..97ed221e7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
@@ -24,20 +24,20 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import cern.jet.math.Arithmetic;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import cern.jet.math.Arithmetic;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
index 5eaa30bf3..48677bbe5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
@@ -1,18 +1,19 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class GCContent implements InfoFieldAnnotation, ExperimentalAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java
index 3a5db2884..cca0ad4bc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GLstats.java
@@ -1,19 +1,20 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
index bd8c51a41..b175579f1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
@@ -24,25 +24,29 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.genotype.Haplotype;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.genotype.Haplotype;
-import org.broadinstitute.sting.utils.pileup.*;
 
 import java.util.*;
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 
 public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
     private final static boolean DEBUG = false;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
index ecebfbbd2..d86728d5e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
@@ -1,20 +1,21 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation;
 import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class HardyWeinberg implements InfoFieldAnnotation, WorkInProgressAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
index 099780fa7..02efd854c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
@@ -1,19 +1,19 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
index ee8b01d7d..12b48473d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java
@@ -1,14 +1,14 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.IndelUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
index f23433bb5..1d999c531 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
@@ -1,19 +1,19 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class LowMQ implements InfoFieldAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
index 11f86b972..cc62580a9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
@@ -1,16 +1,17 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
+import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
-import java.util.Arrays;
 
 
 public class MappingQualityRankSumTest extends RankSumTest {
@@ -21,7 +22,7 @@ public class MappingQualityRankSumTest extends RankSumTest {
 
     protected void fillQualsFromPileup(byte ref, byte alt, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
         for ( final PileupElement p : pileup ) {
-            if( isUsableBase(p) && p.getMappingQual() < 254 ) { // 254 and 255 are special mapping qualities used as a code by aligners
+            if ( isUsableBase(p) ) {
                 if ( p.getBase() == ref ) {
                     refQuals.add((double)p.getMappingQual());
                 } else if ( p.getBase() == alt ) {
@@ -34,7 +35,7 @@ public class MappingQualityRankSumTest extends RankSumTest {
         // equivalent is whether indel likelihoods for reads corresponding to ref allele are more likely than reads corresponding to alt allele ?
         HashMap<PileupElement,LinkedHashMap<Allele,Double>> indelLikelihoodMap = IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap();
         for (final PileupElement p: pileup) {
-            if (indelLikelihoodMap.containsKey(p) && p.getMappingQual() < 254) {
+            if (indelLikelihoodMap.containsKey(p) && p.getMappingQual() != 0 && p.getMappingQual() != QualityUtils.MAPPING_QUALITY_UNAVAILABLE) {
                 // retrieve likelihood information corresponding to this read
                 LinkedHashMap<Allele,Double> el = indelLikelihoodMap.get(p);
                 // by design, first element in LinkedHashMap was ref allele
@@ -54,8 +55,6 @@ public class MappingQualityRankSumTest extends RankSumTest {
                     refQuals.add((double)p.getMappingQual());
                 else if (altLikelihood > refLikelihood + INDEL_LIKELIHOOD_THRESH)
                     altQuals.add((double)p.getMappingQual());
-
-
             }
         }
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
index 25a7b286d..f240d02bc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
@@ -1,16 +1,16 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
index 00cc30309..0ca53adf2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
@@ -25,22 +25,22 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
index dc4934ade..08a25a7e3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
@@ -1,15 +1,15 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
index ba3e2cc8b..1c70a1b33 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
@@ -1,14 +1,14 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
@@ -47,5 +47,5 @@ public class NBaseCount implements InfoFieldAnnotation {
 
     public List<String> getKeyNames() { return Arrays.asList("PercentNBaseSolid"); }
 
-    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("PercentNBaseSolid", 4, VCFHeaderLineType.Float, "Percentage of N bases in the pileup (counting only SOLiD reads)")); }
+    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("PercentNBaseSolid", 1, VCFHeaderLineType.Float, "Percentage of N bases in the pileup (counting only SOLiD reads)")); }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
index 720984835..2175d39e6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
@@ -1,19 +1,19 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 
 public class QualByDepth extends AnnotationByDepth implements InfoFieldAnnotation, StandardAnnotation {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
index 6e80c7555..d52f07b58 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
@@ -1,19 +1,23 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 
 public class RMSMappingQuality implements InfoFieldAnnotation, StandardAnnotation {
@@ -38,8 +42,10 @@ public class RMSMappingQuality implements InfoFieldAnnotation, StandardAnnotatio
                 pileup = context.getBasePileup();
 
             if (pileup != null) {
-                for (PileupElement p : pileup )
-                    qualities[index++] = p.getRead().getMappingQuality();
+                for (PileupElement p : pileup ) {
+                    if ( p.getMappingQual() != QualityUtils.MAPPING_QUALITY_UNAVAILABLE )
+                        qualities[index++] = p.getMappingQual();
+                }
             }
         }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index 1a967293f..5466828f6 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -1,22 +1,23 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.MannWhitneyU;
+import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.List;
 import java.util.ArrayList;
-import java.util.Map;
 import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 
 
@@ -106,6 +107,9 @@ public abstract class RankSumTest implements InfoFieldAnnotation, StandardAnnota
     protected abstract void fillIndelQualsFromPileup(ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals);
 
     protected static boolean isUsableBase( final PileupElement p ) {
-        return !( p.isDeletion() || p.getMappingQual() == 0 || ((int)p.getQual()) < 6 ); // need the unBAQed quality score here
+        return !( p.isDeletion() ||
+                  p.getMappingQual() == 0 ||
+                  p.getMappingQual() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE ||
+                  ((int)p.getQual()) < QualityUtils.MIN_USABLE_Q_SCORE ); // need the unBAQed quality score here
     }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
index f287549bb..c56e2622d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
@@ -26,24 +26,24 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
-import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCompoundHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Arrays;
+import java.util.Map;
 
 /**
  * Created by IntelliJ IDEA.
@@ -200,8 +200,8 @@ public class ReadDepthAndAllelicFractionBySample implements GenotypeAnnotation {
                             1,
                             VCFHeaderLineType.Integer,
                             "Total read depth per sample, including MQ0"),
-                    new VCFFormatHeaderLine(getKeyNames().get(1),
-                            VCFCompoundHeaderLine.UNBOUNDED,
+                            new VCFFormatHeaderLine(getKeyNames().get(1),
+                            VCFHeaderLineCount.UNBOUNDED,
                             VCFHeaderLineType.Float,
                             "Fractions of reads (excluding MQ0 from both ref and alt) supporting each reported alternative allele, per sample"));
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
index 727904a3b..aabfb2970 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
@@ -1,14 +1,17 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import net.sf.samtools.Cigar;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
 import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
-import net.sf.samtools.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java
index fc769ac54..a5ebd8db2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
index 82f16be42..ff9092a71 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
@@ -25,14 +25,15 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
@@ -65,5 +66,5 @@ public class SampleList implements InfoFieldAnnotation {
 
     public List<String> getKeyNames() { return Arrays.asList("Samples"); }
 
-    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("Samples", VCFInfoHeaderLine.UNBOUNDED, VCFHeaderLineType.String, "List of polymorphic samples")); }
+    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("Samples", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "List of polymorphic samples")); }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
index 0b6cbcc2e..a4668eeb6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
@@ -1,14 +1,14 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
index 351117809..b46d82d8b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
@@ -5,7 +5,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.utils.IndelUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
@@ -13,7 +12,10 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index cd5b6694b..acbeee3b2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -25,24 +25,23 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
index 54c8be73a..fdf498a3d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@@ -25,30 +25,27 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedHashMap;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.Map.Entry;
-
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.*;
+import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.GenomicAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.JoinTable;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationInterfaceManager;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.util.*;
+import java.util.Map.Entry;
 
 
 public class VariantAnnotatorEngine {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
index e02c62baf..05c1b3c52 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
@@ -25,13 +25,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
 
-import java.util.*;
-import java.util.Map.Entry;
-
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -39,7 +32,14 @@ import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTa
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.util.*;
+import java.util.Map.Entry;
 
 /**
  * This plugin for {@link VariantAnnotatorEngine} serves as the core
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
index 69a35a584..b42310780 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
@@ -26,28 +26,28 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.*;
-import java.util.Map.Entry;
-
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableCodec;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.*;
+import java.util.Map.Entry;
 
 /**
  * Annotates variant calls with information from user-specified tabular files.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java
index c57aacb5b..714f374cf 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java
@@ -25,6 +25,9 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
 
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
@@ -33,9 +36,6 @@ import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-
 /**
  * This is a container that holds all data corresponding to a single join table as specified by one -J arg (ex: -J bindingName1,/path/to/file,bindingName1.columnName=bindingName2.columnName2).
  * Some terminology:
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java
index d3fcfd42a..3b6c87f90 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java
@@ -25,16 +25,16 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
 
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-
 /**
  * Used to parse files passed to the GenomicAnnotator via the -J arg.
  * The files must be tab-delimited, and the first non-empty/non-commented line
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
index 0ed61fc48..0bbfa51b4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
@@ -24,9 +24,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator;
 
-import java.io.*;
-import java.util.*;
-
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -36,17 +33,15 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableCodec;
 import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.gatk.walkers.By;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.RMD;
-import org.broadinstitute.sting.gatk.walkers.Reference;
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.gatk.walkers.Window;
+import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
+import java.io.IOException;
+import java.io.PrintStream;
+import java.util.*;
+
 /**
  *  Takes a table of transcripts (eg. UCSC refGene, knownGene, and CCDS tables) and generates the big table which contains
  *  annotations for each possible variant at each transcript position (eg. 4 variants at each genomic position).
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
index 29b256479..57bc44ab8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
@@ -1,14 +1,14 @@
 package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 
-import java.util.Map;
 import java.util.List;
+import java.util.Map;
 
 public interface GenotypeAnnotation {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
index 5b33395b5..4e850d01b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Map;
 import java.util.List;
+import java.util.Map;
 
 public interface InfoFieldAnnotation {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
index aa23abc67..21c8ec430 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
@@ -25,26 +25,26 @@
 
 package org.broadinstitute.sting.gatk.walkers.beagle;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
+
 import static java.lang.Math.log10;
 
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
index 93ee0b085..3eed12992 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
@@ -25,10 +25,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.beagle;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Input;
@@ -36,17 +32,20 @@ import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibrationCurve;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.File;
 import java.io.PrintStream;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
index 18aa3e257..f6cd1d636 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
@@ -25,28 +25,29 @@
 
 package org.broadinstitute.sting.gatk.walkers.beagle;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.PrintStream;
-import java.util.*;
+import java.util.Arrays;
+import java.util.Set;
 
 /**
  * Produces an input file to Beagle imputation engine, listing unphased, hard-called genotypes for a single sample
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
index 2c67265d6..90e6fcd77 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
@@ -22,6 +22,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.coverage;
 
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -31,12 +33,10 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
 
 import java.io.File;
-import java.io.PrintStream;
 import java.io.FileNotFoundException;
+import java.io.PrintStream;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java
index ae947eac1..405a44c29 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java
@@ -26,12 +26,11 @@
 package org.broadinstitute.sting.gatk.walkers.coverage;
 
 import net.sf.samtools.SAMRecord;
-
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 
 import java.io.PrintStream;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java
index 5a9c62b7f..6b91b0198 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java
@@ -22,19 +22,19 @@
 
 package org.broadinstitute.sting.gatk.walkers.coverage;
 
+import org.broad.tribble.bed.FullBEDFeature;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broad.tribble.bed.FullBEDFeature;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.util.*;
 import java.io.PrintStream;
+import java.util.Arrays;
+import java.util.List;
 
 /**
  * Test routine for new VariantContext object
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
index 298aa90b9..a41e55166 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
@@ -8,7 +8,9 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 
-import java.util.*;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
index 91ae81cd5..c1956f1d7 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
@@ -26,6 +26,8 @@
 package org.broadinstitute.sting.gatk.walkers.coverage;
 
 import net.sf.samtools.SAMReadGroupRecord;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -34,12 +36,13 @@ import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
 import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
-import org.broadinstitute.sting.gatk.refdata.utils.*;
+import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
+import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
+import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
new file mode 100644
index 000000000..15b16ca6b
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
@@ -0,0 +1,114 @@
+/*
+ * 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.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMRecordIterator;
+import net.sf.samtools.util.BlockCompressedInputStream;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.Arrays;
+
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 1:09 PM
+ *
+ * Class implementing diffnode reader for VCF
+ */
+public class BAMDiffableReader implements DiffableReader {
+    @Override
+    public String getName() { return "BAM"; }
+
+    @Override
+    public DiffElement readFromFile(File file, int maxElementsToRead) {
+        final SAMFileReader reader = new SAMFileReader(file, null); // null because we don't want it to look for the index
+        reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
+
+        DiffNode root = DiffNode.rooted(file.getName());
+        SAMRecordIterator iterator = reader.iterator();
+
+        int count = 0;
+        while ( iterator.hasNext() ) {
+            if ( count++ > maxElementsToRead && maxElementsToRead != -1)
+                break;
+            final SAMRecord record = iterator.next();
+
+            // name is the read name + first of pair
+            String name = record.getReadName().replace('.', '_');
+            if ( record.getReadPairedFlag() ) {
+                name += record.getFirstOfPairFlag() ? "_1" : "_2";
+            }
+
+            DiffNode readRoot = DiffNode.empty(name, root);
+
+            // add fields
+            readRoot.add("NAME", record.getReadName());
+            readRoot.add("FLAGS", record.getFlags());
+            readRoot.add("RNAME", record.getReferenceName());
+            readRoot.add("POS", record.getAlignmentStart());
+            readRoot.add("MAPQ", record.getMappingQuality());
+            readRoot.add("CIGAR", record.getCigarString());
+            readRoot.add("RNEXT", record.getMateReferenceName());
+            readRoot.add("PNEXT", record.getMateAlignmentStart());
+            readRoot.add("TLEN", record.getInferredInsertSize());
+            readRoot.add("SEQ", record.getReadString());
+            readRoot.add("QUAL", record.getBaseQualityString());
+
+            for ( SAMRecord.SAMTagAndValue xt : record.getAttributes() ) {
+                readRoot.add(xt.tag, xt.value);
+            }
+
+            // add record to root
+            if ( ! root.hasElement(name) )
+                // protect ourselves from malformed files
+                root.add(readRoot);
+        }
+
+        reader.close();
+
+        return root.getBinding();
+    }
+
+    @Override
+    public boolean canRead(File file) {
+        final byte[] BAM_MAGIC = "BAM\1".getBytes();
+        final byte[] buffer = new byte[BAM_MAGIC.length];
+        try {
+            FileInputStream fstream = new FileInputStream(file);
+            new BlockCompressedInputStream(fstream).read(buffer,0,BAM_MAGIC.length);
+            return Arrays.equals(buffer, BAM_MAGIC);
+        } catch ( IOException e ) {
+            return false;
+        } catch ( net.sf.samtools.FileTruncatedException e ) {
+            return false;
+        }
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
new file mode 100644
index 000000000..eb8a71c2c
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
@@ -0,0 +1,124 @@
+/*
+ * 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.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Invariant;
+import com.google.java.contract.Requires;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 12:55 PM
+ *
+ * An interface that must be implemented to allow us to calculate differences
+ * between structured objects
+ */
+@Invariant({
+        "name != null",
+        "value != null",
+        "parent != null || name.equals(\"ROOT\")",
+        "value == null || value.getBinding() == this"})
+public class DiffElement {
+    public final static DiffElement ROOT = new DiffElement();
+
+    final private String name;
+    final private DiffElement parent;
+    final private DiffValue value;
+
+    /**
+     * For ROOT only
+     */
+    private DiffElement() {
+        this.name = "ROOT";
+        this.parent = null;
+        this.value = new DiffValue(this, "ROOT");
+    }
+
+    @Requires({"name != null", "parent != null", "value != null"})
+    public DiffElement(String name, DiffElement parent, DiffValue value) {
+        if ( name.equals("ROOT") ) throw new IllegalArgumentException("Cannot use reserved name ROOT");
+        this.name = name;
+        this.parent = parent;
+        this.value = value;
+        this.value.setBinding(this);
+    }
+
+    @Ensures({"result != null"})
+    public String getName() {
+        return name;
+    }
+
+    public DiffElement getParent() {
+        return parent;
+    }
+
+    @Ensures({"result != null"})
+    public DiffValue getValue() {
+        return value;
+    }
+
+    public boolean isRoot() { return this == ROOT; }
+
+    @Ensures({"result != null"})
+    @Override
+    public String toString() {
+        return getName() + "=" + getValue().toString();
+    }
+
+    public String toString(int offset) {
+        return (offset > 0 ? Utils.dupString(' ', offset) : 0) + getName() + "=" + getValue().toString(offset);
+    }
+
+    @Ensures({"result != null"})
+    public final String fullyQualifiedName() {
+        if ( isRoot() )
+            return "";
+        else if ( parent.isRoot() )
+            return name;
+        else
+            return parent.fullyQualifiedName() + "." + name;
+    }
+
+    @Ensures({"result != null"})
+    public String toOneLineString() {
+        return getName() + "=" + getValue().toOneLineString();
+    }
+
+    @Ensures({"result != null"})
+    public DiffNode getValueAsNode() {
+        if ( getValue().isCompound() )
+            return (DiffNode)getValue();
+        else
+            throw new ReviewedStingException("Illegal request conversion of a DiffValue into a DiffNode: " + this);
+    }
+
+    public int size() {
+        return 1 + getValue().size();
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
new file mode 100644
index 000000000..2f87a900a
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
@@ -0,0 +1,360 @@
+/*
+ * 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.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.report.GATKReport;
+import org.broadinstitute.sting.gatk.report.GATKReportTable;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.*;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 12:51 PM
+ * A generic engine for comparing tree-structured objects
+ */
+public class DiffEngine {
+    final protected static Logger logger = Logger.getLogger(DiffEngine.class);
+
+    private final Map<String, DiffableReader> readers = new HashMap<String, DiffableReader>();
+
+    public DiffEngine() {
+        loadDiffableReaders();
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // difference calculation
+    //
+    // --------------------------------------------------------------------------------
+
+    public List<SpecificDifference> diff(DiffElement master, DiffElement test) {
+        DiffValue masterValue = master.getValue();
+        DiffValue testValue = test.getValue();
+
+        if ( masterValue.isCompound() && masterValue.isCompound() ) {
+            return diff(master.getValueAsNode(), test.getValueAsNode());
+        } else if ( masterValue.isAtomic() && testValue.isAtomic() ) {
+            return diff(masterValue, testValue);
+        } else {
+            // structural difference in types.  one is node, other is leaf
+            return Arrays.asList(new SpecificDifference(master, test));
+        }
+    }
+
+    public List<SpecificDifference> diff(DiffNode master, DiffNode test) {
+        Set<String> allNames = new HashSet<String>(master.getElementNames());
+        allNames.addAll(test.getElementNames());
+        List<SpecificDifference> diffs = new ArrayList<SpecificDifference>();
+
+        for ( String name : allNames ) {
+            DiffElement masterElt = master.getElement(name);
+            DiffElement testElt = test.getElement(name);
+            if ( masterElt == null && testElt == null ) {
+                throw new ReviewedStingException("BUG: unexceptedly got two null elements for field: " + name);
+            } else if ( masterElt == null || testElt == null ) { // if either is null, we are missing a value
+                // todo -- should one of these be a special MISSING item?
+                diffs.add(new SpecificDifference(masterElt, testElt));
+            } else {
+                diffs.addAll(diff(masterElt, testElt));
+            }
+        }
+
+        return diffs;
+    }
+
+    public List<SpecificDifference> diff(DiffValue master, DiffValue test) {
+        if ( master.getValue().equals(test.getValue()) ) {
+            return Collections.emptyList();
+        } else {
+            return Arrays.asList(new SpecificDifference(master.getBinding(), test.getBinding()));
+        }
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // Summarizing differences
+    //
+    // --------------------------------------------------------------------------------
+
+    /**
+     * Emits a summary of the diffs to out.  Suppose you have the following three differences:
+     *
+     *   A.X.Z:1!=2
+     *   A.Y.Z:3!=4
+     *   B.X.Z:5!=6
+     *
+     * The above is the itemized list of the differences.  The summary looks for common differences
+     * in the name hierarchy, counts those shared elements, and emits the differences that occur
+     * in order of decreasing counts.
+     *
+     * So, in the above example, what are the shared elements?
+     *
+     * A.X.Z and B.X.Z share X.Z, so there's a *.X.Z with count 2
+     * A.X.Z, A.Y.Z, and B.X.Z all share *.*.Z, with count 3
+     * Each of A.X.Z, A.Y.Z, and B.X.Z are individually unique, with count 1
+     *
+     * So we would emit the following summary:
+     *
+     * *.*.Z: 3
+     * *.X.Z: 2
+     * A.X.Z: 1 [specific difference: 1!=2]
+     * A.Y.Z: 1 [specific difference: 3!=4]
+     * B.X.Z: 1 [specific difference: 5!=6]
+     *
+     * The algorithm to accomplish this calculation is relatively simple. Start with all of the
+     * concrete differences.  For each pair of differences A1.A2....AN and B1.B2....BN:
+     *
+     * find the longest common subsequence Si.Si+1...SN where Ai = Bi = Si
+     * If i == 0, then there's no shared substructure
+     * If i > 0, then generate the summarized value X = *.*...Si.Si+1...SN
+     * if X is a known summary, increment it's count, otherwise set its count to 1
+     *
+     * Not that only pairs of the same length are considered as potentially equivalent
+     *
+     * @param params determines how we display the items
+     * @param diffs
+     */
+    public void reportSummarizedDifferences(List<SpecificDifference> diffs, SummaryReportParams params ) {
+        printSummaryReport(summarizeDifferences(diffs), params );
+    }
+
+    public List<Difference> summarizeDifferences(List<SpecificDifference> diffs) {
+        return summarizedDifferencesOfPaths(diffs);
+    }
+
+    final protected static String[] diffNameToPath(String diffName) {
+        return diffName.split("\\.");
+    }
+
+    protected List<Difference> summarizedDifferencesOfPathsFromString(List<String> singletonDiffs) {
+        List<Difference> diffs = new ArrayList<Difference>();
+
+        for ( String diff : singletonDiffs ) {
+            diffs.add(new Difference(diff));
+        }
+
+        return summarizedDifferencesOfPaths(diffs);
+    }
+
+    protected List<Difference> summarizedDifferencesOfPaths(List<? extends Difference> singletonDiffs) {
+        Map<String, Difference> summaries = new HashMap<String, Difference>();
+
+        // create the initial set of differences
+        for ( int i = 0; i < singletonDiffs.size(); i++ ) {
+            for ( int j = 0; j <= i; j++ ) {
+                Difference diffPath1 = singletonDiffs.get(i);
+                Difference diffPath2 = singletonDiffs.get(j);
+                if ( diffPath1.length() == diffPath2.length() ) {
+                    int lcp = longestCommonPostfix(diffPath1.getParts(), diffPath2.getParts());
+                    String path = lcp > 0 ? summarizedPath(diffPath2.getParts(), lcp) : diffPath2.getPath();
+                    addSummary(summaries, path, true);
+                }
+            }
+        }
+
+        // count differences
+        for ( Difference diffPath : singletonDiffs ) {
+            for ( Difference sumDiff : summaries.values() ) {
+                if ( sumDiff.matches(diffPath.getParts()) )
+                    addSummary(summaries, sumDiff.getPath(), false);
+            }
+        }
+
+        List<Difference> sortedSummaries = new ArrayList<Difference>(summaries.values());
+        Collections.sort(sortedSummaries);
+        return sortedSummaries;
+    }
+
+    private static void addSummary(Map<String, Difference> summaries, String path, boolean onlyCatalog) {
+        if ( summaries.containsKey(path) ) {
+            if ( ! onlyCatalog )
+                summaries.get(path).incCount();
+        } else {
+            Difference sumDiff = new Difference(path);
+            summaries.put(sumDiff.getPath(), sumDiff);
+        }
+    }
+
+    protected void printSummaryReport(List<Difference> sortedSummaries, SummaryReportParams params ) {
+        GATKReport report = new GATKReport();
+        final String tableName = "diffences";
+        report.addTable(tableName, "Summarized differences between the master and test files.\nSee http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information");
+        GATKReportTable table = report.getTable(tableName);
+        table.addPrimaryKey("Difference", true);
+        table.addColumn("NumberOfOccurrences", 0);
+
+        int count = 0, count1 = 0;
+        for ( Difference diff : sortedSummaries ) {
+            if ( diff.getCount() < params.minSumDiffToShow )
+                // in order, so break as soon as the count is too low
+                break;
+
+            if ( params.maxItemsToDisplay != 0 && count++ > params.maxItemsToDisplay )
+                break;
+
+            if ( diff.getCount() == 1 ) {
+                count1++;
+                if ( params.maxCountOneItems != 0 && count1 > params.maxCountOneItems )
+                    break;
+            }
+
+            table.set(diff.getPath(), "NumberOfOccurrences", diff.getCount());
+        }
+
+        table.write(params.out);
+    }
+
+    protected static int longestCommonPostfix(String[] diffPath1, String[] diffPath2) {
+        int i = 0;
+        for ( ; i < diffPath1.length; i++ ) {
+            int j = diffPath1.length - i - 1;
+            if ( ! diffPath1[j].equals(diffPath2[j]) )
+                break;
+        }
+        return i;
+    }
+
+    /**
+     * parts is [A B C D]
+     * commonPostfixLength: how many parts are shared at the end, suppose its 2
+     * We want to create a string *.*.C.D
+     *
+     * @param parts
+     * @param commonPostfixLength
+     * @return
+     */
+    protected static String summarizedPath(String[] parts, int commonPostfixLength) {
+        int stop = parts.length - commonPostfixLength;
+        if ( stop > 0 ) parts = parts.clone();
+        for ( int i = 0; i < stop; i++ ) {
+            parts[i] = "*";
+        }
+        return Utils.join(".", parts);
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // plugin manager
+    //
+    // --------------------------------------------------------------------------------
+
+    public void loadDiffableReaders() {
+        List<Class<? extends DiffableReader>> drClasses = new PluginManager<DiffableReader>( DiffableReader.class ).getPlugins();
+
+        logger.info("Loading diffable modules:");
+        for (Class<? extends DiffableReader> drClass : drClasses ) {
+            logger.info("\t" + drClass.getSimpleName());
+
+            try {
+                DiffableReader dr = drClass.newInstance();
+                readers.put(dr.getName(), dr);
+            } catch (InstantiationException e) {
+                throw new ReviewedStingException("Unable to instantiate module '" + drClass.getSimpleName() + "'");
+            } catch (IllegalAccessException e) {
+                throw new ReviewedStingException("Illegal access error when trying to instantiate '" + drClass.getSimpleName() + "'");
+            }
+        }
+    }
+
+    protected Map<String, DiffableReader> getReaders() {
+        return readers;
+    }
+
+    protected DiffableReader getReader(String name) {
+        return readers.get(name);
+    }
+
+    /**
+     * Returns a reader appropriate for this file, or null if no such reader exists
+     * @param file
+     * @return
+     */
+    public DiffableReader findReaderForFile(File file) {
+        for ( DiffableReader reader : readers.values() )
+            if (reader.canRead(file) )
+                return reader;
+
+        return null;
+    }
+
+    /**
+     * Returns true if reader appropriate for this file, or false if no such reader exists
+     * @param file
+     * @return
+     */
+    public boolean canRead(File file) {
+        return findReaderForFile(file) != null;
+    }
+
+
+    public DiffElement createDiffableFromFile(File file) {
+        return createDiffableFromFile(file, -1);
+    }
+
+    public DiffElement createDiffableFromFile(File file, int maxElementsToRead) {
+        DiffableReader reader = findReaderForFile(file);
+        if ( reader == null )
+            throw new UserException("Unsupported file type: " + file);
+        else
+            return reader.readFromFile(file, maxElementsToRead);
+    }
+
+    public static boolean simpleDiffFiles(File masterFile, File testFile, DiffEngine.SummaryReportParams params) {
+        DiffEngine diffEngine = new DiffEngine();
+
+        if ( diffEngine.canRead(masterFile) && diffEngine.canRead(testFile) ) {
+            DiffElement master = diffEngine.createDiffableFromFile(masterFile);
+            DiffElement test = diffEngine.createDiffableFromFile(testFile);
+            List<SpecificDifference> diffs = diffEngine.diff(master, test);
+            diffEngine.reportSummarizedDifferences(diffs, params);
+            return true;
+        } else {
+            return false;
+        }
+    }
+
+    public static class SummaryReportParams {
+        PrintStream out = System.out;
+        int maxItemsToDisplay = 0;
+        int maxCountOneItems = 0;
+        int minSumDiffToShow = 0;
+
+        public SummaryReportParams(PrintStream out, int maxItemsToDisplay, int maxCountOneItems, int minSumDiffToShow) {
+            this.out = out;
+            this.maxItemsToDisplay = maxItemsToDisplay;
+            this.maxCountOneItems = maxCountOneItems;
+            this.minSumDiffToShow = minSumDiffToShow;
+        }
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
new file mode 100644
index 000000000..2f48de2d3
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
@@ -0,0 +1,248 @@
+/*
+ * 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.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+import com.google.java.contract.Requires;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+import java.util.*;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 12:55 PM
+ *
+ * An interface that must be implemented to allow us to calculate differences
+ * between structured objects
+ */
+public class DiffNode extends DiffValue {
+    private Map<String, DiffElement> getElementMap() {
+        return (Map<String, DiffElement>)super.getValue();
+    }
+    private static Map<String, DiffElement> emptyElements() { return new HashMap<String, DiffElement>(); }
+
+    private DiffNode(Map<String, DiffElement> elements) {
+        super(elements);
+    }
+
+    private DiffNode(DiffElement binding, Map<String, DiffElement> elements) {
+        super(binding, elements);
+    }
+
+    // ---------------------------------------------------------------------------
+    //
+    // constructors
+    //
+    // ---------------------------------------------------------------------------
+
+    public static DiffNode rooted(String name) {
+        return empty(name, DiffElement.ROOT);
+    }
+
+    public static DiffNode empty(String name, DiffElement parent) {
+        DiffNode df = new DiffNode(emptyElements());
+        DiffElement elt = new DiffElement(name, parent, df);
+        df.setBinding(elt);
+        return df;
+    }
+
+    public static DiffNode empty(String name, DiffValue parent) {
+        return empty(name, parent.getBinding());
+    }
+
+    // ---------------------------------------------------------------------------
+    //
+    // accessors
+    //
+    // ---------------------------------------------------------------------------
+
+    @Override
+    public boolean isAtomic() { return false; }
+
+    public Collection<String> getElementNames() {
+        return getElementMap().keySet();
+    }
+
+    public Collection<DiffElement> getElements() {
+        return getElementMap().values();
+    }
+
+    private Collection<DiffElement> getElements(boolean atomicOnly) {
+        List<DiffElement> elts = new ArrayList<DiffElement>();
+        for ( DiffElement elt : getElements() )
+            if ( (atomicOnly && elt.getValue().isAtomic()) || (! atomicOnly && elt.getValue().isCompound()))
+                elts.add(elt);
+        return elts;
+    }
+
+    public Collection<DiffElement> getAtomicElements() {
+        return getElements(true);
+    }
+
+    public Collection<DiffElement> getCompoundElements() {
+        return getElements(false);
+    }
+
+    /**
+     * Returns the element bound to name, or null if no such binding exists
+     * @param name
+     * @return
+     */
+    public DiffElement getElement(String name) {
+        return getElementMap().get(name);
+    }
+
+    /**
+     * Returns true if name is bound in this node
+     * @param name
+     * @return
+     */
+    public boolean hasElement(String name) {
+        return getElement(name) != null;
+    }
+
+    // ---------------------------------------------------------------------------
+    //
+    // add
+    //
+    // ---------------------------------------------------------------------------
+
+    @Requires("elt != null")
+    public void add(DiffElement elt) {
+        if ( getElementMap().containsKey(elt.getName()) )
+            throw new IllegalArgumentException("Attempting to rebind already existing binding: " + elt + " node=" + this);
+        getElementMap().put(elt.getName(), elt);
+    }
+
+    @Requires("elt != null")
+    public void add(DiffValue elt) {
+        add(elt.getBinding());
+    }
+
+    @Requires("elts != null")
+    public void add(Collection<DiffElement> elts) {
+        for ( DiffElement e : elts )
+            add(e);
+    }
+
+    public void add(String name, Object value) {
+        add(new DiffElement(name, this.getBinding(), new DiffValue(value)));
+    }
+
+    public int size() {
+        int count = 0;
+        for ( DiffElement value : getElements() )
+            count += value.size();
+        return count;
+    }
+
+    // ---------------------------------------------------------------------------
+    //
+    // toString
+    //
+    // ---------------------------------------------------------------------------
+
+    @Override
+    public String toString() {
+        return toString(0);
+    }
+
+    @Override
+    public String toString(int offset) {
+        String off = offset > 0 ? Utils.dupString(' ', offset) : "";
+        StringBuilder b = new StringBuilder();
+
+        b.append("(").append("\n");
+        Collection<DiffElement> atomicElts = getAtomicElements();
+        for ( DiffElement elt : atomicElts ) {
+            b.append(elt.toString(offset + 2)).append('\n');
+        }
+
+        for ( DiffElement elt : getCompoundElements() ) {
+            b.append(elt.toString(offset + 4)).append('\n');
+        }
+        b.append(off).append(")").append("\n");
+
+        return b.toString();
+    }
+
+    @Override
+    public String toOneLineString() {
+        StringBuilder b = new StringBuilder();
+
+        b.append('(');
+        List<String> parts = new ArrayList<String>();
+        for ( DiffElement elt : getElements() )
+            parts.add(elt.toOneLineString());
+        b.append(Utils.join(" ", parts));
+        b.append(')');
+
+        return b.toString();
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // fromString and toOneLineString
+    //
+    // --------------------------------------------------------------------------------
+
+    public static DiffElement fromString(String tree) {
+        return fromString(tree, DiffElement.ROOT);
+    }
+
+    /**
+     * Doesn't support full tree structure parsing
+     * @param tree
+     * @param parent
+     * @return
+     */
+    private static DiffElement fromString(String tree, DiffElement parent) {
+        // X=(A=A B=B C=(D=D))
+        String[] parts = tree.split("=", 2);
+        if ( parts.length != 2 )
+            throw new ReviewedStingException("Unexpected tree structure: " + tree + " parts=" + parts);
+        String name = parts[0];
+        String value = parts[1];
+
+        if ( value.length() == 0 )
+            throw new ReviewedStingException("Illegal tree structure: " + value + " at " + tree);
+
+        if ( value.charAt(0) == '(' ) {
+            if ( ! value.endsWith(")") )
+                throw new ReviewedStingException("Illegal tree structure.  Missing ): " + value + " at " + tree);
+            String subtree = value.substring(1, value.length()-1);
+            DiffNode rec = DiffNode.empty(name, parent);
+            String[] subParts = subtree.split(" ");
+            for ( String subPart : subParts ) {
+                rec.add(fromString(subPart, rec.getBinding()));
+            }
+            return rec.getBinding();
+        } else {
+            return new DiffValue(name, parent, value).getBinding();
+        }
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
new file mode 100644
index 000000000..ecb836af9
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
@@ -0,0 +1,117 @@
+/*
+ * 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.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+
+import java.io.File;
+import java.io.PrintStream;
+import java.util.List;
+
+/**
+ * Compares two record-oriented files, itemizing specific difference between equivalent
+ * records in the two files.  Reports both itemized and summarized differences.
+ * @author Mark DePristo
+ * @version 0.1
+ */
+@Requires(value={})
+public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
+    @Output(doc="File to which results should be written",required=true)
+    protected PrintStream out;
+
+    @Argument(fullName="maxObjectsToRead", shortName="motr", doc="Max. number of objects to read from the files.  -1 [default] means unlimited", required=false)
+    int MAX_OBJECTS_TO_READ = -1;
+
+    @Argument(fullName="maxDiffs", shortName="M", doc="Max. number of diffs to process", required=false)
+    int MAX_DIFFS = 0;
+
+    @Argument(fullName="maxCount1Diffs", shortName="M1", doc="Max. number of diffs occuring exactly once in the file to process", required=false)
+    int MAX_COUNT1_DIFFS = 0;
+
+    @Argument(fullName="minCountForDiff", shortName="MCFD", doc="Min number of observations for a records to display", required=false)
+    int minCountForDiff = 1;
+
+    @Argument(fullName="showItemizedDifferences", shortName="SID", doc="Should we enumerate all differences between the files?", required=false)
+    boolean showItemizedDifferences = false;
+
+    @Argument(fullName="master", shortName="m", doc="Master file: expected results", required=true)
+    File masterFile;
+
+    @Argument(fullName="test", shortName="t", doc="Test file: new results to compare to the master file", required=true)
+    File testFile;
+
+    final DiffEngine diffEngine = new DiffEngine();
+
+    @Override
+    public void initialize() {
+
+    }
+
+    @Override
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        return 0;
+    }
+
+    @Override
+    public Integer reduceInit() {
+        return 0;
+    }
+
+    @Override
+    public Integer reduce(Integer counter, Integer sum) {
+        return counter + sum;
+    }
+
+    @Override
+    public void onTraversalDone(Integer sum) {
+        out.printf("Reading master file %s%n", masterFile);
+        DiffElement master = diffEngine.createDiffableFromFile(masterFile, MAX_OBJECTS_TO_READ);
+        out.printf("  Read %d objects%n", master.size());
+        out.printf("Reading test file %s%n", testFile);
+        DiffElement test = diffEngine.createDiffableFromFile(testFile, MAX_OBJECTS_TO_READ);
+        out.printf("  Read %d objects%n", test.size());
+
+//        out.printf("Master diff objects%n");
+//        out.println(master.toString());
+//        out.printf("Test diff objects%n");
+//        out.println(test.toString());
+
+        List<SpecificDifference> diffs = diffEngine.diff(master, test);
+        if ( showItemizedDifferences ) {
+            out.printf("Itemized results%n");
+            for ( SpecificDifference diff : diffs )
+                out.printf("DIFF: %s%n", diff.toString());
+        }
+
+        DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out, MAX_DIFFS, MAX_COUNT1_DIFFS, minCountForDiff);
+        diffEngine.reportSummarizedDifferences(diffs, params);
+    }
+}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
new file mode 100644
index 000000000..963191446
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
@@ -0,0 +1,89 @@
+/*
+ * 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.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 12:55 PM
+ *
+ * An interface that must be implemented to allow us to calculate differences
+ * between structured objects
+ */
+public class DiffValue {
+    private DiffElement binding = null;
+    final private Object value;
+
+    public DiffValue(Object value) {
+        this.value = value;
+    }
+
+    public DiffValue(DiffElement binding, Object value) {
+        this.binding = binding;
+        this.value = value;
+    }
+
+    public DiffValue(DiffValue parent, Object value) {
+        this(parent.getBinding(), value);
+    }
+
+    public DiffValue(String name, DiffElement parent, Object value) {
+        this.binding = new DiffElement(name, parent, this);
+        this.value = value;
+    }
+
+    public DiffValue(String name, DiffValue parent, Object value) {
+        this(name, parent.getBinding(), value);
+    }
+
+    public DiffElement getBinding() {
+        return binding;
+    }
+
+    protected void setBinding(DiffElement binding) {
+        this.binding = binding;
+    }
+
+    public Object getValue() {
+        return value;
+    }
+
+    public String toString() {
+        return getValue().toString();
+    }
+
+    public String toString(int offset) {
+        return toString();
+    }
+
+    public String toOneLineString() {
+        return getValue().toString();
+    }
+
+    public boolean isAtomic() { return true; }
+    public boolean isCompound() { return ! isAtomic(); }
+    public int size() { return 1; }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
new file mode 100644
index 000000000..a117206f1
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
@@ -0,0 +1,65 @@
+/*
+ * 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.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Requires;
+
+import java.io.File;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 1:09 PM
+ *
+ * Interface for readers creating diffable objects from a file
+ */
+public interface DiffableReader {
+    @Ensures("result != null")
+    /**
+     * Return the name of this DiffableReader type.  For example, the VCF reader returns 'VCF' and the
+     * bam reader 'BAM'
+     */
+    public String getName();
+
+    @Ensures("result != null")
+    @Requires("file != null")
+    /**
+     * Read up to maxElementsToRead DiffElements from file, and return them.
+     */
+    public DiffElement readFromFile(File file, int maxElementsToRead);
+
+    /**
+     * Return true if the file can be read into DiffElement objects with this reader. This should
+     * be uniquely true/false for all readers, as the system will use the first reader that can read the
+     * file.  This routine should never throw an exception.  The VCF reader, for example, looks at the
+     * first line of the file for the ##format=VCF4.1 header, and the BAM reader for the BAM_MAGIC value
+     * @param file
+     * @return
+     */
+    @Requires("file != null")
+    public boolean canRead(File file);
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
new file mode 100644
index 000000000..efc6ef160
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
@@ -0,0 +1,95 @@
+/*
+ * 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.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+public class Difference implements Comparable<Difference> {
+    final String path; // X.Y.Z
+    final String[] parts;
+    int count = 0;
+
+    public Difference(String path) {
+        this.path = path;
+        this.parts = DiffEngine.diffNameToPath(path);
+    }
+
+    public String[] getParts() {
+        return parts;
+    }
+
+    public void incCount() { count++; }
+
+    public int getCount() {
+        return count;
+    }
+
+    /**
+     * The fully qualified path object A.B.C etc
+     * @return
+     */
+    public String getPath() {
+        return path;
+    }
+
+    /**
+     * @return the length of the parts of this summary
+     */
+    public int length() {
+        return this.parts.length;
+    }
+
+    /**
+     * Returns true if the string parts matches this summary.  Matches are
+     * must be equal() everywhere where this summary isn't *.
+     * @param otherParts
+     * @return
+     */
+    public boolean matches(String[] otherParts) {
+        if ( otherParts.length != length() )
+            return false;
+
+        // TODO optimization: can start at right most non-star element
+        for ( int i = 0; i < length(); i++ ) {
+            String part = parts[i];
+            if ( ! part.equals("*") && ! part.equals(otherParts[i]) )
+                return false;
+        }
+
+        return true;
+    }
+
+    @Override
+    public String toString() {
+        return String.format("%s:%d", getPath(), getCount());
+    }
+
+    @Override
+    public int compareTo(Difference other) {
+        // sort first highest to lowest count, then by lowest to highest path
+        int countCmp = Integer.valueOf(count).compareTo(other.count);
+        return countCmp != 0 ? -1 * countCmp : path.compareTo(other.path);
+    }
+
+
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/SpecificDifference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/SpecificDifference.java
new file mode 100644
index 000000000..2fe9b47f8
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/SpecificDifference.java
@@ -0,0 +1,59 @@
+/*
+ * 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.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 12:53 PM
+ *
+ * Represents a specific difference between two specific DiffElements
+ */
+public class SpecificDifference extends Difference {
+    DiffElement master, test;
+
+    public SpecificDifference(DiffElement master, DiffElement test) {
+        super(createName(master, test));
+        if ( master == null && test == null ) throw new IllegalArgumentException("Master and test both cannot be null");
+        this.master = master;
+        this.test = test;
+    }
+
+    public String toString() {
+        return String.format("%s:%s!=%s",
+                getPath(),
+                getOneLineString(master),
+                getOneLineString(test));
+    }
+
+    private static String createName(DiffElement master, DiffElement test) {
+        return (master == null ? test : master).fullyQualifiedName();
+    }
+
+    private static String getOneLineString(DiffElement elt) {
+        return elt == null ? "MISSING" : elt.getValue().toOneLineString();
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
new file mode 100644
index 000000000..4e44578c7
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
@@ -0,0 +1,130 @@
+/*
+ * 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.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+import org.broad.tribble.readers.AsciiLineReader;
+import org.broad.tribble.readers.LineReader;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.Map;
+
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/4/11
+ * Time: 1:09 PM
+ *
+ * Class implementing diffnode reader for VCF
+ */
+public class VCFDiffableReader implements DiffableReader {
+    @Override
+    public String getName() { return "VCF"; }
+
+    @Override
+    public DiffElement readFromFile(File file, int maxElementsToRead) {
+        DiffNode root = DiffNode.rooted(file.getName());
+        try {
+            LineReader lineReader = new AsciiLineReader(new FileInputStream(file));
+            VCFCodec vcfCodec = new VCFCodec();
+
+            // must be read as state is stored in reader itself
+            VCFHeader header = (VCFHeader)vcfCodec.readHeader(lineReader);
+            for ( VCFHeaderLine headerLine : header.getMetaData() ) {
+                String key = headerLine.getKey();
+                if ( headerLine instanceof VCFNamedHeaderLine )
+                    key += "_" + ((VCFNamedHeaderLine) headerLine).getName();
+                root.add(key, headerLine.toString());
+            }
+
+            String line = lineReader.readLine();
+            int count = 0;
+            while ( line != null ) {
+                if ( count++ > maxElementsToRead && maxElementsToRead != -1)
+                    break;
+
+                VariantContext vc = (VariantContext)vcfCodec.decode(line);
+                String name = vc.getChr() + ":" + vc.getStart();
+                DiffNode vcRoot = DiffNode.empty(name, root);
+
+                // add fields
+                vcRoot.add("CHROM", vc.getChr());
+                vcRoot.add("POS", vc.getStart());
+                vcRoot.add("ID", vc.hasID() ? vc.getID() : VCFConstants.MISSING_VALUE_v4);
+                vcRoot.add("REF", vc.getReference());
+                vcRoot.add("ALT", vc.getAlternateAlleles());
+                vcRoot.add("QUAL", vc.hasNegLog10PError() ? vc.getNegLog10PError() * 10 : VCFConstants.MISSING_VALUE_v4);
+                vcRoot.add("FILTER", vc.getFilters());
+
+                // add info fields
+                for (Map.Entry<String, Object> attribute : vc.getAttributes().entrySet()) {
+                    if ( ! attribute.getKey().startsWith("_") && ! attribute.getKey().equals(VariantContext.ID_KEY))
+                        vcRoot.add(attribute.getKey(), attribute.getValue());
+                }
+
+                for (Genotype g : vc.getGenotypes().values() ) {
+                    DiffNode gRoot = DiffNode.empty(g.getSampleName(), vcRoot);
+                    gRoot.add("GT", g.getGenotypeString());
+                    gRoot.add("GQ", g.hasNegLog10PError() ? g.getNegLog10PError() * 10 : VCFConstants.MISSING_VALUE_v4 );
+
+                    for (Map.Entry<String, Object> attribute : g.getAttributes().entrySet()) {
+                        if ( ! attribute.getKey().startsWith("_") )
+                            gRoot.add(attribute.getKey(), attribute.getValue());
+                    }
+
+                    vcRoot.add(gRoot);
+                }
+
+                root.add(vcRoot);
+                line = lineReader.readLine();
+            }
+
+            lineReader.close();
+        } catch ( IOException e ) {
+            return null;
+        }
+
+        return root.getBinding();
+    }
+
+    @Override
+    public boolean canRead(File file) {
+        try {
+            final String VCF4_HEADER = "##fileformat=VCFv4";
+            char[] buff = new char[VCF4_HEADER.length()];
+            new FileReader(file).read(buff, 0, VCF4_HEADER.length());
+            String firstLine = new String(buff);
+            return firstLine.startsWith(VCF4_HEADER);
+        } catch ( IOException e ) {
+            return false;
+        }
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
index 828d39717..efc101618 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
@@ -25,13 +25,13 @@
 
 package org.broadinstitute.sting.gatk.walkers.fasta;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.Collection;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
index 6be2336c0..2dbfc76ff 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
@@ -25,16 +25,15 @@
 
 package org.broadinstitute.sting.gatk.walkers.fasta;
 
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
 
 import java.io.PrintStream;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
index b31526987..2c009f7f2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.filters;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 public class ClusteredSnps {
     private GenomeLocParser genomeLocParser;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
index c3849e240..ede19746a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
@@ -25,8 +25,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.filters;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 
 public class FiltrationContext {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
index 225cdecc3..d7c0dd4d5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
@@ -27,7 +27,9 @@ package org.broadinstitute.sting.gatk.walkers.filters;
 
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.*;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.ListIterator;
 
 /**
  * A window of variants surrounding the current variant being investigated
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
index 884d0ac24..6c023573a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
@@ -25,21 +25,20 @@
 
 package org.broadinstitute.sting.gatk.walkers.filters;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
index 47be7e6fe..83a8ce7d7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
@@ -26,14 +26,15 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.PrintStream;
-import java.util.*;
+import java.util.Map;
+import java.util.Set;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java
index 22c9dcf91..696a74de8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java
@@ -4,8 +4,6 @@ import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 
-import java.util.Arrays;
-
 /**
  * Created by IntelliJ IDEA.
  * User: delangel
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
index ab075eaf2..2014801e4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
@@ -26,13 +26,14 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import net.sf.samtools.SAMUtils;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.pileup.FragmentPileup;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.sting.utils.pileup.FragmentPileup;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import static java.lang.Math.log10;
 import static java.lang.Math.pow;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
index 89504b371..5c27bc943 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
@@ -26,17 +26,22 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.SimpleTimer;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import sun.reflect.generics.reflectiveObjects.NotImplementedException;
 
-import java.util.*;
 import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
 
 public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
     //
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
index 3902a0b7f..8261cd588 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
@@ -30,11 +30,11 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 import java.util.Map;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java
index c4e315f68..10b646d63 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java
@@ -26,18 +26,18 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
 import java.io.PrintStream;
+import java.util.*;
 
 public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 1f430548b..be2039780 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -25,16 +25,14 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel;
 import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
-import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.genotype.Haplotype;
@@ -42,11 +40,10 @@ import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java
index 2cf149fd0..3652763de 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 import java.util.ArrayList;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index 9f4d4182f..3e3cd128b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -25,23 +25,25 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
 
 public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
index cf1c57a05..22c3081a3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
@@ -25,8 +25,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.DownsampleType;
@@ -36,8 +34,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.TreeSet;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
index 1533e8777..68d8f9b54 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
@@ -24,19 +24,19 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 055eb0b97..2b25df4aa 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.commandline.Input;
 
 import java.io.File;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 7a765c602..2a0338bca 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -25,22 +25,25 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.gatk.contexts.*;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.ArgumentCollection;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.DownsampleType;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.filters.BadMateFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
-import org.broadinstitute.sting.gatk.DownsampleType;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 
-import java.util.*;
 import java.io.PrintStream;
+import java.util.*;
 
 
 /**
@@ -48,7 +51,7 @@ import java.io.PrintStream;
  * multi-sample data.  The user can choose from several different incorporated calculation models.
  */
 @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
-@ReadFilters( {BadMateFilter.class} )
+@ReadFilters( {BadMateFilter.class, MappingQualityUnavailableReadFilter.class} )
 @Reference(window=@Window(start=-200,stop=200))
 @By(DataSource.REFERENCE)
 @Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
@@ -158,7 +161,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         }
 
         // FORMAT and INFO fields
-        headerInfo.addAll(VCFUtils.getSupportedHeaderStrings());
+        headerInfo.addAll(getSupportedHeaderStrings());
 
         // FILTER fields
         if ( UAC.STANDARD_CONFIDENCE_FOR_EMITTING < UAC.STANDARD_CONFIDENCE_FOR_CALLING )
@@ -167,6 +170,20 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         return headerInfo;
     }
 
+    /**
+     * return a set of supported format lines; what we currently support for output in the genotype fields of a VCF
+     * @return a set of VCF format lines
+     */
+    private static Set<VCFFormatHeaderLine> getSupportedHeaderStrings() {
+        Set<VCFFormatHeaderLine> result = new HashSet<VCFFormatHeaderLine>();
+        result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
+        result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Genotype Quality"));
+        result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)"));
+        result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
+
+        return result;
+    }
+
     /**
      * Compute at a given locus.
      *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 4c9080884..a10897172 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -25,22 +25,24 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
+import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.pileup.*;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import com.google.java.contract.*;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.PrintStream;
 import java.util.*;
@@ -634,17 +636,27 @@ public class UnifiedGenotyperEngine {
                 if (vcInput == null)
                     return null;
 
-                if (vcInput.isSNP() &&  ( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.SNP))
-                    return GenotypeLikelihoodsCalculationModel.Model.SNP;
+                // todo - no support to genotype MNP's yet
+                if  (vcInput.isMNP())
+                    return null;
+
+                if (vcInput.isSNP())  {
+                    if (( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.SNP))
+                        return GenotypeLikelihoodsCalculationModel.Model.SNP;
+                    else
+                        // ignore SNP's if user chose INDEL mode
+                        return null;
+                }
                 else if ((vcInput.isIndel() || vcInput.isMixed()) && (UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.INDEL))
                     return GenotypeLikelihoodsCalculationModel.Model.INDEL;
-            }   else {
+            }
+            else {
                 // todo - this assumes SNP's take priority when BOTH is selected, should do a smarter way once extended events are removed
                 if( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.SNP)
                     return GenotypeLikelihoodsCalculationModel.Model.SNP;
                 else if (UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.INDEL)
                     return GenotypeLikelihoodsCalculationModel.Model.INDEL;
-                }
+            }
         }
         return null;
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
index aebb0e3eb..adb7c4c38 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
@@ -1,7 +1,10 @@
 package org.broadinstitute.sting.gatk.walkers.indels;
 
 import net.sf.picard.sam.SamPairUtil;
-import net.sf.samtools.*;
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMRecordComparator;
+import net.sf.samtools.SAMRecordCoordinateComparator;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
@@ -113,9 +116,10 @@ public class ConstrainedMateFixingManager {
     HashMap<String, SAMRecordHashObject> forMateMatching = new HashMap<String, SAMRecordHashObject>();
     TreeSet<SAMRecord> waitingReads = new TreeSet<SAMRecord>(comparer);
 
-    private <T> T remove(TreeSet<T> treeSet) {
-        final T first = treeSet.first();
-        treeSet.remove(first);
+    private SAMRecord remove(TreeSet<SAMRecord> treeSet) {
+        final SAMRecord first = treeSet.first();
+        if ( !treeSet.remove(first) )
+            throw new UserException("Error caching SAM record " + first.getReadName() + ", which is usually caused by malformed SAM/BAM files in which multiple identical copies of a read are present.");
         return first;
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
index 7617aa9de..e68aa31e0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
@@ -25,21 +25,16 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import net.sf.samtools.AlignmentBlock;
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.genotype.Haplotype;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 import java.util.Arrays;
 import java.util.HashMap;
-import java.util.List;
 
 public class HaplotypeIndelErrorModel {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index a53665d64..61f21c488 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -25,39 +25,41 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.samtools.*;
 import net.sf.samtools.util.RuntimeIOException;
-import net.sf.samtools.util.StringUtil;
 import net.sf.samtools.util.SequenceUtil;
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.commandline.*;
+import net.sf.samtools.util.StringUtil;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.commandline.Input;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
-import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.BAQMode;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
+import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
+import org.broadinstitute.sting.gatk.walkers.BAQMode;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
+import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
+import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.utils.interval.NwayIntervalMergingIterator;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.NWaySAMFileWriter;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
index 010e0cf6f..af8051334 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
@@ -25,8 +25,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import net.sf.samtools.*;
-import org.broadinstitute.sting.commandline.*;
+import net.sf.samtools.Cigar;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index ab7ae4184..60262d6f4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -28,30 +28,25 @@ package org.broadinstitute.sting.gatk.walkers.indels;
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-/*import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.Covariate;
-import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDataManager;
-import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDatum;
-import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalibrationArgumentCollection;
-*/import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.collections.NestedHashMap;
-import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.genotype.Haplotype;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.text.XReadLines;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 import java.io.File;
-import java.io.FileNotFoundException;
-import java.util.*;
-import java.util.regex.Pattern;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+
+/*import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.Covariate;
+import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDataManager;
+import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalDatum;
+import org.broadinstitute.sting.oneoffprojects.walkers.IndelCountCovariates.RecalibrationArgumentCollection;
+*/
 
 
 public class PairHMMIndelErrorModel {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignedReadCounter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignedReadCounter.java
index fc196e712..2c89b907b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignedReadCounter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignedReadCounter.java
@@ -25,19 +25,23 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import net.sf.samtools.*;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.filters.BadMateFilter;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
-import org.broadinstitute.sting.utils.sam.ReadUtils;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.filters.BadMateFilter;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.By;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
+import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.io.File;
-import java.util.*;
+import java.util.Iterator;
 
 @By(DataSource.READS)
 // walker to count realigned reads
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index 048dbd8cb..488e37f26 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -25,32 +25,32 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.filters.BadCigarFilter;
-import org.broadinstitute.sting.gatk.filters.Platform454Filter;
-import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.gatk.filters.BadMateFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
+import org.broadinstitute.sting.gatk.filters.Platform454Filter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.ArrayList;
 import java.io.PrintStream;
+import java.util.ArrayList;
 
 /**
  * Emits intervals for the Local Indel Realigner to target for cleaning.  Ignores 454 reads, MQ0 reads, and reads with consecutive indel operators in the CIGAR string.
  */
-@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class, BadCigarFilter.class})
+@ReadFilters({Platform454Filter.class, MappingQualityZeroReadFilter.class, BadCigarFilter.class})
 @Reference(window=@Window(start=-1,stop=50))
 @Allows(value={DataSource.READS, DataSource.REFERENCE})
 @By(DataSource.REFERENCE)
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java
index 1fe3fdd04..3854a4a8c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java
@@ -23,7 +23,8 @@
  */
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import net.sf.samtools.*;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMRecordCoordinateComparator;
 
 /**
  * Extends Picard's Comparator for sorting SAMRecords by coordinate.  This one actually deals with unmapped reads
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
index c2953d1d7..443e6e9f2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
@@ -25,15 +25,21 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import net.sf.samtools.*;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.commandline.Tags;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
-import org.broadinstitute.sting.gatk.filters.*;
-import org.broadinstitute.sting.gatk.refdata.*;
+import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
+import org.broadinstitute.sting.gatk.filters.Platform454Filter;
+import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter;
+import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
+import org.broadinstitute.sting.gatk.refdata.Transcript;
 import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
 import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
@@ -42,22 +48,22 @@ import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODItera
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.gatk.walkers.ReadFilters;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.interval.IntervalUtils;
-import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
-import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
-import org.broadinstitute.sting.utils.interval.OverlappingIntervalIterator;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.collections.CircularArray;
 import org.broadinstitute.sting.utils.collections.PrimitivePair;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.Hidden;
-
-import net.sf.samtools.*;
+import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
+import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
+import org.broadinstitute.sting.utils.interval.IntervalUtils;
+import org.broadinstitute.sting.utils.interval.OverlappingIntervalIterator;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.*;
 import java.util.*;
@@ -72,7 +78,7 @@ import java.util.*;
  * if first bam has coverage at the site but no indication for an indel. In the --somatic mode, BED output contains
  * only somatic calls, while --verbose output contains all calls annotated with GERMLINE/SOMATIC keywords.
  */
-@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class, PlatformUnitFilter.class})
+@ReadFilters({Platform454Filter.class, MappingQualityZeroReadFilter.class, PlatformUnitFilter.class})
 public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
 //    @Output
 //    PrintStream out;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
index 869edf784..cb123c868 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
@@ -23,9 +23,9 @@
  */
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
index 81d9b4ddb..9aa370d3f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
@@ -24,14 +24,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.features.annotator.AnnotatorInputTableFeature;
@@ -41,9 +37,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.AminoAci
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
index 709bc44ce..5bd438605 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java
@@ -24,10 +24,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -35,7 +31,11 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
index abced442e..b0491a281 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
@@ -24,20 +24,19 @@
 
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
index ec6f5c648..be15d4541 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java
@@ -24,20 +24,22 @@
 
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index e59b29502..9702fd18c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -23,27 +23,28 @@
  */
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
-import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.DisjointSet;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.HasGenomeLocation;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriter;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.*;
 import java.util.*;
@@ -58,7 +59,7 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
 @Requires(value = {DataSource.READS, DataSource.REFERENCE}, referenceMetaData = @RMD(name = "variant", type = ReferenceOrderedDatum.class))
 @By(DataSource.READS)
 
-@ReadFilters({ZeroMappingQualityReadFilter.class})
+@ReadFilters({MappingQualityZeroReadFilter.class})
 // Filter out all reads with zero mapping quality
 
 public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
@@ -220,6 +221,9 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
             }
             else {
                 unprocessedList.add(vc); // Finished with the unprocessed variant, and writer can enforce sorting on-the-fly
+
+                if (DEBUG)
+                    logger.debug("Unprocessed variant = " + VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc));
             }
 
             int numReads = 0;
@@ -239,7 +243,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         return new PhasingStatsAndOutput(phaseStats, completedList);
     }
 
-    private static final Set<String> KEYS_TO_KEEP_IN_REDUCED_VCF = new HashSet<String>(Arrays.asList("PQ"));
+    private static final Set<String> KEYS_TO_KEEP_IN_REDUCED_VCF = new HashSet<String>(Arrays.asList(PQ_KEY));
 
     private VariantContext reduceVCToSamples(VariantContext vc, List<String> samplesToPhase) {
 //        for ( String sample : samplesToPhase )
@@ -1105,7 +1109,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
             this.alleles = vc.getAlleles();
             this.genotypes = new HashMap<String, Genotype>(vc.getGenotypes()); // since vc.getGenotypes() is unmodifiable
             this.negLog10PError = vc.getNegLog10PError();
-            this.filters = vc.getFilters();
+            this.filters = vc.filtersWereApplied() ? vc.getFilters() : null;
             this.attributes = new HashMap<String, Object>(vc.getAttributes());
         }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
index db1f888a1..153c4a23f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
@@ -23,10 +23,10 @@
  */
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
 
 public class SNPallelePair extends AllelePair {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java
index f82e48abd..2851ace0d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java
@@ -24,9 +24,9 @@
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 
 public class WriteVCF {
     public static void writeVCF(VariantContext vc, VCFWriter writer, Logger logger) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java
index feb5f62af..2bdd4558f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java
@@ -6,14 +6,12 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 
-import java.util.List;
 import java.io.PrintStream;
+import java.util.List;
 
 /**
  * Counts the number of contiguous regions the walker traverses over. Slower than it needs to be, but
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java
index ef6ff04f2..0d68c8493 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
-import net.sf.samtools.SAMFileWriter;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java
index cece04fcf..df89efe6d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java
@@ -25,14 +25,14 @@
 
 package org.broadinstitute.sting.gatk.walkers.qc;
 
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.walkers.ReadPairWalker;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
-import org.broadinstitute.sting.commandline.Output;
-import net.sf.samtools.SAMRecord;
 
+import java.io.PrintStream;
 import java.util.Collection;
 import java.util.List;
-import java.io.PrintStream;
 
 /**
  * Counts the number of read pairs encountered in a file sorted in
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java
index 74f63aa2f..87c0409b9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java
@@ -1,11 +1,11 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.walkers.Requires;
 
 /**
  * Walks over the input data set, calculating the number of reads seen for diagnostic purposes.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java
index a4e80138f..d1545f159 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java
@@ -25,13 +25,13 @@
 
 package org.broadinstitute.sting.gatk.walkers.qc;
 
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.commandline.Argument;
 
 /**
  * Prints out counts of the number of reference ordered data objects are
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
index 92867e1a9..8a03dea44 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
@@ -27,23 +27,24 @@ package org.broadinstitute.sting.gatk.walkers.qc;
 
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
 
+import java.io.PrintStream;
 import java.util.ArrayList;
-import java.util.List;
 import java.util.Collection;
 import java.util.LinkedList;
-import java.io.PrintStream;
+import java.util.List;
 
 /**
  * Prints out counts of the number of reference ordered data objects are
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java
index 5ae35416a..b5f5442cd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java
@@ -25,22 +25,22 @@
 
 package org.broadinstitute.sting.gatk.walkers.qc;
 
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.collections.PrimitivePair;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMReadGroupRecord;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.utils.collections.PrimitivePair;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 
-import java.util.*;
 import java.io.*;
+import java.util.*;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java
index 39b69ba29..d3b992cb5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java
@@ -1,16 +1,16 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 
-import java.util.List;
-import java.util.Arrays;
 import java.io.PrintStream;
-
-import net.sf.samtools.SAMRecord;
+import java.util.Arrays;
+import java.util.List;
 
 /**
  * At each locus in the input data set, prints the reference base, genomic location, and
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java
index 2f1773d01..908e389a8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java
@@ -22,21 +22,24 @@
 
 package org.broadinstitute.sting.gatk.walkers.qc;
 
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.sam.AlignmentUtils;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
-import net.sf.samtools.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 
-import java.util.*;
-import java.io.*;
+import java.io.PrintStream;
+import java.util.Arrays;
 
 /**
  * User: depristo
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
index 6ad0340a4..fa1bb4d55 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
@@ -1,16 +1,16 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMFileWriter;
 
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
-import java.util.List;
 import java.util.ArrayList;
+import java.util.List;
 
 
 /*
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java
index 9cb715507..170630b77 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -8,8 +7,11 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.walkers.Reference;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.*;
 import java.math.BigInteger;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
index bc68be592..e1e6c4b69 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
@@ -25,20 +25,20 @@
 
 package org.broadinstitute.sting.gatk.walkers.qc;
 
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.features.sampileup.SAMPileupFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
-import java.util.Arrays;
 import java.io.PrintStream;
+import java.util.Arrays;
 
 /**
  * At every locus in the input set, compares the pileup data (reference base, aligned base from
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java
index 568e1b638..fc6b3daee 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java
@@ -7,7 +7,6 @@ import org.broadinstitute.sting.utils.text.XReadLines;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.PrintStream;
-import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.regex.Pattern;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
index ee504b6e7..8c6539f8d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
@@ -27,23 +27,25 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import org.broad.tribble.bed.BEDCodec;
 import org.broad.tribble.dbsnp.DbSNPCodec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Gather;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
+import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.collections.NestedHashMap;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
@@ -75,7 +77,7 @@ import java.util.Map;
 
 @BAQMode(ApplicationTime = BAQ.ApplicationTime.FORBIDDEN)
 @By( DataSource.READS ) // Only look at covered loci, not every loci of the reference file
-@ReadFilters( {ZeroMappingQualityReadFilter.class} ) // Filter out all reads with zero mapping quality
+@ReadFilters( {MappingQualityZeroReadFilter.class, MappingQualityUnavailableReadFilter.class} ) // Filter out all reads with zero or unavailable mapping quality
 @Requires( {DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES} ) // This walker requires both -I input.bam and -R reference.fasta
 @PartitionBy(PartitionType.LOCUS)
 public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.CountedData, CountCovariatesWalker.CountedData> implements TreeReducible<CountCovariatesWalker.CountedData> {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
index 64e0864c0..945d02837 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import net.sf.samtools.SAMRecord;
-
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java
index 0de6897d0..a7717161a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java
@@ -1,11 +1,10 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import java.util.HashMap;
-
 import net.sf.samtools.SAMRecord;
-
 import org.broadinstitute.sting.utils.BaseUtils;
 
+import java.util.HashMap;
+
 /*
  * Copyright (c) 2009 The Broad Institute
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
index fdbeb6a31..e6d0b306c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -25,19 +25,21 @@
 
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMUtils;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.collections.NestedHashMap;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
-import java.util.*;
-
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMReadGroupRecord;
-import net.sf.samtools.SAMUtils;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java
index 7ba441ccc..f04989fa5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 
-import java.util.*;
+import java.util.List;
 
 /*
  * Copyright (c) 2010 The Broad Institute
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index 0eaa1245e..0277fda0d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -25,31 +25,33 @@
 
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.util.*;
-import java.util.regex.Pattern;
-
 import net.sf.samtools.*;
 import net.sf.samtools.util.SequenceUtil;
-
+import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.sting.utils.collections.NestedHashMap;
+import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.text.TextFormattingUtils;
+import org.broadinstitute.sting.utils.text.XReadLines;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.MissingResourceException;
+import java.util.ResourceBundle;
+import java.util.regex.Pattern;
 
 /**
  * This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
index c1c17bda5..b3b63bb96 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
@@ -1,12 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers.sequenom;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.PrintStream;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
index fde233b5d..b877ff70b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
@@ -25,29 +25,27 @@
 
 package org.broadinstitute.sting.gatk.walkers.sequenom;
 
-import net.sf.samtools.util.CloseableIterator;
 import org.broad.tribble.bed.BEDCodec;
-import org.broad.tribble.dbsnp.DbSNPCodec;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.*;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
+import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
-import java.util.*;
 import java.io.PrintStream;
+import java.util.*;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index 15d808ebe..fe3173506 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -1,14 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
@@ -20,23 +18,21 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
 import org.broadinstitute.sting.gatk.walkers.variantrecalibration.Tranche;
 import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
-import net.sf.picard.reference.FastaSequenceFile;
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import net.sf.picard.reference.ReferenceSequence;
-import java.io.FileNotFoundException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.PrintStream;
 import java.lang.reflect.Field;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java
index 787dbe9af..925bff9c0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
 
 class NewCompEvalGenotypes {
     private GenomeLoc loc;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
index 76db330ed..255a54737 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
@@ -1,12 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 /**
  * The Broad Institute
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
index c4277adc9..8c281b2f8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 @Analysis(description = "Counts different classes of variants in the sample")
 public class CountVariants extends VariantEvaluator implements StandardEval {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
index 4b56cf130..bbd3f5f54 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
@@ -1,18 +1,18 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
index 3d14dd0e5..a476a2680 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
@@ -1,20 +1,20 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.phasing.AllelePair;
 import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.NewEvaluationContext;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.HashMap;
 import java.util.HashSet;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
index 5daf33a9f..77def0f30 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 /**
  * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
index eca6c5193..6e1b76acd 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java
@@ -1,14 +1,14 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
index 48b06d532..d99196ecf 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
@@ -1,15 +1,15 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
 import org.broadinstitute.sting.utils.IndelUtils;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
index 85e0b5889..a0cc393d9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
@@ -1,21 +1,15 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.MendelianViolation;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-
-import java.util.Arrays;
-import java.util.List;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 /**
  * Mendelian violation detection and counting
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
index 7d54d0df8..b209ee13d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
@@ -24,12 +24,12 @@
 
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 @Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites")
 public class PrintMissingComp extends VariantEvaluator {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java
index 5f3e6b0fa..751f61a97 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
 
 import java.util.HashMap;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
index deed05508..d466645ea 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
@@ -1,18 +1,18 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Degeneracy;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Sample;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.ArrayList;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
index 89c67cfe9..ec43cbd55 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.ConcurrentMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
index 8811dc001..be957abd7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
@@ -1,13 +1,13 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 @Analysis(description = "Ti/Tv Variant Evaluator")
 public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEval {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
index 405f35635..9c331b577 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
@@ -1,17 +1,16 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.Set;
 
 /**
  * The Broad Institute
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
index 6017ecca3..e29e7ed50 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
@@ -1,12 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.NewEvaluationContext;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 public abstract class VariantEvaluator {
     public void initialize(VariantEvalWalker walker) {}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
index 4af14810b..b6ad55b18 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java
@@ -25,16 +25,16 @@
 
 package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
+import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
 import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.ArrayList;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
index ff59c9e29..411493d4f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
@@ -1,12 +1,11 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
-import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
@@ -43,9 +42,9 @@ public class AlleleCount extends VariantStratifier {
 
         if (eval != null) {
             int AC = -1;
-            if ( eval.hasAttribute("AC") )
+            if ( eval.hasAttribute("AC") && eval.getAttribute("AC") instanceof Integer ) {
                 AC = eval.getAttributeAsInt("AC");
-            else if ( eval.isVariant() ) {
+            } else if ( eval.isVariant() ) {
                 for (Allele allele : eval.getAlternateAlleles())
                     AC = Math.max(AC, eval.getChromosomeCount(allele));
             } else
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
index 48b4ffa91..2ffc7716c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
@@ -1,10 +1,10 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
index 9942ba8d6..c6975808f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
index 1a9d31085..c14355035 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
index 15b1d41c1..3e8a6ed17 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
index 65af6090c..155a66186 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
@@ -1,14 +1,14 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.Set;
 import java.util.HashSet;
+import java.util.Set;
 
 public class Degeneracy extends VariantStratifier {
     private ArrayList<String> states;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
index 7bd15a974..40f952fd2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
index 8d8782ab7..3b7a419f2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
index fd724d6d1..c6c094f8e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
index a7ccd3182..76efedbf4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
@@ -1,10 +1,10 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
index 39d2e6b4d..a0973a088 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Collection;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
index f909de4f3..a2a3eb3fb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
index 218cb23ca..2c4b8bc46 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
@@ -1,11 +1,10 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java
similarity index 80%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java
index 129d5a95d..2b37ce210 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/Analysis.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.walkers.varianteval.tags;
+package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
 import java.lang.annotation.Retention;
 import java.lang.annotation.RetentionPolicy;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java
index c8d917040..db44e9e28 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java
@@ -23,8 +23,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.lang.annotation.Annotation;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java
similarity index 77%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java
index 3ba448049..396843252 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/tags/DataPoint.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.walkers.varianteval.tags;
+package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
 import java.lang.annotation.Retention;
 import java.lang.annotation.RetentionPolicy;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java
index 3208c26bb..8112ae97f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -9,6 +8,7 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvalu
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.HashMap;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
index 0281653af..38f7a7f40 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
-import org.apache.commons.jexl2.*;
+import org.apache.commons.jexl2.Expression;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 public class SortableJexlVCMatchExp extends VariantContextUtils.JexlVCMatchExp implements Comparable<SortableJexlVCMatchExp> {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
index b8e45e462..0a915db37 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
@@ -1,24 +1,21 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.report.GATKReport;
 import org.broadinstitute.sting.gatk.report.GATKReportTable;
-import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.StandardEval;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.RequiredStratification;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.StandardStratification;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.lang.reflect.Field;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index d4e07dccf..403c67d3e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -25,23 +25,23 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Input;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
 import java.io.FileNotFoundException;
-import java.lang.Double;
 import java.util.*;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
index 1f622afc8..17461de2f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
@@ -97,7 +97,7 @@ public class GaussianMixtureModel {
 
         int ttt = 0;
         while( ttt++ < numIterations ) {
-            // Estep: assign each variant to the nearest cluster
+            // E step: assign each variant to the nearest cluster
             for( final VariantDatum datum : data ) {
                 double minDistance = Double.MAX_VALUE;
                 MultivariateGaussian minGaussian = null;
@@ -112,7 +112,7 @@ public class GaussianMixtureModel {
                 datum.assignment = minGaussian;
             }
 
-            // Mstep: update gaussian means based on assigned variants
+            // M step: update gaussian means based on assigned variants
             for( final MultivariateGaussian gaussian : gaussians ) {
                 gaussian.zeroOutMu();
                 int numAssigned = 0;
@@ -229,26 +229,29 @@ public class GaussianMixtureModel {
     }
 
     public double evaluateDatumMarginalized( final VariantDatum datum ) {
-        int numVals = 0;
+        int numSamples = 0;
         double sumPVarInGaussian = 0.0;
-        int numIter = 10;
+        final int numIterPerMissingAnnotation = 10; // Trade off here between speed of computation and accuracy of the marginalization
         final double[] pVarInGaussianLog10 = new double[gaussians.size()];
+        // for each dimension
         for( int iii = 0; iii < datum.annotations.length; iii++ ) {
-            // marginalize over the missing dimension by drawing X random values for the missing annotation and averaging the lod
+            // if it is missing marginalize over the missing dimension by drawing X random values for the missing annotation and averaging the lod
             if( datum.isNull[iii] ) {
-                for( int ttt = 0; ttt < numIter; ttt++ ) {
-                    datum.annotations[iii] = Normal.staticNextDouble(0.0, 1.0);
+                for( int ttt = 0; ttt < numIterPerMissingAnnotation; ttt++ ) {
+                    datum.annotations[iii] = GenomeAnalysisEngine.getRandomGenerator().nextGaussian(); // draw a random sample from the standard normal distribution
 
+                    // evaluate this random data point
                     int gaussianIndex = 0;
                     for( final MultivariateGaussian gaussian : gaussians ) {
                         pVarInGaussianLog10[gaussianIndex++] = gaussian.pMixtureLog10 + gaussian.evaluateDatumLog10( datum );
                     }
 
-                    sumPVarInGaussian += Math.pow(10.0, MathUtils.log10sumLog10(pVarInGaussianLog10));
-                    numVals++;
+                    // add this sample's probability to the pile in order to take an average in the end
+                    sumPVarInGaussian += Math.pow(10.0, MathUtils.log10sumLog10(pVarInGaussianLog10)); // p = 10 ^ Sum(pi_k * p(v|n,k))
+                    numSamples++;
                 }
             }
         }
-        return Math.log10( sumPVarInGaussian / ((double) numVals) );
+        return Math.log10( sumPVarInGaussian / ((double) numSamples) );
     }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
index 64fe36637..15424f0f7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
@@ -25,11 +25,14 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
-import java.io.*;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintStream;
 import java.util.*;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
index 5deb5d8c2..bc7252ec2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
@@ -26,10 +26,10 @@
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 357bbaa24..67d54a408 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -25,9 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
-import cern.jet.random.Normal;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -35,9 +33,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.PrintStream;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
 
 /**
  * Created by IntelliJ IDEA.
@@ -83,19 +84,11 @@ public class VariantDataManager {
             }
 
             foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-6);
-            if( annotationKeys.get(iii).toLowerCase().contains("ranksum") ) { // BUGBUG: to clean up
-                for( final VariantDatum datum : data ) {
-                    if( datum.annotations[iii] > 0.0 ) { datum.annotations[iii] /= 3.0; }
-                }
-            }
             meanVector[iii] = theMean;
             varianceVector[iii] = theSTD;
             for( final VariantDatum datum : data ) {
-                datum.annotations[iii] = ( datum.isNull[iii] ? Normal.staticNextDouble(0.0, 1.0) : ( datum.annotations[iii] - theMean ) / theSTD );
-                // Each data point is now [ (x - mean) / standard deviation ]
-                if( annotationKeys.get(iii).toLowerCase().contains("ranksum") && datum.isNull[iii] && datum.annotations[iii] > 0.0 ) {
-                    datum.annotations[iii] /= 3.0;
-                }
+                // Transform each data point via: (x - mean) / standard deviation
+                datum.annotations[iii] = ( datum.isNull[iii] ? GenomeAnalysisEngine.getRandomGenerator().nextGaussian() : ( datum.annotations[iii] - theMean ) / theSTD );
             }
         }
         if( foundZeroVarianceAnnotation ) {
@@ -164,7 +157,7 @@ public class VariantDataManager {
         final int numBadSitesAdded = trainingData.size();
         logger.info( "Found " + numBadSitesAdded + " variants overlapping bad sites training tracks." );
 
-        // Next, sort the variants by the LOD coming from the positive model and add to the list the bottom X percent of variants
+        // Next sort the variants by the LOD coming from the positive model and add to the list the bottom X percent of variants
         Collections.sort( data );
         final int numToAdd = Math.max( minimumNumber - trainingData.size(), Math.round((float)bottomPercentage * data.size()) );
         if( numToAdd > data.size() ) {
@@ -242,23 +235,15 @@ public class VariantDataManager {
         double value;
 
         try {
-            if( annotationKey.equalsIgnoreCase("QUAL") ) {
-                value = vc.getPhredScaledQual();
-            } else if( annotationKey.equalsIgnoreCase("DP") ) {
-                value = Double.parseDouble( (String)vc.getAttribute( "DP" ) ) / Double.parseDouble( (String)vc.getAttribute( "AN" ) );
-            } else {
-                value = Double.parseDouble( (String)vc.getAttribute( annotationKey ) );
-                if( Double.isInfinite(value) ) { value = Double.NaN; }
-                if( annotationKey.equalsIgnoreCase("InbreedingCoeff") && value > 0.05 ) { value = Double.NaN; }
-                if( jitter && annotationKey.equalsIgnoreCase("HRUN") ) { // Integer valued annotations must be jittered a bit to work in this GMM
-                      value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble();
-                }
-                if( annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.0001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
-                if( annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
+            value = Double.parseDouble( (String)vc.getAttribute( annotationKey ) );
+            if( Double.isInfinite(value) ) { value = Double.NaN; }
+            if( jitter && annotationKey.equalsIgnoreCase("HRUN") ) { // Integer valued annotations must be jittered a bit to work in this GMM
+                  value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble();
             }
-
+            if( jitter && annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.0001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
+            if( jitter && annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, 0.001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
         } catch( Exception e ) {
-            value = Double.NaN; // The VQSR works with missing data now by marginalizing over the missing dimension when evaluating Gaussians
+            value = Double.NaN; // The VQSR works with missing data by marginalizing over the missing dimension when evaluating the Gaussian mixture model
         }
 
         return value;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 2c51f02d6..8179463eb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -25,14 +25,12 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
@@ -42,6 +40,8 @@ import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -284,7 +284,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             throw new UserException.CouldNotCreateOutputFile(RSCRIPT_FILE, "", e);
         }
 
-        // We make extensive use of the ggplot2 library: http://had.co.nz/ggplot2/
+        // We make extensive use of the ggplot2 R library: http://had.co.nz/ggplot2/
         stream.println("library(ggplot2)");
 
         createArrangeFunction( stream );
@@ -378,6 +378,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         }
      }
 
+    // The Arrange function is how we place the 4 model plots on one page
     // from http://gettinggeneticsdone.blogspot.com/2010/03/arrange-multiple-ggplot2-plots-in-same.html
     private void createArrangeFunction( final PrintStream stream ) {
         stream.println("vp.layout <- function(x, y) viewport(layout.pos.row=x, layout.pos.col=y)");
@@ -402,5 +403,4 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         stream.println("}");
         stream.println("}");
     }
-
- }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
index f597fb128..e1a815913 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
@@ -60,7 +60,7 @@ public class VariantRecalibratorArgumentCollection {
     @Argument(fullName="priorCounts", shortName="priorCounts", doc="The number of prior counts to use in variational Bayes algorithm.", required=false)
     public double PRIOR_COUNTS = 20.0;
     @Argument(fullName="percentBadVariants", shortName="percentBad", doc="What percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent.", required=false)
-    public double PERCENT_BAD_VARIANTS = 0.015;
+    public double PERCENT_BAD_VARIANTS = 0.03;
     @Argument(fullName="minNumBadVariants", shortName="minNumBad", doc="The minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary.", required=false)
     public int MIN_NUM_BAD_VARIANTS = 2000;
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index 597a54dc1..837f352f8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -25,12 +25,12 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.Requires;
@@ -38,11 +38,10 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
-import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
index ba6f5e513..b45ee1b67 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
@@ -24,18 +24,21 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
-import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Map;
+import java.util.Set;
 
 /**
  * Filters a lifted-over VCF file for ref bases that have been changed.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
index d9dd85f0c..2ebd183f4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
@@ -28,21 +28,17 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriter;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
index 7eda54387..4f05c8aac 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -24,27 +24,27 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-
-import java.io.File;
-import java.util.*;
-
 import net.sf.picard.PicardException;
 import net.sf.picard.liftover.LiftOver;
 import net.sf.picard.util.Interval;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileReader;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.RMD;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+
+import java.io.File;
+import java.util.*;
 
 /**
  * Lifts a VCF file over from one build to another.  Note that the resulting VCF could be mis-sorted.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
index 0c41a9728..f0756d884 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
@@ -24,11 +24,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@@ -39,11 +34,15 @@ import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
 
 /**
  * Takes a VCF file, randomly splits variants into two different sets, and outputs 2 new VCFs with the results.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index cbac54326..1db692e9f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -24,27 +24,26 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.MendelianViolation;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.MendelianViolation;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.File;
-import java.lang.annotation.AnnotationFormatError;
 import java.util.*;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
index 1bd73414c..0644c669b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
@@ -25,22 +25,25 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broad.tribble.TribbleException;
+import org.broad.tribble.dbsnp.DbSNPFeature;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
 import java.io.File;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
index 482679593..86bb3b0e8 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
@@ -25,20 +25,19 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
index 71dd5df3f..8d90af65a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
@@ -24,18 +24,17 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.PrintStream;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
index 7eb49da34..aa0e5987f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
@@ -28,26 +28,26 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
 import net.sf.samtools.util.CloseableIterator;
 import org.broad.tribble.dbsnp.DbSNPCodec;
 import org.broad.tribble.dbsnp.DbSNPFeature;
-import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
@@ -199,8 +199,8 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
             // setup the header fields
             Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
             hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
-            hInfo.add(new VCFHeaderLine("source", "VariantsToVCF"));
-            hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
+            //hInfo.add(new VCFHeaderLine("source", "VariantsToVCF"));
+            //hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
 
             allowedGenotypeFormatStrings.add(VCFConstants.GENOTYPE_KEY);
             for ( VCFHeaderLine field : hInfo ) {
diff --git a/public/java/src/org/broadinstitute/sting/jna/clibrary/LibC.java b/public/java/src/org/broadinstitute/sting/jna/clibrary/LibC.java
index b01533ee6..b5efcc153 100644
--- a/public/java/src/org/broadinstitute/sting/jna/clibrary/LibC.java
+++ b/public/java/src/org/broadinstitute/sting/jna/clibrary/LibC.java
@@ -24,7 +24,10 @@
 
 package org.broadinstitute.sting.jna.clibrary;
 
-import com.sun.jna.*;
+import com.sun.jna.LastErrorException;
+import com.sun.jna.Native;
+import com.sun.jna.NativeLong;
+import com.sun.jna.Structure;
 import com.sun.jna.ptr.NativeLongByReference;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java b/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java
index 0c0579d6f..c7b3de6cf 100644
--- a/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java
+++ b/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java
@@ -29,7 +29,7 @@ import com.sun.jna.ptr.FloatByReference;
 import com.sun.jna.ptr.IntByReference;
 import com.sun.jna.ptr.PointerByReference;
 import org.broadinstitute.sting.jna.clibrary.JNAUtils;
-import org.broadinstitute.sting.jna.clibrary.LibC.*;
+import org.broadinstitute.sting.jna.clibrary.LibC.timeval;
 
 /*
   NOTE: This library uses Pointer for some Struct.ByReference members going
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
index fe6758e76..c09c4037e 100644
--- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
+++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
@@ -27,13 +27,16 @@ package org.broadinstitute.sting.queue.extensions.gatk;
 import net.sf.samtools.BAMIndex;
 import net.sf.samtools.SAMFileWriter;
 import org.broad.tribble.Tribble;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
 
 import java.io.File;
 import java.lang.annotation.Annotation;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
 
 public abstract class ArgumentDefinitionField extends ArgumentField {
 
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
index 2da427d44..e90933504 100644
--- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
+++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
@@ -35,7 +35,10 @@ import java.io.File;
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.lang.annotation.Annotation;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
 
 public abstract class ArgumentField {
 
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
index 21fb44733..5095bd6e5 100644
--- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
+++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
@@ -27,17 +27,20 @@ package org.broadinstitute.sting.queue.extensions.gatk;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.commandline.ParsingEngine;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.WalkerManager;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
 import org.broadinstitute.sting.gatk.filters.ReadFilter;
-import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
+import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.walkers.PartitionBy;
 import org.broadinstitute.sting.gatk.walkers.PartitionType;
diff --git a/public/java/src/org/broadinstitute/sting/utils/DisjointSet.java b/public/java/src/org/broadinstitute/sting/utils/DisjointSet.java
index 5f68d3414..52c18e6d6 100644
--- a/public/java/src/org/broadinstitute/sting/utils/DisjointSet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/DisjointSet.java
@@ -23,7 +23,9 @@
  */
 package org.broadinstitute.sting.utils;
 
-import java.util.*;
+import java.util.Collection;
+import java.util.Set;
+import java.util.TreeSet;
 
 public class DisjointSet {
     private ItemNode[] nodes;
diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index 1f8800542..b96923589 100644
--- a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -2,7 +2,6 @@ package org.broadinstitute.sting.utils;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.Serializable;
diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index 18a1e7ffd..a5c6e0537 100644
--- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -25,12 +25,14 @@
 
 package org.broadinstitute.sting.utils;
 
-import com.google.java.contract.*;
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Invariant;
+import com.google.java.contract.Requires;
+import com.google.java.contract.ThrowEnsures;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
-
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
diff --git a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java
index 30e1a3f5b..af69ebca6 100755
--- a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.utils;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Arrays;
diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
index 50aa0f707..36ed506aa 100755
--- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -25,17 +25,14 @@
 
 package org.broadinstitute.sting.utils;
 
-import cern.jet.math.Arithmetic;
-
-import java.math.BigDecimal;
-import java.util.*;
-
 import com.google.java.contract.Requires;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.collections.PrimitivePair;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
+import java.math.BigDecimal;
+import java.util.*;
+
 /**
  * MathUtils is a static class (no instantiation allowed!) with some useful math methods.
  *
diff --git a/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java b/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
index a8089ffe8..c6a07b5ce 100755
--- a/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
@@ -1,12 +1,13 @@
 package org.broadinstitute.sting.utils;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.Collection;
+import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/PathUtils.java b/public/java/src/org/broadinstitute/sting/utils/PathUtils.java
index 47466be20..822d04dfd 100755
--- a/public/java/src/org/broadinstitute/sting/utils/PathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/PathUtils.java
@@ -2,10 +2,10 @@ package org.broadinstitute.sting.utils;
 
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.List;
-import java.util.ArrayList;
 import java.io.File;
 import java.io.FilenameFilter;
+import java.util.ArrayList;
+import java.util.List;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java b/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
index 23054e95f..fad2320fc 100755
--- a/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
@@ -9,9 +9,13 @@ import net.sf.samtools.SAMUtils;
  * @author Kiran Garimella
  */
 public class QualityUtils {
+
     public final static byte MAX_QUAL_SCORE = SAMUtils.MAX_PHRED_SCORE;
     public final static double MIN_REASONABLE_ERROR = 0.0001;
     public final static byte MAX_REASONABLE_Q_SCORE = 40;
+    public final static byte MIN_USABLE_Q_SCORE = 6;
+
+    public final static int MAPPING_QUALITY_UNAVAILABLE = 255;
 
     /**
      * Private constructor.  No instantiating this class!
diff --git a/public/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java b/public/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java
index 30257d967..a758df431 100644
--- a/public/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java
@@ -3,7 +3,9 @@ package org.broadinstitute.sting.utils;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
 
 /**
  * Randomly downsample from a stream of elements.  This algorithm is a direct,
diff --git a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java
index 4b7fa3e41..92d73a5ce 100755
--- a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java
+++ b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java
@@ -24,15 +24,14 @@
 
 package org.broadinstitute.sting.utils;
 
+import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
-import net.sf.samtools.Cigar;
-
-import java.util.*;
-
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 
+import java.util.*;
+
 /**
  * Created by IntelliJ IDEA.
  * User: asivache
diff --git a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
index c0370064d..f9997bfd8 100755
--- a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
@@ -27,12 +27,12 @@ package org.broadinstitute.sting.utils;
 
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMReadGroupRecord;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java b/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java
index a59c5134a..342087b41 100644
--- a/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java
+++ b/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java
@@ -1,7 +1,10 @@
 package org.broadinstitute.sting.utils;
 
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Invariant;
+import com.google.java.contract.Requires;
+
 import java.io.PrintStream;
-import com.google.java.contract.*;
 
 /**
  * A useful simple system for timing code.  This code is not thread safe!
diff --git a/public/java/src/org/broadinstitute/sting/utils/Utils.java b/public/java/src/org/broadinstitute/sting/utils/Utils.java
index 4c13d8b18..6a50badce 100755
--- a/public/java/src/org/broadinstitute/sting/utils/Utils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/Utils.java
@@ -25,13 +25,12 @@
 
 package org.broadinstitute.sting.utils;
 
-import java.util.*;
-
 import net.sf.samtools.util.StringUtil;
-
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.collections.Pair;
 
+import java.util.*;
+
 /**
  * Created by IntelliJ IDEA.
  * User: depristo
diff --git a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
index 456f0fa0f..ef7cf751e 100644
--- a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
+++ b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
@@ -1,10 +1,10 @@
 package org.broadinstitute.sting.utils.baq;
 
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.CigarElement;
-import net.sf.samtools.CigarOperator;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.picard.reference.ReferenceSequence;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
diff --git a/public/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java b/public/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java
index 24d4152a5..26356a4a4 100644
--- a/public/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java
@@ -2,11 +2,10 @@ package org.broadinstitute.sting.utils.baq;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import net.sf.samtools.SAMRecord;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.Iterator;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/bed/BedParser.java b/public/java/src/org/broadinstitute/sting/utils/bed/BedParser.java
index abcae066f..b95165841 100644
--- a/public/java/src/org/broadinstitute/sting/utils/bed/BedParser.java
+++ b/public/java/src/org/broadinstitute/sting/utils/bed/BedParser.java
@@ -1,11 +1,12 @@
 package org.broadinstitute.sting.utils.bed;
 
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.*;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java b/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
index 404bd80b6..e65b8f921 100755
--- a/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
@@ -29,9 +29,9 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.reflections.util.ClasspathHelper;
 
-import java.lang.reflect.*;
 import java.io.File;
 import java.io.IOException;
+import java.lang.reflect.*;
 import java.net.URL;
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
index 95f3e160c..5449906b2 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
@@ -4,9 +4,6 @@ import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.walkers.ClipReadsWalker;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.util.Vector;
diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
index 031467ed9..988d297f6 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.utils.clipreads;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.walkers.ClipReadsWalker;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java
index a286ce789..fef6c4ea0 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java
@@ -30,7 +30,6 @@ import org.broad.tribble.readers.LineReader;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.io.IOException;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.regex.Matcher;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java
index 618d9ce79..e169dbdfc 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java
@@ -4,11 +4,11 @@ import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.NameAwareCodec;
 import org.broad.tribble.TribbleException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broad.tribble.exception.CodecLineParsingException;
 import org.broad.tribble.readers.LineReader;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
index cd0f52c68..710127f7a 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
@@ -7,6 +7,8 @@ import org.broad.tribble.NameAwareCodec;
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.readers.LineReader;
 import org.broad.tribble.util.ParsingUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -96,6 +98,9 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
         for ( String str : headerStrings ) {
             if ( !str.startsWith(VCFHeader.METADATA_INDICATOR) ) {
                 String[] strings = str.substring(1).split(VCFConstants.FIELD_SEPARATOR);
+                if ( strings.length < VCFHeader.HEADER_FIELDS.values().length )
+                    throw new TribbleException.InvalidHeader("there are not enough columns present in the header line: " + str);
+
                 int arrayIndex = 0;
                 for (VCFHeader.HEADER_FIELDS field : VCFHeader.HEADER_FIELDS.values()) {
                     try {
@@ -159,12 +164,11 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
     }
 
     private Feature reallyDecode(String line) {
-        try {
             // the same line reader is not used for parsing the header and parsing lines, if we see a #, we've seen a header line
             if (line.startsWith(VCFHeader.HEADER_INDICATOR)) return null;
 
             // our header cannot be null, we need the genotype sample names and counts
-            if (header == null) throw new IllegalStateException("VCF Header cannot be null when decoding a record");
+            if (header == null) throw new ReviewedStingException("VCF Header cannot be null when decoding a record");
 
             if (parts == null)
                 parts = new String[Math.min(header.getColumnCount(), NUM_STANDARD_FIELDS+1)];
@@ -174,17 +178,18 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
             // if we have don't have a header, or we have a header with no genotyping data check that we have eight columns.  Otherwise check that we have nine (normal colummns + genotyping data)
             if (( (header == null || (header != null && !header.hasGenotypingData())) && nParts != NUM_STANDARD_FIELDS) ||
                  (header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) )
-                throw new IllegalArgumentException("There aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) +
-                        " tokens, and saw " + nParts + " )");
+                throw new UserException.MalformedVCF("there aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) +
+                        " tokens, and saw " + nParts + " )", lineNo);
 
             return parseVCFLine(parts);
-        } catch (TribbleException e) {
-            throw new TribbleException.InvalidDecodeLine(e.getMessage(), line);
-        }
     }
 
     protected void generateException(String message) {
-        throw new TribbleException.InvalidDecodeLine(message, lineNo);
+        throw new UserException.MalformedVCF(message, lineNo);
+    }
+
+    private static void generateException(String message, int lineNo) {
+        throw new UserException.MalformedVCF(message, lineNo);
     }
 
     /**
@@ -225,7 +230,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
             loc = pos + alleles.get(0).length() - 1;
         } else if ( !isSingleNucleotideEvent(alleles) ) {
             ArrayList<Allele> newAlleles = new ArrayList<Allele>();
-            loc = clipAlleles(pos, ref, alleles, newAlleles);
+            loc = clipAlleles(pos, ref, alleles, newAlleles, lineNo);
             alleles = newAlleles;
         }
 
@@ -472,10 +477,6 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
         return true;
     }
 
-    private static void generateException(String message, int lineNo) {
-        throw new TribbleException.InvalidDecodeLine(message, lineNo);
-    }
-
     private static int computeForwardClipping(List<Allele> unclippedAlleles, String ref) {
         boolean clipping = true;
         // Note that the computation of forward clipping here is meant only to see whether there is a common
@@ -504,7 +505,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
      * @param clippedAlleles output list of clipped alleles
      * @return a list of alleles, clipped to the reference
      */
-    protected static long clipAlleles(long position, String ref, List<Allele> unclippedAlleles, List<Allele> clippedAlleles) {
+    protected static long clipAlleles(long position, String ref, List<Allele> unclippedAlleles, List<Allele> clippedAlleles, int lineNo) {
 
         // Note that the computation of forward clipping here is meant only to see whether there is a common
         // base to all alleles, and to correctly compute reverse clipping,
@@ -522,6 +523,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
                 }
                 if (a.length() - reverseClipped <= forwardClipping || a.length() - forwardClipping == 0)
                     clipping = false;
+                else if (ref.length() == reverseClipped)
+                    generateException("bad alleles encountered", lineNo);
                 else if (a.getBases()[a.length()-reverseClipped-1] != ref.getBytes()[ref.length()-reverseClipped-1])
                     clipping = false;
             }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
index 31251c089..b7f4be39a 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
@@ -32,13 +32,14 @@ import org.broad.tribble.index.IndexFactory;
 import org.broad.tribble.util.LittleEndianOutputStream;
 import org.broad.tribble.util.ParsingUtils;
 import org.broad.tribble.util.PositionalStream;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.*;
-import java.util.*;
 import java.lang.reflect.Array;
+import java.util.*;
 
 /**
  * this class writes VCF files
@@ -123,12 +124,10 @@ public class StandardVCFWriter implements VCFWriter {
         
         try {
             // the file format field needs to be written first
-            mWriter.write(VCFHeader.METADATA_INDICATOR + VCFHeaderVersion.VCF4_0.getFormatString() + "=" + VCFHeaderVersion.VCF4_0.getVersionString() + "\n");
+            mWriter.write(VCFHeader.METADATA_INDICATOR + VCFHeaderVersion.VCF4_1.getFormatString() + "=" + VCFHeaderVersion.VCF4_1.getVersionString() + "\n");
 
             for ( VCFHeaderLine line : mHeader.getMetaData() ) {
-                if ( line.getKey().equals(VCFHeaderVersion.VCF4_0.getFormatString()) ||
-                        line.getKey().equals(VCFHeaderVersion.VCF3_3.getFormatString()) ||
-                        line.getKey().equals(VCFHeaderVersion.VCF3_2.getFormatString()) )
+                if ( VCFHeaderVersion.isFormatString(line.getKey()) )
                     continue;
 
                 // are the records filtered (so we know what to put in the FILTER column of passing records) ?
@@ -302,10 +301,7 @@ public class StandardVCFWriter implements VCFWriter {
             } else {
                 List<String> genotypeAttributeKeys = new ArrayList<String>();
                 if ( vc.hasGenotypes() ) {
-                    genotypeAttributeKeys.add(VCFConstants.GENOTYPE_KEY);
-                    for ( String key : calcVCFGenotypeKeys(vc) ) {
-                        genotypeAttributeKeys.add(key);
-                    }
+                    genotypeAttributeKeys.addAll(calcVCFGenotypeKeys(vc));
                 } else if ( mHeader.hasGenotypingData() ) {
                     // this needs to be done in case all samples are no-calls
                     genotypeAttributeKeys.add(VCFConstants.GENOTYPE_KEY);
@@ -358,16 +354,8 @@ public class StandardVCFWriter implements VCFWriter {
             mWriter.write(key);
 
             if ( !entry.getValue().equals("") ) {
-                int numVals = 1;
                 VCFInfoHeaderLine metaData = mHeader.getInfoHeaderLine(key);
-                if ( metaData != null )
-                    numVals = metaData.getCount();
-
-                // take care of unbounded encoding
-                if ( numVals == VCFInfoHeaderLine.UNBOUNDED )
-                    numVals = 1;
-
-                if ( numVals > 0 ) {
+                if ( metaData == null || metaData.getCountType() != VCFHeaderLineCount.INTEGER || metaData.getCount() != 0 ) {
                     mWriter.write("=");
                     mWriter.write(entry.getValue());
                 }
@@ -397,16 +385,22 @@ public class StandardVCFWriter implements VCFWriter {
                 continue;
             }
 
-            writeAllele(g.getAllele(0), alleleMap);
-            for (int i = 1; i < g.getPloidy(); i++) {
-                mWriter.write(g.isPhased() ? VCFConstants.PHASED : VCFConstants.UNPHASED);
-                writeAllele(g.getAllele(i), alleleMap);
-            }
-
             List<String> attrs = new ArrayList<String>(genotypeFormatKeys.size());
             for ( String key : genotypeFormatKeys ) {
-                if ( key.equals(VCFConstants.GENOTYPE_KEY) )
+
+                if ( key.equals(VCFConstants.GENOTYPE_KEY) ) {
+                    if ( !g.isAvailable() ) {
+                        throw new ReviewedStingException("GTs cannot be missing for some samples if they are available for others in the record");
+                    }
+
+                    writeAllele(g.getAllele(0), alleleMap);
+                    for (int i = 1; i < g.getPloidy(); i++) {
+                        mWriter.write(g.isPhased() ? VCFConstants.PHASED : VCFConstants.UNPHASED);
+                        writeAllele(g.getAllele(i), alleleMap);
+                    }
+
                     continue;
+                }
 
                 Object val = g.hasAttribute(key) ? g.getAttribute(key) : VCFConstants.MISSING_VALUE_v4;
 
@@ -423,7 +417,7 @@ public class StandardVCFWriter implements VCFWriter {
 
                 VCFFormatHeaderLine metaData = mHeader.getFormatHeaderLine(key);
                 if ( metaData != null ) {
-                    int numInFormatField = metaData.getCount();
+                    int numInFormatField = metaData.getCount(vc.getAlternateAlleles().size());
                     if ( numInFormatField > 1 && val.equals(VCFConstants.MISSING_VALUE_v4) ) {
                         // If we have a missing field but multiple values are expected, we need to construct a new string with all fields.
                         // For example, if Number=2, the string has to be ".,."
@@ -450,9 +444,10 @@ public class StandardVCFWriter implements VCFWriter {
                     break;
             }
 
-            for (String s : attrs ) {
-                mWriter.write(VCFConstants.GENOTYPE_FIELD_SEPARATOR);
-                mWriter.write(s);
+            for (int i = 0; i < attrs.size(); i++) {
+                if ( i > 0 || genotypeFormatKeys.contains(VCFConstants.GENOTYPE_KEY) )
+                    mWriter.write(VCFConstants.GENOTYPE_FIELD_SEPARATOR);
+                mWriter.write(attrs.get(i));
             }
         }
     }
@@ -498,10 +493,13 @@ public class StandardVCFWriter implements VCFWriter {
     private static List<String> calcVCFGenotypeKeys(VariantContext vc) {
         Set<String> keys = new HashSet<String>();
 
+        boolean sawGoodGT = false;
         boolean sawGoodQual = false;
         boolean sawGenotypeFilter = false;
         for ( Genotype g : vc.getGenotypes().values() ) {
             keys.addAll(g.getAttributes().keySet());
+            if ( g.isAvailable() )
+                sawGoodGT = true;
             if ( g.hasNegLog10PError() )
                 sawGoodQual = true;
             if (g.isFiltered() && g.isCalled())
@@ -514,7 +512,17 @@ public class StandardVCFWriter implements VCFWriter {
         if (sawGenotypeFilter)
             keys.add(VCFConstants.GENOTYPE_FILTER_KEY);
 
-        return ParsingUtils.sortList(new ArrayList<String>(keys));
+        List<String> sortedList = ParsingUtils.sortList(new ArrayList<String>(keys));
+
+        // make sure the GT is first
+        if ( sawGoodGT ) {
+            List<String> newList = new ArrayList<String>(sortedList.size()+1);
+            newList.add(VCFConstants.GENOTYPE_KEY);
+            newList.addAll(sortedList);
+            sortedList = newList;
+        }
+
+        return sortedList;
     }
 
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
index f3c99e963..c29f2ba8b 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
@@ -141,8 +141,6 @@ public class VCF3Codec extends AbstractVCFCodec {
                     boolean missing = i >= GTValueSplitSize;
 
                     if (gtKey.equals(VCFConstants.GENOTYPE_KEY)) {
-                        if (i != 0)
-                            generateException("Saw GT at position " + i + ", but it must be at the first position for genotypes");
                         genotypeAlleleLocation = i;
                     } else if (gtKey.equals(VCFConstants.GENOTYPE_QUALITY_KEY)) {
                         GTQual = missing ? parseQual(VCFConstants.MISSING_VALUE_v4) : parseQual(GTValueArray[i]);
@@ -156,12 +154,13 @@ public class VCF3Codec extends AbstractVCFCodec {
                 }
             }
 
-            // check to make sure we found a gentoype field
-            if (genotypeAlleleLocation < 0) generateException("Unable to find required field GT for the record; we don't yet support a missing GT field");
+            // check to make sure we found a genotype field
+            if ( genotypeAlleleLocation < 0 )
+                generateException("Unable to find the GT field for the record; the GT field is required");
+            if ( genotypeAlleleLocation > 0 )
+                generateException("Saw GT field at position " + genotypeAlleleLocation + ", but it must be at the first position for genotypes");
 
-            // todo -- assuming allele list length in the single digits is bad.  Fix me.
-            // Check for > 1 for haploid genotypes
-            boolean phased = GTValueArray[genotypeAlleleLocation].length() > 1 && GTValueArray[genotypeAlleleLocation].charAt(1) == '|';
+            boolean phased = GTValueArray[genotypeAlleleLocation].indexOf(VCFConstants.PHASED) != -1;
 
             // add it to the list
             try {
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFAltHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFAltHeaderLine.java
new file mode 100644
index 000000000..a9de949d8
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFAltHeaderLine.java
@@ -0,0 +1,28 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+/**
+ * @author ebanks
+ * A class representing a key=value entry for ALT fields in the VCF header
+ */
+public class VCFAltHeaderLine extends VCFSimpleHeaderLine  {
+
+    /**
+     * create a VCF filter header line
+     *
+     * @param name         the name for this header line
+     * @param description  the description for this header line
+     */
+    public VCFAltHeaderLine(String name, String description) {
+        super(name, description, SupportedHeaderLineType.ALT);
+    }
+
+    /**
+     * create a VCF info header line
+     *
+     * @param line      the header line
+     * @param version   the vcf header version
+     */
+    protected VCFAltHeaderLine(String line, VCFHeaderVersion version) {
+        super(line, version, SupportedHeaderLineType.ALT);
+    }
+}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
index 0fb2940bb..05fff5d9e 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
@@ -145,8 +145,6 @@ public class VCFCodec extends AbstractVCFCodec {
 
                     // todo -- all of these on the fly parsing of the missing value should be static constants
                     if (gtKey.equals(VCFConstants.GENOTYPE_KEY)) {
-                        if (i != 0)
-                            generateException("Saw GT at position " + i + ", but it must be at the first position for genotypes");
                         genotypeAlleleLocation = i;
                     } else if (gtKey.equals(VCFConstants.GENOTYPE_QUALITY_KEY)) {
                         GTQual = missing ? parseQual(VCFConstants.MISSING_VALUE_v4) : parseQual(GTValueArray[i]);
@@ -160,22 +158,24 @@ public class VCFCodec extends AbstractVCFCodec {
                 }
             }
 
-            // check to make sure we found a gentoype field
-            // TODO -- This is no longer required in v4.1
-            if (genotypeAlleleLocation < 0) generateException("Unable to find required field GT for the record; we don't yet support a missing GT field");
+            // check to make sure we found a genotype field if we are a VCF4.0 file
+            if ( version == VCFHeaderVersion.VCF4_0 && genotypeAlleleLocation == -1 )
+                generateException("Unable to find the GT field for the record; the GT field is required in VCF4.0");
+            if ( genotypeAlleleLocation > 0 )
+                generateException("Saw GT field at position " + genotypeAlleleLocation + ", but it must be at the first position for genotypes when present");
 
-            // todo -- assuming allele list length in the single digits is bad.  Fix me.
-            // Check for > 1 for haploid genotypes
-            boolean phased = GTValueArray[genotypeAlleleLocation].length() > 1 && GTValueArray[genotypeAlleleLocation].charAt(1) == '|';
+            List<Allele> GTalleles = (genotypeAlleleLocation == -1 ? null : parseGenotypeAlleles(GTValueArray[genotypeAlleleLocation], alleles, alleleMap));
+            boolean phased = genotypeAlleleLocation != -1 && GTValueArray[genotypeAlleleLocation].indexOf(VCFConstants.PHASED) != -1;
 
             // add it to the list
             try {
-                genotypes.put(sampleName, new Genotype(sampleName,
-                        parseGenotypeAlleles(GTValueArray[genotypeAlleleLocation], alleles, alleleMap),
-                        GTQual,
-                        genotypeFilters,
-                        gtAttributes,
-                        phased));
+                genotypes.put(sampleName,
+                        new Genotype(sampleName,
+                                GTalleles,
+                                GTQual,
+                                genotypeFilters,
+                                gtAttributes,
+                                phased));
             } catch (TribbleException e) {
                 throw new TribbleException.InternalCodecException(e.getMessage() + ", at position " + chr+":"+pos);
             }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
index a799161ad..bb822f2ed 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
@@ -24,6 +24,8 @@
 
 package org.broadinstitute.sting.utils.codecs.vcf;
 
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
 import java.util.Arrays;
 import java.util.LinkedHashMap;
 import java.util.Map;
@@ -43,26 +45,43 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
 
     // the field types
     private String name;
-    private int count;
+    private int count = -1;
+    private VCFHeaderLineCount countType;
     private String description;
     private VCFHeaderLineType type;
 
     // access methods
     public String getName() { return name; }
-    public int getCount() { return count; }
     public String getDescription() { return description; }
     public VCFHeaderLineType getType() { return type; }
+    public VCFHeaderLineCount getCountType() { return countType; }
+    public int getCount() {
+        if ( countType != VCFHeaderLineCount.INTEGER )
+            throw new ReviewedStingException("Asking for header line count when type is not an integer");
+        return count;
+    }
 
-    //
-    public void setNumberToUnbounded() { this.count = UNBOUNDED; }
+    // utility method
+    public int getCount(int numAltAlleles) {
+        int myCount;
+        switch ( countType ) {
+            case INTEGER: myCount = count; break;
+            case UNBOUNDED: myCount = -1; break;
+            case A: myCount = numAltAlleles; break;
+            case G: myCount = ((numAltAlleles + 1) * (numAltAlleles + 2) / 2); break;
+            default: throw new ReviewedStingException("Unknown count type: " + countType);
+        }
+        return myCount;
+    }
+
+    public void setNumberToUnbounded() {
+        countType = VCFHeaderLineCount.UNBOUNDED;
+        count = -1;
+    }
 
     // our type of line, i.e. format, info, etc
     private final SupportedHeaderLineType lineType;
 
-    // line numerical values are allowed to be unbounded (or unknown), which is
-    // marked with a dot (.)
-    public static final int UNBOUNDED = -1;    // the value we store internally for unbounded types
-
     /**
      * create a VCF format header line
      *
@@ -70,10 +89,12 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
      * @param count        the count for this header line
      * @param type         the type for this header line
      * @param description  the description for this header line
+     * @param lineType     the header line type
      */
     protected VCFCompoundHeaderLine(String name, int count, VCFHeaderLineType type, String description, SupportedHeaderLineType lineType) {
         super(lineType.toString(), "");
         this.name = name;
+        this.countType = VCFHeaderLineCount.INTEGER;
         this.count = count;
         this.type = type;
         this.description = description;
@@ -81,20 +102,53 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
         validate();
     }
 
+    /**
+     * create a VCF format header line
+     *
+     * @param name         the name for this header line
+     * @param count        the count type for this header line
+     * @param type         the type for this header line
+     * @param description  the description for this header line
+     * @param lineType     the header line type
+     */
+    protected VCFCompoundHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description, SupportedHeaderLineType lineType) {
+        super(lineType.toString(), "");
+        this.name = name;
+        this.countType = count;
+        this.type = type;
+        this.description = description;
+        this.lineType = lineType;
+        validate();
+    }
+
     /**
      * create a VCF format header line
      *
      * @param line   the header line
      * @param version      the VCF header version
+     * @param lineType     the header line type
      *
      */
     protected VCFCompoundHeaderLine(String line, VCFHeaderVersion version, SupportedHeaderLineType lineType) {
         super(lineType.toString(), "");
         Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Number","Type","Description"));
         name = mapping.get("ID");
-        count = (version == VCFHeaderVersion.VCF4_0 || version == VCFHeaderVersion.VCF4_1) ?
-                        mapping.get("Number").equals(VCFConstants.UNBOUNDED_ENCODING_v4) ? UNBOUNDED : Integer.valueOf(mapping.get("Number")) :
-                        mapping.get("Number").equals(VCFConstants.UNBOUNDED_ENCODING_v3) ? UNBOUNDED : Integer.valueOf(mapping.get("Number"));
+        count = -1;
+        final String numberStr = mapping.get("Number");
+        if ( numberStr.equals(VCFConstants.PER_ALLELE_COUNT) ) {
+            countType = VCFHeaderLineCount.A;
+        } else if ( numberStr.equals(VCFConstants.PER_GENOTYPE_COUNT) ) {
+            countType = VCFHeaderLineCount.G;
+        } else if ( ((version == VCFHeaderVersion.VCF4_0 || version == VCFHeaderVersion.VCF4_1) &&
+                     numberStr.equals(VCFConstants.UNBOUNDED_ENCODING_v4)) ||
+                    ((version == VCFHeaderVersion.VCF3_2 || version == VCFHeaderVersion.VCF3_3) &&
+                     numberStr.equals(VCFConstants.UNBOUNDED_ENCODING_v3)) ) {
+            countType = VCFHeaderLineCount.UNBOUNDED;
+        } else {
+            countType = VCFHeaderLineCount.INTEGER;
+            count = Integer.valueOf(numberStr);
+
+        }
         type = VCFHeaderLineType.valueOf(mapping.get("Type"));
         if (type == VCFHeaderLineType.Flag && !allowFlagValues())
             throw new IllegalArgumentException("Flag is an unsupported type for this kind of field");
@@ -121,7 +175,15 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
     protected String toStringEncoding() {
         Map<String,Object> map = new LinkedHashMap<String,Object>();
         map.put("ID", name);
-        map.put("Number", count == UNBOUNDED ? VCFConstants.UNBOUNDED_ENCODING_v4 : count);
+        Object number;
+        switch ( countType ) {
+            case A: number = VCFConstants.PER_ALLELE_COUNT; break;
+            case G: number = VCFConstants.PER_GENOTYPE_COUNT; break;
+            case UNBOUNDED: number = VCFConstants.UNBOUNDED_ENCODING_v4; break;
+            case INTEGER:
+            default: number = count;
+        }
+        map.put("Number", number);
         map.put("Type", type);
         map.put("Description", description);
         return lineType.toString() + "=" + VCFHeaderLine.toStringEncoding(map);
@@ -136,15 +198,13 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
         if ( !(o instanceof VCFCompoundHeaderLine) )
             return false;
         VCFCompoundHeaderLine other = (VCFCompoundHeaderLine)o;
-        return name.equals(other.name) &&
-                count == other.count &&
-                description.equals(other.description) &&
-                type == other.type &&
-                lineType == other.lineType;
+        return equalsExcludingDescription(other) &&
+                description.equals(other.description);
     }
 
     public boolean equalsExcludingDescription(VCFCompoundHeaderLine other) {
         return count == other.count &&
+                countType == other.countType &&
                 type == other.type &&
                 lineType == other.lineType &&
                 name.equals(other.name);
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java
index 695c46c27..91cf86c70 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java
@@ -99,6 +99,8 @@ public final class VCFConstants {
     public static final String MISSING_DEPTH_v3 = "-1";
     public static final String UNBOUNDED_ENCODING_v4 = ".";
     public static final String UNBOUNDED_ENCODING_v3 = "-1";
+    public static final String PER_ALLELE_COUNT = "A";
+    public static final String PER_GENOTYPE_COUNT = "G";
     public static final String EMPTY_ALLELE = ".";
     public static final String EMPTY_GENOTYPE = "./.";
     public static final double MAX_GENOTYPE_QUAL = 99.0;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java
index 9176fc16e..418b80074 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java
@@ -1,19 +1,10 @@
 package org.broadinstitute.sting.utils.codecs.vcf;
 
-import java.util.Arrays;
-import java.util.LinkedHashMap;
-import java.util.Map;
-
-
 /**
  * @author ebanks
  * A class representing a key=value entry for FILTER fields in the VCF header
  */
-public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeaderLine  {
-
-    private String name;
-    private String description;
-
+public class VCFFilterHeaderLine extends VCFSimpleHeaderLine  {
 
     /**
      * create a VCF filter header line
@@ -22,12 +13,7 @@ public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeader
      * @param description  the description for this header line
      */
     public VCFFilterHeaderLine(String name, String description) {
-        super("FILTER", "");
-        this.name = name;
-        this.description = description;
-
-        if ( name == null || description == null )
-            throw new IllegalArgumentException(String.format("Invalid VCFCompoundHeaderLine: key=%s name=%s desc=%s", super.getKey(), name, description ));
+        super(name, description, SupportedHeaderLineType.FILTER);
     }
 
     /**
@@ -37,34 +23,6 @@ public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeader
      * @param version   the vcf header version
      */
     protected VCFFilterHeaderLine(String line, VCFHeaderVersion version) {
-        super("FILTER", "");
-        Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Description"));
-        name = mapping.get("ID");
-        description = mapping.get("Description");
-        if ( description == null && ALLOW_UNBOUND_DESCRIPTIONS ) // handle the case where there's no description provided 
-            description = UNBOUND_DESCRIPTION;
-    }
-
-    protected String toStringEncoding() {
-        Map<String,Object> map = new LinkedHashMap<String,Object>();
-        map.put("ID", name);
-        map.put("Description", description);
-        return "FILTER=" + VCFHeaderLine.toStringEncoding(map);
-    }
-
-    public boolean equals(Object o) {
-        if ( !(o instanceof VCFFilterHeaderLine) )
-            return false;
-        VCFFilterHeaderLine other = (VCFFilterHeaderLine)o;
-        return name.equals(other.name) &&
-               description.equals(other.description);
-    }
-
-    public String getName() {
-        return name;
-    }
-
-    public String getDescription() {
-        return description;
+        super(line, version, SupportedHeaderLineType.FILTER);
     }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
index 352be3e97..474c8dd14 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
@@ -16,6 +16,10 @@ public class VCFFormatHeaderLine extends VCFCompoundHeaderLine {
             throw new IllegalArgumentException("Flag is an unsupported type for format fields");
     }
 
+    public VCFFormatHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description) {
+        super(name, count, type, description, SupportedHeaderLineType.FORMAT);
+    }
+
     protected VCFFormatHeaderLine(String line, VCFHeaderVersion version) {
         super(line, version, SupportedHeaderLineType.FORMAT);
     }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineCount.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineCount.java
new file mode 100644
index 000000000..d615c7c78
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineCount.java
@@ -0,0 +1,8 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+/**
+ * the count encodings we use for fields in VCF header lines
+ */
+public enum VCFHeaderLineCount {
+    INTEGER, A, G, UNBOUNDED;
+}
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java
index 135a5c1a1..9b20f38a1 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java
@@ -13,6 +13,10 @@ public class VCFInfoHeaderLine extends VCFCompoundHeaderLine {
         super(name, count, type, description, SupportedHeaderLineType.INFO);
     }
 
+    public VCFInfoHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description) {
+        super(name, count, type, description, SupportedHeaderLineType.INFO);
+    }
+
     protected VCFInfoHeaderLine(String line, VCFHeaderVersion version) {
         super(line, version, SupportedHeaderLineType.INFO);
     }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java
index dac996494..1dba351e2 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java
@@ -2,7 +2,9 @@ package org.broadinstitute.sting.utils.codecs.vcf;
 
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import java.util.*;
+
+import java.util.List;
+import java.util.Map;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java
new file mode 100644
index 000000000..152043f28
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java
@@ -0,0 +1,81 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+
+/**
+ * @author ebanks
+ * A class representing a key=value entry for simple VCF header types
+ */
+public abstract class VCFSimpleHeaderLine extends VCFHeaderLine implements VCFNamedHeaderLine  {
+
+    public enum SupportedHeaderLineType {
+        FILTER, ALT;
+    }
+
+    private String name;
+    private String description;
+
+    // our type of line, i.e. filter, alt, etc
+    private final SupportedHeaderLineType lineType;
+
+
+    /**
+     * create a VCF filter header line
+     *
+     * @param name         the name for this header line
+     * @param description  the description for this header line
+     * @param lineType     the header line type
+     */
+    public VCFSimpleHeaderLine(String name, String description, SupportedHeaderLineType lineType) {
+        super(lineType.toString(), "");
+        this.lineType = lineType;
+        this.name = name;
+        this.description = description;
+
+        if ( name == null || description == null )
+            throw new IllegalArgumentException(String.format("Invalid VCFSimpleHeaderLine: key=%s name=%s desc=%s", super.getKey(), name, description ));
+    }
+
+    /**
+     * create a VCF info header line
+     *
+     * @param line      the header line
+     * @param version   the vcf header version
+     * @param lineType     the header line type
+     */
+    protected VCFSimpleHeaderLine(String line, VCFHeaderVersion version, SupportedHeaderLineType lineType) {
+        super(lineType.toString(), "");
+        this.lineType = lineType;
+        Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Description"));
+        name = mapping.get("ID");
+        description = mapping.get("Description");
+        if ( description == null && ALLOW_UNBOUND_DESCRIPTIONS ) // handle the case where there's no description provided 
+            description = UNBOUND_DESCRIPTION;
+    }
+
+    protected String toStringEncoding() {
+        Map<String,Object> map = new LinkedHashMap<String,Object>();
+        map.put("ID", name);
+        map.put("Description", description);
+        return lineType.toString() + "=" + VCFHeaderLine.toStringEncoding(map);
+    }
+
+    public boolean equals(Object o) {
+        if ( !(o instanceof VCFSimpleHeaderLine) )
+            return false;
+        VCFSimpleHeaderLine other = (VCFSimpleHeaderLine)o;
+        return name.equals(other.name) &&
+               description.equals(other.description);
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public String getDescription() {
+        return description;
+    }
+}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
index ecede068e..f43891e77 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
@@ -25,10 +25,10 @@
 
 package org.broadinstitute.sting.utils.codecs.vcf;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.*;
 
@@ -180,19 +180,4 @@ public class VCFUtils {
 
         return new HashSet<VCFHeaderLine>(map.values());
     }
-
-    /**
-     * return a set of supported format lines; what we currently support for output in the genotype fields of a VCF
-     * @return a set of VCF format lines
-     */
-    public static Set<VCFFormatHeaderLine> getSupportedHeaderStrings() {
-        Set<VCFFormatHeaderLine> result = new HashSet<VCFFormatHeaderLine>();
-        result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
-        result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Genotype Quality"));
-        result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)"));
-        result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, -1, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; if site is not biallelic, number of likelihoods if n*(n+1)/2"));
-
-        return result;
-    }
-    
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java b/public/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java
index a36ed9ac6..d280ac804 100755
--- a/public/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java
+++ b/public/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java
@@ -25,7 +25,8 @@
 
 package org.broadinstitute.sting.utils.collections;
 
-import java.util.*;
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/utils/collections/RODMergingIterator.java b/public/java/src/org/broadinstitute/sting/utils/collections/RODMergingIterator.java
index 3a731c2fd..6d6cb8272 100644
--- a/public/java/src/org/broadinstitute/sting/utils/collections/RODMergingIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/collections/RODMergingIterator.java
@@ -27,10 +27,13 @@ package org.broadinstitute.sting.utils.collections;
 
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.*;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.PriorityQueue;
 
 public class RODMergingIterator implements Iterator<RODRecordList>, Iterable<RODRecordList> {
     PriorityQueue<Element> queue = new PriorityQueue<Element>();
diff --git a/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java b/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java
index 41de5ef96..bba47c76c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java
@@ -26,15 +26,18 @@
 package org.broadinstitute.sting.utils.duplicates;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 
-import java.util.List;
 import java.util.Arrays;
+import java.util.List;
 
 public class DupUtils {
     private static SAMRecord tmpCopyRead(SAMRecord read) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index 0be4bec91..7eab6f6c9 100755
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -28,9 +28,8 @@ import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
 import java.util.Arrays;
@@ -154,6 +153,16 @@ public class UserException extends ReviewedStingException {
         }
     }
 
+    public static class MalformedVCF extends UserException {
+        public MalformedVCF(String message, String line) {
+            super(String.format("The provided VCF file is malformed at line %s: %s", line, message));
+        }
+
+        public MalformedVCF(String message, int lineNo) {
+            super(String.format("The provided VCF file is malformed at line nmber %d: %s", lineNo, message));
+        }
+    }
+
     public static class ReadMissingReadGroup extends MalformedBAM {
         public ReadMissingReadGroup(SAMRecord read) {
             super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK.  Please use http://www.broadinstitute.org/gsa/wiki/index.php/ReplaceReadGroups to fix this problem", read.getReadName()));
diff --git a/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
index 0c5085cc7..43ef4aa74 100644
--- a/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
+++ b/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
@@ -25,15 +25,16 @@
 package org.broadinstitute.sting.utils.fasta;
 
 import net.sf.picard.PicardException;
-import net.sf.picard.reference.*;
+import net.sf.picard.reference.FastaSequenceIndex;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.picard.reference.ReferenceSequence;
 import net.sf.samtools.SAMSequenceRecord;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.util.Arrays;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-
 /**
  * A caching version of the IndexedFastaSequenceFile that avoids going to disk as often as the raw indexer.
  *
diff --git a/public/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java b/public/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
index cbfba848c..1c2cfe2e1 100755
--- a/public/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.utils.genotype;
 
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.MathUtils;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
index cb6557408..a17e81461 100755
--- a/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/genotype/Haplotype.java
@@ -24,14 +24,14 @@
 
 package org.broadinstitute.sting.utils.genotype;
 
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.List;
 
 public class Haplotype {
     protected byte[] bases = null;
@@ -133,8 +133,12 @@ public class Haplotype {
 
 
         byte[] basesBeforeVariant = Arrays.copyOfRange(refBases,startIdxInReference,startIdxInReference+numPrefBases);
+        int startAfter = startIdxInReference+numPrefBases+ refAllele.getBases().length;
+        // protect against long events that overrun available reference context
+        if (startAfter > refBases.length)
+            startAfter = refBases.length;
         byte[] basesAfterVariant = Arrays.copyOfRange(refBases,
-                startIdxInReference+numPrefBases+ refAllele.getBases().length, refBases.length);
+                startAfter, refBases.length);
 
 
         // Create location for all haplotypes
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java b/public/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java
index d9e74640f..483c874dc 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java
@@ -25,13 +25,13 @@
 
 package org.broadinstitute.sting.utils.help;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.List;
-import java.util.Collections;
 import java.io.IOException;
+import java.util.Collections;
+import java.util.List;
 
 /**
  * Contains details additional details that the program can
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/DescriptionTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/DescriptionTaglet.java
index 68633a2b3..65c332048 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/DescriptionTaglet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/DescriptionTaglet.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.utils.help;
 
 import com.sun.tools.doclets.Taglet;
-import com.sun.javadoc.Tag;
 
 import java.util.Map;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/DisplayNameTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/DisplayNameTaglet.java
index be6f7f3eb..6c6dad736 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/DisplayNameTaglet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/DisplayNameTaglet.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.utils.help;
 
 import com.sun.tools.doclets.Taglet;
-import com.sun.javadoc.Tag;
 
 import java.util.Map;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java
index 493f26e76..a9d71ef98 100755
--- a/public/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java
@@ -25,22 +25,16 @@
 
 package org.broadinstitute.sting.utils.help;
 
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.commandline.ArgumentDefinition;
 import org.broadinstitute.sting.commandline.ArgumentDefinitionGroup;
 import org.broadinstitute.sting.commandline.ArgumentDefinitions;
-import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 
-import java.util.Formatter;
-import java.util.List;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.Comparator;
-import java.util.Collection;
-import java.util.Collections;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
+import java.util.*;
 /**
  * Print out help for Sting command-line applications.
  */
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpTaglet.java
index b962664eb..b350b1a29 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/HelpTaglet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpTaglet.java
@@ -1,9 +1,7 @@
 package org.broadinstitute.sting.utils.help;
 
-import com.sun.tools.doclets.Taglet;
 import com.sun.javadoc.Tag;
-
-import java.util.Map;
+import com.sun.tools.doclets.Taglet;
 
 /**
  * Basic functionality for the help taglet.
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java b/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
index 4afac69c3..6ee12d42e 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
@@ -26,14 +26,16 @@
 package org.broadinstitute.sting.utils.help;
 
 import com.sun.javadoc.*;
+import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.*;
-import java.util.*;
-
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.gatk.walkers.Walker;
+import java.util.HashSet;
+import java.util.Properties;
+import java.util.Scanner;
+import java.util.Set;
 
 /**
  * Extracts certain types of javadoc (specifically package and class descriptions) and makes them available
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/SummaryTaglet.java b/public/java/src/org/broadinstitute/sting/utils/help/SummaryTaglet.java
index 036bbec4f..db8b55940 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/SummaryTaglet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/SummaryTaglet.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.utils.help;
 
 import com.sun.tools.doclets.Taglet;
-import com.sun.javadoc.Tag;
 
 import java.util.Map;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java b/public/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java
index 3420c9876..73a29ba4f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java
+++ b/public/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java
@@ -27,9 +27,9 @@ package org.broadinstitute.sting.utils.instrumentation;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.lang.instrument.Instrumentation;
+import java.lang.reflect.Array;
 import java.lang.reflect.Field;
 import java.lang.reflect.Modifier;
-import java.lang.reflect.Array;
 import java.util.IdentityHashMap;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalFileMergingIterator.java b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalFileMergingIterator.java
index e722ac196..988240ef9 100644
--- a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalFileMergingIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalFileMergingIterator.java
@@ -25,16 +25,16 @@
 
 package org.broadinstitute.sting.utils.interval;
 
+import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
+import org.broadinstitute.sting.gatk.refdata.utils.StringToGenomeLocIteratorAdapter;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
-import org.broadinstitute.sting.gatk.refdata.utils.StringToGenomeLocIteratorAdapter;
 
-import java.util.Iterator;
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.util.Iterator;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
index 80dc35455..f551e1368 100644
--- a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
@@ -5,17 +5,17 @@ import net.sf.picard.util.IntervalList;
 import net.sf.samtools.SAMFileHeader;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.bed.BedParser;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.*;
-import java.io.File;
 
 /**
  * Parse text representations of interval strings that
diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/NwayIntervalMergingIterator.java b/public/java/src/org/broadinstitute/sting/utils/interval/NwayIntervalMergingIterator.java
index 31a2f41fb..7e87ce8b5 100644
--- a/public/java/src/org/broadinstitute/sting/utils/interval/NwayIntervalMergingIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/interval/NwayIntervalMergingIterator.java
@@ -26,11 +26,10 @@
 package org.broadinstitute.sting.utils.interval;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.util.PriorityQueue;
 import java.util.Iterator;
+import java.util.PriorityQueue;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/OverlappingIntervalIterator.java b/public/java/src/org/broadinstitute/sting/utils/interval/OverlappingIntervalIterator.java
index 0b63d582e..29ffb13e4 100755
--- a/public/java/src/org/broadinstitute/sting/utils/interval/OverlappingIntervalIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/interval/OverlappingIntervalIterator.java
@@ -25,9 +25,8 @@
 
 package org.broadinstitute.sting.utils.interval;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
+import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.util.Iterator;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
index 543302446..3821c9c8a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
@@ -24,19 +24,16 @@
 
 package org.broadinstitute.sting.utils.pileup;
 
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
-import org.broadinstitute.sting.utils.HasGenomeLocation;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.gatk.iterators.IterableIterator;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.StingException;
 
 import java.util.*;
 
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.exceptions.StingException;
-
 /**
  * A generic implementation of read-backed pileups.
  *
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java
index b6f3e9f09..26e66014c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java
@@ -1,8 +1,5 @@
 package org.broadinstitute.sting.utils.pileup;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.BaseUtils;
 import net.sf.samtools.SAMRecord;
 
 import java.util.Arrays;
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/FragmentPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/FragmentPileup.java
index 6c855c1c7..f7d237401 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/FragmentPileup.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/FragmentPileup.java
@@ -1,6 +1,9 @@
 package org.broadinstitute.sting.utils.pileup;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  * An easy to access fragment-based pileup, which contains two separate pileups.  The first
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java b/public/java/src/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java
index d8af2ea8f..7005cf869 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java
@@ -27,9 +27,9 @@ package org.broadinstitute.sting.utils.pileup;
 import net.sf.picard.util.PeekableIterator;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 
-import java.util.PriorityQueue;
 import java.util.Comparator;
 import java.util.Iterator;
+import java.util.PriorityQueue;
 
 /**
  * Merges multiple pileups broken down by sample.
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
index 51e02bf74..66e1afecb 100755
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
@@ -1,9 +1,10 @@
 package org.broadinstitute.sting.utils.pileup;
 
-import org.broadinstitute.sting.utils.*;
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Requires;
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import com.google.java.contract.*;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
index a32aa5645..8d43a368a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
@@ -24,15 +24,13 @@
 
 package org.broadinstitute.sting.utils.pileup;
 
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 
-import java.util.Iterator;
-import java.util.List;
 import java.util.Collection;
-
-import net.sf.samtools.SAMRecord;
+import java.util.List;
 
 /**
  * A clean interface for working with extended event pileups.
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
index a1a08c95f..31d29430a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
@@ -23,15 +23,14 @@
  */
 package org.broadinstitute.sting.utils.pileup;
 
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.*;
 
-import net.sf.samtools.SAMRecord;
-
 public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<ReadBackedExtendedEventPileupImpl,ExtendedEventPileupElement> implements ReadBackedExtendedEventPileup {
     private int nInsertions;
     private int maxDeletionLength;      // cached value of the length of the longest deletion observed at the site
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
index c52cc0b52..36b8a8c65 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
@@ -24,14 +24,13 @@
 
 package org.broadinstitute.sting.utils.pileup;
 
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.gatk.iterators.IterableIterator;
-import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.HasGenomeLocation;
 
-import java.util.List;
 import java.util.Collection;
+import java.util.List;
 
 /**
  * A data retrieval interface for accessing parts of the pileup.
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
index 70eba577c..e5b054961 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java
@@ -23,9 +23,9 @@
  */
 package org.broadinstitute.sting.utils.pileup;
 
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import net.sf.samtools.SAMRecord;
 
 import java.util.List;
 import java.util.Map;
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
index 4e4294b20..344eccb83 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -25,15 +25,16 @@
 
 package org.broadinstitute.sting.utils.sam;
 
-import net.sf.samtools.CigarOperator;
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.pileup.*;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.util.ArrayList;
 import java.util.Arrays;
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java
index 5812c9aec..5f7db458a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java
@@ -1,15 +1,13 @@
 package org.broadinstitute.sting.utils.sam;
 
-import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.apache.log4j.Logger;
-
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMRecord;
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
+import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.Walker;
 
 
 /*
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java
index ce6ca570c..adf60b16b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java
@@ -1,15 +1,17 @@
 package org.broadinstitute.sting.utils.sam;
 
 import net.sf.samtools.*;
-
-import java.io.InputStream;
-import java.io.ByteArrayInputStream;
-import java.io.UnsupportedEncodingException;
-import java.util.*;
-
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
 /**
  * User: hanna
  * Date: Jun 11, 2009
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java
index b683f5247..62e371bc0 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java
@@ -1,9 +1,8 @@
 package org.broadinstitute.sting.utils.sam;
 
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.gatk.ReadProperties;
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 
 import java.util.Iterator;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java
index 4f5dcca61..2b359fe6a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java
@@ -1,13 +1,12 @@
 package org.broadinstitute.sting.utils.sam;
 
 import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMSequenceRecord;
 import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMSequenceRecord;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.List;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-
 
 /*
  * Copyright (c) 2009 The Broad Institute
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java
index 01f1dfe96..31deb7535 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java
@@ -26,8 +26,6 @@
 package org.broadinstitute.sting.utils.sam;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 
 public class ComparableSAMRecord implements Comparable<ComparableSAMRecord> {
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java
index 2b8ac387c..c7ffcab0c 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.utils.sam;
 
-import net.sf.samtools.*;
+import net.sf.samtools.SAMReadGroupRecord;
 
 /**
  * @author ebanks
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index f3d9edab9..517f9f75d 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -1,12 +1,14 @@
 package org.broadinstitute.sting.utils.sam;
 
-import java.lang.reflect.Method;
-import java.util.*;
-
 import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
+import java.lang.reflect.Method;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
 /**
  * @author ebanks
  * GATKSAMRecord
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index 080762039..6c15910b1 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -25,13 +25,14 @@
 
 package org.broadinstitute.sting.utils.sam;
 
-import com.google.java.contract.*;
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Requires;
 import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.*;
 import java.io.File;
+import java.util.*;
 
 /**
  * A miscellaneous collection of utilities for working with SAM files, headers, etc.
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java b/public/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java
index f8a0ca6a7..bb9db5d98 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java
@@ -26,11 +26,10 @@
 package org.broadinstitute.sting.utils.sam;
 
 import net.sf.samtools.SAMFileReader;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-
 /**
  * Allows the user to steadily accumulate information about what
  * components go into a SAM file writer, ultimately using this
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java b/public/java/src/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java
index df2010e8b..60e1d9948 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java
@@ -3,13 +3,6 @@ package org.broadinstitute.sting.utils.sam;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-
-import java.util.Iterator;
-import java.util.NoSuchElementException;
 
 /**
  * XXX
diff --git a/public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java b/public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java
index 9beb7895b..f6aa882ad 100644
--- a/public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java
@@ -26,7 +26,6 @@ package org.broadinstitute.sting.utils.text;
 
 import org.broadinstitute.sting.commandline.ParsingEngine;
 import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
diff --git a/public/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java b/public/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java
index 803d6ac0f..1d4251542 100644
--- a/public/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java
@@ -28,11 +28,11 @@ package org.broadinstitute.sting.utils.text;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.*;
-import java.util.regex.Pattern;
-import java.util.regex.Matcher;
-import java.io.StringReader;
 import java.io.IOException;
+import java.io.StringReader;
+import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 /**
  * Common utilities for dealing with text formatting.
diff --git a/public/java/src/org/broadinstitute/sting/utils/text/XReadLines.java b/public/java/src/org/broadinstitute/sting/utils/text/XReadLines.java
index 064256388..52b6f3b01 100644
--- a/public/java/src/org/broadinstitute/sting/utils/text/XReadLines.java
+++ b/public/java/src/org/broadinstitute/sting/utils/text/XReadLines.java
@@ -25,10 +25,10 @@
 
 package org.broadinstitute.sting.utils.text;
 
-import java.util.Iterator;
-import java.util.List;
-import java.util.LinkedList;
 import java.io.*;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
 
 /**
  * Support for Python-like xreadlines() function as a class.  This is an iterator and iterable over
diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/FileBackedGenomeLocProcessingTracker.java b/public/java/src/org/broadinstitute/sting/utils/threading/FileBackedGenomeLocProcessingTracker.java
index cae099eeb..3763ec67d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/threading/FileBackedGenomeLocProcessingTracker.java
+++ b/public/java/src/org/broadinstitute/sting/utils/threading/FileBackedGenomeLocProcessingTracker.java
@@ -1,18 +1,14 @@
 package org.broadinstitute.sting.utils.threading;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.*;
-import java.nio.ByteBuffer;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
-import java.util.concurrent.locks.ReentrantLock;
 
 /**
  * Keeps a copy of the processing locks in a file
diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/NoOpGenomeLocProcessingTracker.java b/public/java/src/org/broadinstitute/sting/utils/threading/NoOpGenomeLocProcessingTracker.java
index 4e61ef9e1..ad2a6d31b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/threading/NoOpGenomeLocProcessingTracker.java
+++ b/public/java/src/org/broadinstitute/sting/utils/threading/NoOpGenomeLocProcessingTracker.java
@@ -1,9 +1,5 @@
 package org.broadinstitute.sting.utils.threading;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileLock.java b/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileLock.java
index 3eb2be96b..0f47da413 100644
--- a/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileLock.java
+++ b/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileLock.java
@@ -6,10 +6,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.io.RandomAccessFile;
-import java.nio.channels.*;
 
 /**
  * User: depristo
diff --git a/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileThreadSafeLock.java b/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileThreadSafeLock.java
index dec69f7c2..d70879a0a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileThreadSafeLock.java
+++ b/public/java/src/org/broadinstitute/sting/utils/threading/SharedFileThreadSafeLock.java
@@ -2,13 +2,8 @@ package org.broadinstitute.sting.utils.threading;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.RandomAccessFile;
-import java.nio.channels.*;
 
 /**
  * User: depristo
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
index a9ba46159..c3f437f11 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.utils.variantcontext;
 
-import java.util.Arrays;
-import java.util.List;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
+import java.util.List;
 
 /**
  * Immutable representation of an allele
@@ -108,7 +108,7 @@ public class Allele implements Comparable<Allele> {
         this.bases = bases;
 
         if ( ! acceptableAlleleBases(bases) )
-            throw new IllegalArgumentException("Unexpected base in allele bases " + new String(bases));
+            throw new IllegalArgumentException("Unexpected base in allele bases \'" + new String(bases)+"\'");
     }
 
     private Allele(String bases, boolean isRef) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
index 3a87f1196..0b5976c3c 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.utils.variantcontext;
 
 import org.broad.tribble.util.ParsingUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.*;
 
@@ -19,12 +20,14 @@ public class Genotype {
     protected InferredGeneticContext commonInfo;
     public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR;
     protected List<Allele> alleles = null; // new ArrayList<Allele>();
+    protected Type type = null;
 
     protected boolean isPhased = false;
-    private boolean filtersWereAppliedToContext;
+    protected boolean filtersWereAppliedToContext;
 
     public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased) {
-        this.alleles = Collections.unmodifiableList(alleles);
+        if ( alleles != null )
+            this.alleles = Collections.unmodifiableList(alleles);
         commonInfo = new InferredGeneticContext(sampleName, negLog10PError, filters, attributes);
         filtersWereAppliedToContext = filters != null;
         this.isPhased = isPhased;
@@ -66,6 +69,9 @@ public class Genotype {
     }
 
     public List<Allele> getAlleles(Allele allele) {
+        if ( getType() == Type.UNAVAILABLE )
+            throw new ReviewedStingException("Requesting alleles for an UNAVAILABLE genotype");
+
         List<Allele> al = new ArrayList<Allele>();
         for ( Allele a : alleles )
             if ( a.equals(allele) )
@@ -75,6 +81,8 @@ public class Genotype {
     }
 
     public Allele getAllele(int i) {
+        if ( getType() == Type.UNAVAILABLE )
+            throw new ReviewedStingException("Requesting alleles for an UNAVAILABLE genotype");
         return alleles.get(i);
     }
 
@@ -89,10 +97,21 @@ public class Genotype {
         NO_CALL,
         HOM_REF,
         HET,
-        HOM_VAR
+        HOM_VAR,
+        UNAVAILABLE
     }
 
     public Type getType() {
+        if ( type == null ) {
+            type = determineType();
+        }
+        return type;
+    }
+
+    protected Type determineType() {
+        if ( alleles == null )
+            return Type.UNAVAILABLE;
+
         Allele firstAllele = alleles.get(0);
 
         if ( firstAllele.isNoCall() ) {
@@ -122,7 +141,8 @@ public class Genotype {
      * @return true if this genotype is not actually a genotype but a "no call" (e.g. './.' in VCF)
      */
     public boolean isNoCall() { return getType() == Type.NO_CALL; }
-    public boolean isCalled() { return getType() != Type.NO_CALL; }
+    public boolean isCalled() { return getType() != Type.NO_CALL && getType() != Type.UNAVAILABLE; }
+    public boolean isAvailable() { return getType() != Type.UNAVAILABLE; }
 
     //
     // Useful methods for getting genotype likelihoods for a genotype object, if present
@@ -157,8 +177,8 @@ public class Genotype {
     }
 
     public void validate() {
-        if ( alleles == null ) throw new IllegalArgumentException("BUG: alleles cannot be null in setAlleles");
-        if ( alleles.size() == 0) throw new IllegalArgumentException("BUG: alleles cannot be of size 0 in setAlleles");
+        if ( alleles == null ) return;
+        if ( alleles.size() == 0) throw new IllegalArgumentException("BUG: alleles cannot be of size 0");
 
         int nNoCalls = 0;
         for ( Allele allele : alleles ) {
@@ -175,6 +195,9 @@ public class Genotype {
     }
 
     public String getGenotypeString(boolean ignoreRefState) {
+        if ( alleles == null )
+            return null;
+
         // Notes:
         // 1. Make sure to use the appropriate separator depending on whether the genotype is phased
         // 2. If ignoreRefState is true, then we want just the bases of the Alleles (ignoring the '*' indicating a ref Allele)
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
index 3feaf5e1c..dba16cf86 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
@@ -24,8 +24,8 @@
 
 package org.broadinstitute.sting.utils.variantcontext;
 
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broad.tribble.TribbleException;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 
 public class GenotypeLikelihoods {
     public static final boolean CAP_PLS = false;
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java
index 4efba8825..a191670a4 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java
@@ -1,7 +1,10 @@
 package org.broadinstitute.sting.utils.variantcontext;
 
 
-import java.util.*;
+import java.util.Collection;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
 
 /**
  * Mutable version of VariantContext
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 3d375aba2..eab392c4d 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -2,8 +2,8 @@ package org.broadinstitute.sting.utils.variantcontext;
 
 import org.broad.tribble.Feature;
 import org.broad.tribble.TribbleException;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broad.tribble.util.ParsingUtils;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFParser;
 
 import java.util.*;
@@ -867,7 +867,10 @@ public class VariantContext implements Feature { // to enable tribble intergrati
 
         for ( String name : sampleNames ) {
             if ( map.containsKey(name) ) throw new IllegalArgumentException("Duplicate names detected in requested samples " + sampleNames);
-            map.put(name, getGenotype(name));
+            final Genotype g = getGenotype(name);
+            if ( g != null ) {
+                map.put(name, g);
+            }
         }
 
         return map;
@@ -1203,9 +1206,11 @@ public class VariantContext implements Feature { // to enable tribble intergrati
 
             if ( ! name.equals(g.getSampleName()) ) throw new IllegalStateException("Bound sample name " + name + " does not equal the name of the genotype " + g.getSampleName());
 
-            for ( Allele gAllele : g.getAlleles() ) {
-                if ( ! hasAllele(gAllele) && gAllele.isCalled() )
-                    throw new IllegalStateException("Allele in genotype " + gAllele + " not in the variant context " + alleles);
+            if ( g.isAvailable() ) {
+                for ( Allele gAllele : g.getAlleles() ) {
+                    if ( ! hasAllele(gAllele) && gAllele.isCalled() )
+                        throw new IllegalStateException("Allele in genotype " + gAllele + " not in the variant context " + alleles);
+                }
             }
         }
     }
@@ -1343,6 +1348,15 @@ public class VariantContext implements Feature { // to enable tribble intergrati
         return (int)stop;
     }
 
+    private boolean hasSymbolicAlleles() {
+        for (Allele a: getAlleles()) {
+            if (a.isSymbolic()) {
+                return true;
+            }
+        }
+        return false;
+    }
+
     public static VariantContext createVariantContextWithPaddedAlleles(VariantContext inputVC, byte inputRefBase, boolean refBaseShouldBeAppliedToEndOfAlleles) {
         Allele refAllele = inputVC.getReference();
 
@@ -1352,7 +1366,9 @@ public class VariantContext implements Feature { // to enable tribble intergrati
         // We need to pad a VC with a common base if the length of the reference allele is less than the length of the VariantContext.
         // This happens because the position of e.g. an indel is always one before the actual event (as per VCF convention).
         long locLength = (inputVC.getEnd() - inputVC.getStart()) + 1;
-        if (refAllele.length() == locLength)
+        if (inputVC.hasSymbolicAlleles())
+            padVC = true;
+        else if (refAllele.length() == locLength)
             padVC = false;
         else if (refAllele.length() == locLength-1)
             padVC = true;
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
index 5d58954aa..5a5671056 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -23,21 +23,26 @@
 
 package org.broadinstitute.sting.utils.variantcontext;
 
-import java.io.Serializable;
-import java.util.*;
-
-import com.google.java.contract.*;
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Requires;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.samtools.util.StringUtil;
-import org.apache.commons.jexl2.*;
+import org.apache.commons.jexl2.Expression;
+import org.apache.commons.jexl2.JexlEngine;
 import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
-import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec;
 import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
+import java.io.Serializable;
+import java.util.*;
+
 public class VariantContextUtils {
     final public static JexlEngine engine = new JexlEngine();
     static {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
index c5a3b6f2a..a59ed7abe 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
@@ -29,7 +29,10 @@ import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.util.*;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
 
 /**
  *
diff --git a/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java b/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java
index ab91d0e2e..5782c2704 100755
--- a/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.utils.wiggle;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.*;
diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java
index 61bb8b34b..b3e422ba9 100755
--- a/public/java/test/org/broadinstitute/sting/BaseTest.java
+++ b/public/java/test/org/broadinstitute/sting/BaseTest.java
@@ -4,6 +4,7 @@ import org.apache.commons.io.FileUtils;
 import org.apache.log4j.*;
 import org.apache.log4j.spi.LoggingEvent;
 import org.broadinstitute.sting.commandline.CommandLineUtils;
+import org.broadinstitute.sting.gatk.walkers.diffengine.DiffEngine;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.testng.Assert;
 
@@ -12,6 +13,10 @@ import java.io.*;
 import java.math.BigInteger;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 /**
  *
@@ -107,6 +112,57 @@ public abstract class BaseTest {
         }
     }
 
+    /**
+     * Simple generic utility class to creating TestNG data providers:
+     *
+     * 1: inherit this class, as in
+     *
+     *      private class SummarizeDifferenceTest extends TestDataProvider {
+     *         public SummarizeDifferenceTest() {
+     *           super(SummarizeDifferenceTest.class);
+     *         }
+     *         ...
+     *      }
+     *
+     * Provide a reference to your class to the TestDataProvider constructor.
+     *
+     * 2: Create instances of your subclass.  Return from it the call to getTests, providing
+     * the class type of your test
+     *
+     * @DataProvider(name = "summaries")
+     * public Object[][] createSummaries() {
+     *   new SummarizeDifferenceTest().addDiff("A", "A").addSummary("A:2");
+     *   new SummarizeDifferenceTest().addDiff("A", "B").addSummary("A:1", "B:1");
+     *   return SummarizeDifferenceTest.getTests(SummarizeDifferenceTest.class);
+     * }
+     *
+     * This class magically tracks created objects of this
+     */
+    public static class TestDataProvider {
+        private static final Map<Class, List<Object>> tests = new HashMap<Class, List<Object>>();
+
+        /**
+         * Create a new TestDataProvider instance bound to the class variable C
+         * @param c
+         */
+        public TestDataProvider(Class c) {
+            if ( ! tests.containsKey(c) )
+                tests.put(c, new ArrayList<Object>());
+            tests.get(c).add(this);
+        }
+
+        /**
+         * Return all of the data providers in the form expected by TestNG of type class C
+         * @param c
+         * @return
+         */
+        public static Object[][] getTests(Class c) {
+            List<Object[]> params2 = new ArrayList<Object[]>();
+            for ( Object x : tests.get(c) ) params2.add(new Object[]{x});
+            return params2.toArray(new Object[][]{});
+        }
+    }
+
     /**
      * test if the file exists
      *
@@ -279,11 +335,14 @@ public abstract class BaseTest {
         
         if (parameterize || expectedMD5.equals("")) {
             // Don't assert
-        } else {
-            Assert.assertEquals(filemd5sum, expectedMD5, name + " Mismatching MD5s");
+        } else if ( filemd5sum.equals(expectedMD5) ) {
             System.out.println(String.format("  => %s PASSED", name));
+        } else {
+            Assert.fail(String.format("%s has mismatching MD5s: expected=%s observed=%s", name, expectedMD5, filemd5sum));
         }
 
+
+
         return filemd5sum;
     }
 
@@ -326,7 +385,12 @@ public abstract class BaseTest {
                     System.out.printf("##### Path to calculated file (MD5=%s): %s%n", filemd5sum, pathToFileMD5File);
                     System.out.printf("##### Diff command: diff %s %s%n", pathToExpectedMD5File, pathToFileMD5File);
 
-                    // todo -- add support for simple inline display of the first N differences for text file
+                    // inline differences
+                    DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(System.out, 20, 10, 0);
+                    boolean success = DiffEngine.simpleDiffFiles(new File(pathToExpectedMD5File), new File(pathToFileMD5File), params);
+                    if ( success )
+                        System.out.printf("Note that the above list is not comprehensive.  At most 20 lines of output, and 10 specific differences will be listed.  Please use -T DiffObjects -R public/testdata/exampleFASTA.fasta -m %s -t %s to explore the differences more freely%n",
+                                pathToExpectedMD5File, pathToFileMD5File);
                 }
             }
 
diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java
index dacaf2738..22635dfa3 100755
--- a/public/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -26,7 +26,9 @@
 package org.broadinstitute.sting;
 
 import org.apache.commons.lang.StringUtils;
+import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.Tribble;
+import org.broad.tribble.index.Index;
 import org.broad.tribble.index.IndexFactory;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.gatk.CommandLineExecutable;
@@ -63,8 +65,20 @@ public class WalkerTest extends BaseTest {
                 throw new StingException("Found an index created for file " + resultFile + " but we can only validate VCF files.  Extend this code!");
             }
 
-            System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile);
-            Assert.assertTrue(IndexFactory.onDiskIndexEqualToNewlyCreatedIndex(resultFile, indexFile, new VCFCodec()), "Index on disk from indexing on the fly not equal to the index created after the run completed");
+            assertOnDiskIndexEqualToNewlyCreatedIndex(indexFile, name, resultFile);
+        }
+    }
+
+
+    public static void assertOnDiskIndexEqualToNewlyCreatedIndex(final File indexFile, final String name, final File resultFile) {
+        System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile);
+        Index indexFromOutputFile = IndexFactory.createIndex(resultFile, new VCFCodec());
+        Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath());
+
+        if ( ! indexFromOutputFile.equalsIgnoreTimestamp(dynamicIndex) ) {
+            Assert.fail(String.format("Index on disk from indexing on the fly not equal to the index created after the run completed.  FileIndex %s vs. on-the-fly %s%n",
+                    indexFromOutputFile.getProperties(),
+                    dynamicIndex.getProperties()));
         }
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 6ba6926c6..e6300e6c9 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -15,7 +15,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("4cc077eb3d343e6b7ba12bff86ebe347"));
+                Arrays.asList("8a105fa5eebdfffe7326bc5b3d8ffd1c"));
         executeTest("test file has annotations, not asking for annotations, #1", spec);
     }
 
@@ -23,7 +23,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsNotAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("1de8e943fbf55246ebd19efa32f22a58"));
+                Arrays.asList("964f1016ec9a3c55333f62dd834c14d6"));
         executeTest("test file has annotations, not asking for annotations, #2", spec);
     }
 
@@ -31,7 +31,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("93c110e45fd4aedb044a8a5501e23336"));
+                Arrays.asList("8e7de435105499cd71ffc099e268a83e"));
         executeTest("test file has annotations, asking for annotations, #1", spec);
     }
 
@@ -39,7 +39,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("f5cb45910ed719f46159f9f71acaecf4"));
+                Arrays.asList("64b6804cb1e27826e3a47089349be581"));
         executeTest("test file has annotations, asking for annotations, #2", spec);
     }
 
@@ -47,7 +47,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("4b48e7d095ef73e3151542ea976ecd89"));
+                Arrays.asList("42ccee09fa9f8c58f4a0d4f1139c094f"));
         executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
     }
 
@@ -55,7 +55,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsNotAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("28dfbfd178aca071b948cd3dc2365357"));
+                Arrays.asList("f2ddfa8105c290b1f34b7a261a02a1ac"));
         executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
     }
 
@@ -63,7 +63,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("a330a5bc3ee72a51dbeb7e6c97a0db99"));
+                Arrays.asList("fd1ffb669800c2e07df1e2719aa38e49"));
         executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
     }
 
@@ -71,7 +71,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("3a31d1ef471acfb881a2dec7963fe3f4"));
+                Arrays.asList("09f8e840770a9411ff77508e0ed0837f"));
         executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
     }
 
@@ -79,7 +79,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testOverwritingHeader() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
-                Arrays.asList("a63fd8ff7bafbd46b7f009144a7c2ad1"));
+                Arrays.asList("78d2c19f8107d865970dbaf3e12edd92"));
         executeTest("test overwriting header", spec);
     }
 
@@ -87,7 +87,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoReads() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
-                Arrays.asList("36378f1245bb99d902fbfe147605bc42"));
+                Arrays.asList("16e3a1403fc376320d7c69492cad9345"));
         executeTest("not passing it any reads", spec);
     }
 
@@ -95,7 +95,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testDBTagWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
-                Arrays.asList("0257a1cc3c703535b2d3c5046bf88ab7"));
+                Arrays.asList("3da8ca2b6bdaf6e92d94a8c77a71313d"));
         executeTest("getting DB tag with dbSNP", spec);
     }
 
@@ -103,7 +103,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testDBTagWithHapMap() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
-                Arrays.asList("2d7c73489dcf0db433bebdf79a068764"));
+                Arrays.asList("1bc01c5b3bd0b7aef75230310c3ce688"));
         executeTest("getting DB tag with HM3", spec);
     }
 
@@ -111,13 +111,13 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testUsingExpression() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:foo,VCF " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" -B:variant,VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variant", 1,
-                Arrays.asList("2f6efd08d818faa1eb0631844437c64a"));
+                Arrays.asList("e9c0d832dc6b4ed06c955060f830c140"));
         executeTest("using expression", spec);
     }
 
     @Test
     public void testTabixAnnotations() {
-        final String MD5 = "6c7a6a1c0027bf82656542a9b2671a35";
+        final String MD5 = "13269d5a2e16f06fd755cc0fb9271acf";
         for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
             WalkerTestSpec spec = new WalkerTestSpec(
                     baseTestString() + " -A HomopolymerRun -B:variant,VCF " + validationDataLocation + "/" + file + " -BTI variant -NO_HEADER", 1,
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java
index c4f6d5ebc..c75a5b2dc 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java
@@ -29,7 +29,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
         */
 
 
-        String[] md5WithDashSArg = {"3d3b61a83c1189108eabb2df04218099"};
+        String[] md5WithDashSArg = {"efba4ce1641cfa2ef88a64395f2ebce8"};
         WalkerTestSpec specWithSArg = new WalkerTestSpec(
                 "-T GenomicAnnotator -R " + b36KGReference +
                 " -B:variant,vcf3 /humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf" +
@@ -58,7 +58,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("caa562160733aa638e1ba413ede209ae")
+                Arrays.asList("772fc3f43b70770ec6c6acbb8bbbd4c0")
         );
         executeTest("testGenomicAnnotatorOnIndels", testOnIndels);
     }
@@ -76,7 +76,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("a4cf76f08fa90284b6988a464b6e0c17")
+                Arrays.asList("081ade7f3d2d3c5f19cb1e8651a626f3")
         );
         executeTest("testGenomicAnnotatorOnSNPsAndIndels", testOnSNPsAndIndels);
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
index 70c34e729..fef1b6e64 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
@@ -41,7 +41,7 @@ public class BeagleIntegrationTest extends WalkerTest {
                         "-B:beagleR2,BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " +
                         "-B:beagleProbs,BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " +
                         "-B:beaglePhased,BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " +
-                        "-o %s -NO_HEADER", 1, Arrays.asList("6bccee48ad2f06ba5a8c774fed444478"));
+                        "-o %s -NO_HEADER", 1, Arrays.asList("3531451e84208264104040993889aaf4"));
         executeTest("test BeagleOutputToVCF", spec);
     }
    
@@ -60,7 +60,7 @@ public class BeagleIntegrationTest extends WalkerTest {
                 "-T ProduceBeagleInput -B:variant,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_HSQ_chr22_14-16m.vcf "+
                         "-B:validation,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878_OMNI_chr22_14-16m.vcf "+
                         "-L 22:14000000-16000000 -o %s -bvcf %s -bs 0.8 -valp 0.98 -R /humgen/1kg/reference/human_g1k_v37.fasta -NO_HEADER ",2,
-                Arrays.asList("660986891b30cdc937e0f2a3a5743faa","223fb977e8db567dcaf632c6ee51f294"));
+                Arrays.asList("660986891b30cdc937e0f2a3a5743faa","e96ddd51da9f4a797b2aa8c20e404166"));
         executeTest("test BeagleInputWithBootstrap",spec);
     }
 
@@ -72,7 +72,7 @@ public class BeagleIntegrationTest extends WalkerTest {
                 "-B:beagleR2,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.r2 "+
                 "-B:beagleProbs,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.gprobs.bgl "+
                 "-B:beaglePhased,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.phased.bgl "+
-                "-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("24b88ef8cdf6e347daab491f0256be5a"));
+                "-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("8dd6ec53994fb46c5c22af8535d22965"));
 
         executeTest("testBeagleChangesSitesToRef",spec);
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java
new file mode 100644
index 000000000..96dfec6e8
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java
@@ -0,0 +1,229 @@
+/*
+ * 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.
+ */
+
+// our package
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+
+// the imports for unit testing.
+
+import org.broadinstitute.sting.BaseTest;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+/**
+ * Basic unit test for DifferableReaders in reduced reads
+ */
+public class DiffEngineUnitTest extends BaseTest {
+    DiffEngine engine;
+
+    @BeforeClass(enabled = true)
+    public void createDiffEngine() {
+        engine = new DiffEngine();
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // Difference testing routines
+    //
+    // --------------------------------------------------------------------------------
+
+    private class DifferenceTest extends TestDataProvider {
+        public DiffElement tree1, tree2;
+        public List<String> differences;
+
+        private DifferenceTest(String tree1, String tree2) {
+            this(tree1, tree2, Collections.<String>emptyList());
+        }
+
+        private DifferenceTest(String tree1, String tree2, String difference) {
+            this(tree1, tree2, Arrays.asList(difference));
+        }
+
+        private DifferenceTest(String tree1, String tree2, List<String> differences) {
+            super(DifferenceTest.class);
+            this.tree1 = DiffNode.fromString(tree1);
+            this.tree2 = DiffNode.fromString(tree2);
+            this.differences = differences;
+        }
+
+        public String toString() {
+            return String.format("tree1=%s tree2=%s diff=%s",
+                    tree1.toOneLineString(), tree2.toOneLineString(), differences);
+        }
+    }
+
+    @DataProvider(name = "trees")
+    public Object[][] createTrees() {
+        new DifferenceTest("A=X", "A=X");
+        new DifferenceTest("A=X", "A=Y", "A:X!=Y");
+        new DifferenceTest("A=X", "B=X", Arrays.asList("A:X!=MISSING", "B:MISSING!=X"));
+        new DifferenceTest("A=(X=1)", "B=(X=1)", Arrays.asList("A:(X=1)!=MISSING", "B:MISSING!=(X=1)"));
+        new DifferenceTest("A=(X=1)", "A=(X=1)");
+        new DifferenceTest("A=(X=1 Y=2)", "A=(X=1 Y=2)");
+        new DifferenceTest("A=(X=1 Y=2 B=(Z=3))", "A=(X=1 Y=2 B=(Z=3))");
+        new DifferenceTest("A=(X=1)", "A=(X=2)", "A.X:1!=2");
+        new DifferenceTest("A=(X=1 Y=2 B=(Z=3))", "A=(X=1 Y=2 B=(Z=4))", "A.B.Z:3!=4");
+        new DifferenceTest("A=(X=1)", "A=(X=1 Y=2)", "A.Y:MISSING!=2");
+        new DifferenceTest("A=(X=1 Y=2 B=(Z=3))", "A=(X=1 Y=2)", "A.B:(Z=3)!=MISSING");
+        return DifferenceTest.getTests(DifferenceTest.class);
+    }
+
+    @Test(enabled = true, dataProvider = "trees")
+    public void testDiffs(DifferenceTest test) {
+        logger.warn("Test tree1: " + test.tree1.toOneLineString());
+        logger.warn("Test tree2: " + test.tree2.toOneLineString());
+
+        List<SpecificDifference> diffs = engine.diff(test.tree1, test.tree2);
+        logger.warn("Test expected diff : " + test.differences);
+        logger.warn("Observed diffs     : " + diffs);
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // Low-level routines for summarizing differences
+    //
+    // --------------------------------------------------------------------------------
+
+    @Test(enabled = true)
+    public void testLongestCommonPostfix() {
+        testLongestCommonPostfixHelper("A", "A", 1);
+        testLongestCommonPostfixHelper("A", "B", 0);
+        testLongestCommonPostfixHelper("A.B", "A.B", 2);
+        testLongestCommonPostfixHelper("A.B.C", "A.B.C", 3);
+        testLongestCommonPostfixHelper("A.B.C", "X.B.C", 2);
+        testLongestCommonPostfixHelper("A.B.C", "X.Y.C", 1);
+        testLongestCommonPostfixHelper("A.B.C", "X.Y.Z", 0);
+        testLongestCommonPostfixHelper("A.B.C", "A.X.C", 1);
+        testLongestCommonPostfixHelper("A.B.C", "A.X.Z", 0);
+        testLongestCommonPostfixHelper("A.B.C", "A.B.Z", 0);
+    }
+
+    public void testLongestCommonPostfixHelper(String p1, String p2, int expected) {
+        String[] parts1 = p1.split("\\.");
+        String[] parts2 = p2.split("\\.");
+        int obs = DiffEngine.longestCommonPostfix(parts1, parts2);
+        Assert.assertEquals(obs, expected, "p1=" + p1 + " p2=" + p2 + " failed");
+    }
+
+    @Test(enabled = true, dependsOnMethods = "testLongestCommonPostfix")
+    public void testSummarizePath() {
+        testSummarizePathHelper("A", "A", "A");
+        testSummarizePathHelper("A", "B", "*");
+        testSummarizePathHelper("A.B", "A.B", "A.B");
+        testSummarizePathHelper("A.B", "X.B", "*.B");
+        testSummarizePathHelper("A.B", "X.Y", "*.*");
+        testSummarizePathHelper("A.B.C", "A.B.C", "A.B.C");
+        testSummarizePathHelper("A.B.C", "X.B.C", "*.B.C");
+        testSummarizePathHelper("A.B.C", "X.Y.C", "*.*.C");
+        testSummarizePathHelper("A.B.C", "X.Y.Z", "*.*.*");
+        testSummarizePathHelper("A.B.C", "A.X.C", "*.*.C");
+        testSummarizePathHelper("A.B.C", "A.X.Z", "*.*.*");
+        testSummarizePathHelper("A.B.C", "A.B.Z", "*.*.*");
+    }
+
+    public void testSummarizePathHelper(String p1, String p2, String expected) {
+        String[] parts1 = DiffEngine.diffNameToPath(p1);
+        String[] parts2 = DiffEngine.diffNameToPath(p2);
+        int obs = DiffEngine.longestCommonPostfix(parts1, parts2);
+        String path = DiffEngine.summarizedPath(parts2, obs);
+        Assert.assertEquals(path, expected, "p1=" + p1 + " p2=" + p2 + " failed");
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // High-level difference summary
+    //
+    // --------------------------------------------------------------------------------
+
+    private class SummarizeDifferenceTest extends TestDataProvider {
+        List<String> diffs = new ArrayList<String>();
+        List<String> expecteds = new ArrayList<String>();
+
+        public SummarizeDifferenceTest() { super(SummarizeDifferenceTest.class); }
+
+        public SummarizeDifferenceTest addDiff(String... diffsToAdd) {
+            diffs.addAll(Arrays.asList(diffsToAdd));
+            return this;
+        }
+
+        public SummarizeDifferenceTest addSummary(String... expectedSummary) {
+            expecteds.addAll(Arrays.asList(expectedSummary));
+            return this;
+        }
+
+        public String toString() {
+            return String.format("diffs=%s => expected=%s", diffs, expecteds);
+        }
+
+        public void test() {
+            List<String[]> diffPaths = new ArrayList<String[]>(diffs.size());
+            for ( String diff : diffs ) { diffPaths.add(DiffEngine.diffNameToPath(diff)); }
+
+            List<Difference> sumDiffs = engine.summarizedDifferencesOfPathsFromString(diffs);
+
+            Assert.assertEquals(sumDiffs.size(), expecteds.size(), "Unexpected number of summarized differences: " + sumDiffs);
+
+            for ( int i = 0; i < sumDiffs.size(); i++ ) {
+                Difference sumDiff = sumDiffs.get(i);
+                String expected = expecteds.get(i);
+                String[] pathCount = expected.split(":");
+                String path = pathCount[0];
+                int count = Integer.valueOf(pathCount[1]);
+                Assert.assertEquals(sumDiff.getPath(), path, "Unexpected path at: " + expected + " obs=" + sumDiff + " all=" + sumDiffs);
+                Assert.assertEquals(sumDiff.getCount(), count, "Unexpected counts at: " + expected + " obs=" + sumDiff + " all=" + sumDiffs);
+            }
+        }
+    }
+
+    @DataProvider(name = "summaries")
+    public Object[][] createSummaries() {
+        new SummarizeDifferenceTest().addDiff("A", "A").addSummary("A:2");
+        new SummarizeDifferenceTest().addDiff("A", "B").addSummary("A:1", "B:1");
+        new SummarizeDifferenceTest().addDiff("A", "A", "A").addSummary("A:3");
+        new SummarizeDifferenceTest().addDiff("A", "A", "A", "B").addSummary("A:3", "B:1");
+        new SummarizeDifferenceTest().addDiff("A", "A", "A", "B", "B").addSummary("A:3", "B:2");
+        new SummarizeDifferenceTest().addDiff("A", "A", "A", "B", "B", "C").addSummary("A:3", "B:2", "C:1");
+        new SummarizeDifferenceTest().addDiff("A.X", "A.X").addSummary("A.X:2");
+        new SummarizeDifferenceTest().addDiff("A.X", "A.X", "B.X").addSummary("*.X:3", "A.X:2", "B.X:1");
+        new SummarizeDifferenceTest().addDiff("A.X", "A.X", "B.X", "B.X").addSummary("*.X:4", "A.X:2", "B.X:2");
+        new SummarizeDifferenceTest().addDiff("A.B.C", "X.B.C").addSummary("*.B.C:2", "A.B.C:1", "X.B.C:1");
+        new SummarizeDifferenceTest().addDiff("A.B.C", "X.Y.C", "X.Y.C").addSummary("*.*.C:3", "X.Y.C:2", "A.B.C:1");
+        new SummarizeDifferenceTest().addDiff("A.B.C", "A.X.C", "X.Y.C").addSummary("*.*.C:3", "A.B.C:1", "A.X.C:1", "X.Y.C:1");
+        new SummarizeDifferenceTest().addDiff("A.B.C", "A.X.C", "B.X.C").addSummary("*.*.C:3", "*.X.C:2", "A.B.C:1", "A.X.C:1", "B.X.C:1");
+        new SummarizeDifferenceTest().addDiff("A.B.C", "A.X.C", "B.X.C", "B.X.C").addSummary("*.*.C:4", "*.X.C:3", "B.X.C:2", "A.B.C:1", "A.X.C:1");
+
+        return SummarizeDifferenceTest.getTests(SummarizeDifferenceTest.class);
+    }
+
+
+    @Test(enabled = true, dependsOnMethods = "testSummarizePath", dataProvider = "summaries")
+    public void testSummarizeDifferences(SummarizeDifferenceTest test) {
+        test.test();
+    }
+}
\ No newline at end of file
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java
new file mode 100644
index 000000000..534416d29
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java
@@ -0,0 +1,249 @@
+/*
+ * 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.
+ */
+
+// our package
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+
+// the imports for unit testing.
+
+
+import org.broadinstitute.sting.BaseTest;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+/**
+ * Basic unit test for DifferableReaders in reduced reads
+ */
+public class DiffNodeUnitTest extends BaseTest {
+    // Data is:
+    // MY_ROOT
+    //   fields: A=A, B=B
+    //   nodes: C, D
+    //   C: fields: E=E, nodes: none
+    //   D: fields: F=F, G=G, nodes: none
+    static DiffNode MY_ROOT = DiffNode.rooted("MY_ROOT");
+    static DiffValue Value_A = new DiffValue("A", MY_ROOT, "A");
+    static DiffValue Value_B = new DiffValue("B", MY_ROOT, "B");
+    static DiffNode NODE_C = DiffNode.empty("C", MY_ROOT);
+    static DiffNode NODE_D = DiffNode.empty("D", MY_ROOT);
+    static DiffValue Value_E = new DiffValue("E", NODE_C, "E");
+    static DiffValue Value_F = new DiffValue("F", NODE_D, "F");
+    static DiffValue Value_G = new DiffValue("G", NODE_D, "G");
+
+    static {
+        MY_ROOT.add(Value_A);
+        MY_ROOT.add(Value_B);
+        MY_ROOT.add(NODE_C);
+        MY_ROOT.add(NODE_D);
+        NODE_C.add(Value_E);
+        NODE_D.add(Value_F);
+        NODE_D.add(Value_G);
+    }
+
+
+    // --------------------------------------------------------------------------------
+    //
+    // Element testing routines
+    //
+    // --------------------------------------------------------------------------------
+
+    private class ElementTest extends TestDataProvider {
+        public DiffElement elt;
+        public String name;
+        public String fullName;
+        public DiffElement parent;
+
+        private ElementTest(DiffValue elt, DiffValue parent, String name, String fullName) {
+            this(elt.getBinding(), parent.getBinding(), name, fullName);
+        }
+
+        private ElementTest(DiffElement elt, DiffElement parent, String name, String fullName) {
+            super(ElementTest.class);
+            this.elt = elt;
+            this.name = name;
+            this.fullName = fullName;
+            this.parent = parent;
+        }
+
+        public String toString() {
+            return String.format("ElementTest elt=%s name=%s fullName=%s parent=%s",
+                    elt.toOneLineString(), name, fullName, parent.getName());
+        }
+    }
+
+    @DataProvider(name = "elementdata")
+    public Object[][] createElementData() {
+        new ElementTest(MY_ROOT.getBinding(), DiffElement.ROOT, "MY_ROOT", "MY_ROOT");
+        new ElementTest(NODE_C, MY_ROOT, "C", "MY_ROOT.C");
+        new ElementTest(NODE_D, MY_ROOT, "D", "MY_ROOT.D");
+        new ElementTest(Value_A, MY_ROOT, "A", "MY_ROOT.A");
+        new ElementTest(Value_B, MY_ROOT, "B", "MY_ROOT.B");
+        new ElementTest(Value_E, NODE_C, "E", "MY_ROOT.C.E");
+        new ElementTest(Value_F, NODE_D, "F", "MY_ROOT.D.F");
+        new ElementTest(Value_G, NODE_D, "G", "MY_ROOT.D.G");
+        return TestDataProvider.getTests(ElementTest.class);
+    }
+
+    @Test(enabled = true, dataProvider = "elementdata")
+    public void testElementMethods(ElementTest test) {
+        Assert.assertNotNull(test.elt.getName());
+        Assert.assertNotNull(test.elt.getParent());
+        Assert.assertEquals(test.elt.getName(), test.name);
+        Assert.assertEquals(test.elt.getParent(), test.parent);
+        Assert.assertEquals(test.elt.fullyQualifiedName(), test.fullName);
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // DiffValue testing routines
+    //
+    // --------------------------------------------------------------------------------
+
+    private class LeafTest extends TestDataProvider {
+        public DiffValue diffvalue;
+        public Object value;
+
+        private LeafTest(DiffValue diffvalue, Object value) {
+            super(LeafTest.class);
+            this.diffvalue = diffvalue;
+            this.value = value;
+        }
+
+        public String toString() {
+            return String.format("LeafTest diffvalue=%s value=%s", diffvalue.toOneLineString(), value);
+        }
+    }
+
+    @DataProvider(name = "leafdata")
+    public Object[][] createLeafData() {
+        new LeafTest(Value_A, "A");
+        new LeafTest(Value_B, "B");
+        new LeafTest(Value_E, "E");
+        new LeafTest(Value_F, "F");
+        new LeafTest(Value_G, "G");
+        return TestDataProvider.getTests(LeafTest.class);
+    }
+
+    @Test(enabled = true, dataProvider = "leafdata")
+    public void testLeafMethods(LeafTest test) {
+        Assert.assertNotNull(test.diffvalue.getValue());
+        Assert.assertEquals(test.diffvalue.getValue(), test.value);
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // Node testing routines
+    //
+    // --------------------------------------------------------------------------------
+
+    private class NodeTest extends TestDataProvider {
+        public DiffNode node;
+        public Set<String> fields;
+        public Set<String> subnodes;
+        public Set<String> allNames;
+
+        private NodeTest(DiffNode node, List<String> fields, List<String> subnodes) {
+            super(NodeTest.class);
+            this.node = node;
+            this.fields = new HashSet<String>(fields);
+            this.subnodes = new HashSet<String>(subnodes);
+            this.allNames = new HashSet<String>(fields);
+            allNames.addAll(subnodes);
+        }
+
+        public String toString() {
+            return String.format("NodeTest node=%s fields=%s subnodes=%s",
+                    node.toOneLineString(), fields, subnodes);
+        }
+    }
+
+    @DataProvider(name = "nodedata")
+    public Object[][] createData1() {
+        new NodeTest(MY_ROOT, Arrays.asList("A", "B"), Arrays.asList("C", "D"));
+        new NodeTest(NODE_C, Arrays.asList("E"), Collections.<String>emptyList());
+        new NodeTest(NODE_D, Arrays.asList("F", "G"), Collections.<String>emptyList());
+        return TestDataProvider.getTests(NodeTest.class);
+    }
+
+    @Test(enabled = true, dataProvider = "nodedata")
+    public void testNodeAccessors(NodeTest test) {
+        Assert.assertNotNull(test.node.getElements());
+
+        for ( String name : test.allNames ) {
+            DiffElement elt = test.node.getElement(name);
+            Assert.assertNotNull(elt, "Failed to find field " + elt + " in " + test.node);
+            Assert.assertEquals(elt.getName(), name);
+            Assert.assertEquals(elt.getValue().isAtomic(), test.fields.contains(name), "Failed atomic/compound expectation: " + test.node);
+        }
+    }
+
+    // NOTE: add routines are being implicitly tested by the creation of the data structures
+
+    @Test(enabled = true, dataProvider = "nodedata")
+    public void testCounts(NodeTest test) {
+        Assert.assertEquals(test.node.getElements().size(), test.allNames.size());
+        Assert.assertEquals(test.node.getElementNames(), test.allNames);
+    }
+
+    // --------------------------------------------------------------------------------
+    //
+    // fromString testing routines
+    //
+    // --------------------------------------------------------------------------------
+
+    private class FromStringTest extends TestDataProvider {
+        public String string;
+        public DiffElement expected;
+
+        private FromStringTest(String string, DiffElement expected) {
+            super(FromStringTest.class);
+            this.string = string;
+            this.expected = expected;
+        }
+
+        public String toString() {
+            return String.format("FromStringTest string=%s expected=%s", string, expected.toOneLineString());
+        }
+    }
+
+    @DataProvider(name = "fromstringdata")
+    public Object[][] createFromData() {
+        new FromStringTest("A=A", Value_A.getBinding());
+        new FromStringTest("B=B", Value_B.getBinding());
+        new FromStringTest("C=(E=E)", NODE_C.getBinding());
+        new FromStringTest("D=(F=F G=G)", NODE_D.getBinding());
+        return TestDataProvider.getTests(FromStringTest.class);
+    }
+
+    @Test(enabled = true, dataProvider = "fromstringdata")
+    public void parseFromString(FromStringTest test) {
+        logger.warn("Testing from string: " + test.string);
+        DiffElement elt = DiffNode.fromString(test.string);
+        Assert.assertEquals(elt.toOneLineString(), test.expected.toOneLineString());
+    }
+}
\ No newline at end of file
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
new file mode 100644
index 000000000..a0cb47770
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
@@ -0,0 +1,143 @@
+/*
+ * 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.
+ */
+
+// our package
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+
+// the imports for unit testing.
+
+
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.util.*;
+
+/**
+ * Basic unit test for DifferableReaders in reduced reads
+ */
+public class DiffableReaderUnitTest extends BaseTest {
+    DiffEngine engine;
+
+    File vcfFile = new File(testDir + "diffTestMaster.vcf");
+    File bamFile = new File(testDir + "exampleBAM.bam");
+
+    @BeforeClass(enabled = true)
+    public void createDiffEngine() {
+        engine = new DiffEngine();
+    }
+
+    @Test(enabled = true)
+    public void testPluggableDiffableReaders() {
+        logger.warn("testPluggableDiffableReaders");
+        Map<String, DiffableReader> readers = engine.getReaders();
+        Assert.assertNotNull(readers);
+        Assert.assertTrue(readers.size() > 0);
+        Assert.assertNotNull(readers.get("VCF"));
+        for ( Map.Entry<String, DiffableReader> e : engine.getReaders().entrySet() ) {
+            logger.warn("Found diffable reader: " + e.getKey());
+            Assert.assertEquals(e.getValue().getName(), e.getKey());
+            Assert.assertEquals(e.getValue(), engine.getReader(e.getKey()));
+        }
+    }
+
+    private static void testLeaf(DiffNode rec, String field, Object expected) {
+        DiffElement value = rec.getElement(field);
+        Assert.assertNotNull(value, "Expected to see leaf named " + field + " in rec " + rec);
+        Assert.assertEquals(value.getValue().getValue(), expected, "Expected to leaf named " + field + " to have value " + expected + " in rec " + rec);
+    }
+
+    @Test(enabled = true, dependsOnMethods = "testPluggableDiffableReaders")
+    public void testVCF1() {
+        logger.warn("testVCF1");
+        DiffableReader vcfReader = engine.getReader("VCF");
+        Assert.assertTrue(vcfReader.canRead(vcfFile));
+        Assert.assertFalse(vcfReader.canRead(bamFile));
+
+        DiffElement diff = vcfReader.readFromFile(vcfFile, -1);
+        Assert.assertNotNull(diff);
+
+        Assert.assertEquals(diff.getName(), vcfFile.getName());
+        Assert.assertSame(diff.getParent(), DiffElement.ROOT);
+
+        DiffNode node = diff.getValueAsNode();
+        Assert.assertEquals(node.getElements().size(), 10);
+
+        // chr1    2646    rs62635284      G       A       0.15    PASS    AC=2;AF=1.00;AN=2       GT:AD:DP:GL:GQ  1/1:53,75:3:-12.40,-0.90,-0.00:9.03
+        DiffNode rec1 = node.getElement("chr1:2646").getValueAsNode();
+        testLeaf(rec1, "CHROM", "chr1");
+        testLeaf(rec1, "POS", 2646);
+        testLeaf(rec1, "ID", "rs62635284");
+        testLeaf(rec1, "REF", Allele.create("G", true));
+        testLeaf(rec1, "ALT", new HashSet<Allele>(Arrays.asList(Allele.create("A"))));
+        testLeaf(rec1, "QUAL", 0.15);
+        testLeaf(rec1, "FILTER", Collections.<Object>emptySet());
+        testLeaf(rec1, "AC", "2");
+        testLeaf(rec1, "AF", "1.00");
+        testLeaf(rec1, "AN", "2");
+    }
+
+    @Test(enabled = true, dependsOnMethods = "testPluggableDiffableReaders")
+    public void testBAM() {
+        logger.warn("testBAM");
+        DiffableReader bamReader = engine.getReader("BAM");
+        Assert.assertTrue(bamReader.canRead(bamFile));
+        Assert.assertFalse(bamReader.canRead(vcfFile));
+
+        DiffElement diff = bamReader.readFromFile(bamFile, -1);
+        Assert.assertNotNull(diff);
+
+        Assert.assertEquals(diff.getName(), bamFile.getName());
+        Assert.assertSame(diff.getParent(), DiffElement.ROOT);
+
+        DiffNode node = diff.getValueAsNode();
+        Assert.assertEquals(node.getElements().size(), 33);
+
+        // 30PPJAAXX090125:1:42:512:1817#0 99      chr1    200     0       76M     =
+        // 255     -130    ACCCTAACCCTAACCCTAACCCTAACCATAACCCTAAGACTAACCCTAAACCTAACCCTCATAATCGAAATACAAC
+        // BBBBC@C?AABCBB<63>=B@>+B9-9+)2B8,+@327B5A>90((>-+''3?(/'''A)(''19('7.,**%)3:
+        // PG:Z:0  RG:Z:exampleBAM.bam     SM:Z:exampleBAM.bam
+
+        DiffNode rec1 = node.getElement("30PPJAAXX090125:1:42:512:1817#0_1").getValueAsNode();
+        testLeaf(rec1, "NAME", "30PPJAAXX090125:1:42:512:1817#0");
+        testLeaf(rec1, "FLAGS", 99);
+        testLeaf(rec1, "RNAME", "chr1");
+        testLeaf(rec1, "POS", 200);
+        testLeaf(rec1, "MAPQ", 0);
+        testLeaf(rec1, "CIGAR", "76M");
+        testLeaf(rec1, "RNEXT", "chr1");
+        testLeaf(rec1, "PNEXT", 255);
+        testLeaf(rec1, "TLEN", -130);
+        testLeaf(rec1, "SEQ", "ACCCTAACCCTAACCCTAACCCTAACCATAACCCTAAGACTAACCCTAAACCTAACCCTCATAATCGAAATACAAC");
+        testLeaf(rec1, "QUAL", "BBBBC@C?AABCBB<63>=B@>+B9-9+)2B8,+@327B5A>90((>-+''3?(/'''A)(''19('7.,**%)3:");
+        testLeaf(rec1, "PG", "0");
+        testLeaf(rec1, "RG", "exampleBAM.bam");
+        testLeaf(rec1, "SM", "exampleBAM.bam");
+    }
+}
\ No newline at end of file
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java
new file mode 100644
index 000000000..64579a01b
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java
@@ -0,0 +1,95 @@
+/*
+ * 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.
+ */
+
+// our package
+package org.broadinstitute.sting.gatk.walkers.diffengine;
+
+
+// the imports for unit testing.
+
+
+import org.broadinstitute.sting.BaseTest;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+/**
+ * Basic unit test for DifferableReaders in reduced reads
+ */
+public class DifferenceUnitTest extends BaseTest {
+    // --------------------------------------------------------------------------------
+    //
+    // testing routines
+    //
+    // --------------------------------------------------------------------------------
+
+    private class DifferenceTest extends TestDataProvider {
+        public DiffElement tree1, tree2;
+        public String difference;
+
+        private DifferenceTest(String tree1, String tree2, String difference) {
+            this(DiffNode.fromString(tree1), DiffNode.fromString(tree2), difference);
+        }
+
+        private DifferenceTest(DiffElement tree1, DiffElement tree2, String difference) {
+            super(DifferenceTest.class);
+            this.tree1 = tree1;
+            this.tree2 = tree2;
+            this.difference = difference;
+        }
+
+        public String toString() {
+            return String.format("tree1=%s tree2=%s diff=%s",
+                    tree1 == null ? "null" : tree1.toOneLineString(),
+                    tree2 == null ? "null" : tree2.toOneLineString(),
+                    difference);
+        }
+    }
+
+    @DataProvider(name = "data")
+    public Object[][] createTrees() {
+        new DifferenceTest("A=X", "A=Y", "A:X!=Y");
+        new DifferenceTest("A=Y", "A=X", "A:Y!=X");
+        new DifferenceTest(DiffNode.fromString("A=X"), null, "A:X!=MISSING");
+        new DifferenceTest(null, DiffNode.fromString("A=X"), "A:MISSING!=X");
+        return DifferenceTest.getTests(DifferenceTest.class);
+    }
+
+    @Test(enabled = true, dataProvider = "data")
+    public void testDiffToString(DifferenceTest test) {
+        logger.warn("Test tree1: " + (test.tree1 == null ? "null" : test.tree1.toOneLineString()));
+        logger.warn("Test tree2: " + (test.tree2 == null ? "null" : test.tree2.toOneLineString()));
+        logger.warn("Test expected diff : " + test.difference);
+        SpecificDifference diff = new SpecificDifference(test.tree1, test.tree2);
+        logger.warn("Observed diffs     : " + diff);
+        Assert.assertEquals(diff.toString(), test.difference, "Observed diff string " + diff + " not equal to expected difference string " + test.difference );
+
+    }
+}
\ No newline at end of file
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
index 3d75fdc44..7bec67d2e 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
@@ -16,7 +16,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testNoAction() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("4cc077eb3d343e6b7ba12bff86ebe347"));
+                Arrays.asList("8a105fa5eebdfffe7326bc5b3d8ffd1c"));
         executeTest("test no action", spec);
     }
 
@@ -24,7 +24,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testClusteredSnps() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -window 10 -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("ada5540bb3d9b6eb8f1337ba01e90a94"));
+                Arrays.asList("27b13f179bb4920615dff3a32730d845"));
         executeTest("test clustered SNPs", spec);
     }
 
@@ -32,17 +32,17 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testMasks() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseTestString() + " -mask foo -B:mask,VCF3 " + validationDataLocation + "vcfexample2.vcf -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("b0fcac4af3526e3b2a37602ab4c0e6ae"));
+                Arrays.asList("578f9e774784c25871678e6464fd212b"));
         executeTest("test mask all", spec1);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 baseTestString() + " -mask foo -B:mask,VCF " + validationDataLocation + "vcfMask.vcf -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("b64baabe905a5d197cc1ab594147d3d5"));
+                Arrays.asList("bfa86a674aefca1b13d341cb14ab3c4f"));
         executeTest("test mask some", spec2);
 
         WalkerTestSpec spec3 = new WalkerTestSpec(
                 baseTestString() + " -mask foo -maskExtend 10 -B:mask,VCF " + validationDataLocation + "vcfMask.vcf -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("0eff92fe72024d535c44b98e1e9e1993"));
+                Arrays.asList("5939f80d14b32d88587373532d7b90e5"));
         executeTest("test mask extend", spec3);
     }
 
@@ -50,7 +50,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("7a40795147cbfa92941489d7239aad92"));
+                Arrays.asList("45219dbcfb6f81bba2ea0c35f5bfd368"));
         executeTest("test filter #1", spec);
     }
 
@@ -58,7 +58,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilter2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("e9dd4991b1e325847c77d053dfe8ee54"));
+                Arrays.asList("c95845e817da7352b9b72bc9794f18fb"));
         executeTest("test filter #2", spec);
     }
 
@@ -66,7 +66,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testFilterWithSeparateNames() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --filterName ABF -filter 'AlleleBalance < 0.7' --filterName FSF -filter 'FisherStrand == 1.4' -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("9ded2cce63b8d97550079047051d80a3"));
+                Arrays.asList("b8cdd7f44ff1a395e0a9b06a87e1e530"));
         executeTest("test filter with separate names #2", spec);
     }
 
@@ -74,12 +74,12 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testGenotypeFilters() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("6696e3f65a62ce912230d47cdb0c129b"));
+                Arrays.asList("96b61e4543a73fe725e433f007260039"));
         executeTest("test genotype filter #1", spec1);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo -B:variant,VCF3 " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("26e5b4ee954c9e0b5eb044afd4b88ee9"));
+                Arrays.asList("6c8112ab17ce39c8022c891ae73bf38e"));
         executeTest("test genotype filter #2", spec2);
     }
 
@@ -87,7 +87,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testDeletions() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --filterExpression 'QUAL < 100' --filterName foo -B:variant,VCF " + validationDataLocation + "twoDeletions.vcf", 1,
-                Arrays.asList("e63b58be33c9126ad6cc55489aac539b"));
+                Arrays.asList("569546fd798afa0e65c5b61b440d07ac"));
         executeTest("test deletions", spec);
     }
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 20fa7719f..1f23d262e 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -28,7 +28,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot1() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
-                Arrays.asList("258e1954e6ae55c89abc6a716e19cbe0"));
+                Arrays.asList("c97829259463d04b0159591bb6fb44af"));
         executeTest("test MultiSample Pilot1", spec);
     }
 
@@ -54,12 +54,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testWithAllelesPassedIn() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("edeb1db288a24baff59575ceedd94243"));
+                Arrays.asList("2b69667f4770e8c0c894066b7f27e440"));
         executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("581990130d90071b084024f4cd7caf91"));
+                Arrays.asList("b77fe007c2a97fcd59dfd5eef94d8b95"));
         executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
     }
 
@@ -67,7 +67,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testSingleSamplePilot2() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
-                Arrays.asList("d120db27d694a6da32367cc4fb5770fa"));
+                Arrays.asList("ee8a5e63ddd470726a749e69c0c20f60"));
         executeTest("test SingleSample Pilot2", spec);
     }
 
@@ -77,7 +77,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     //
     // --------------------------------------------------------------------------------------------------------------
 
-    private final static String COMPRESSED_OUTPUT_MD5 = "75e5c430ed39f79f24e375037a388dc4";
+    private final static String COMPRESSED_OUTPUT_MD5 = "ef31654a2b85b9b2d3bba4f4a75a17b6";
 
     @Test
     public void testCompressedOutput() {
@@ -107,7 +107,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
         // Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
 
-        String md5 = "a29615dd37222a11b8dadd341b53e43c";
+        String md5 = "46868a9c4134651c54535fb46b408aee";
 
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
@@ -138,9 +138,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testCallingParameters() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "--min_base_quality_score 26", "93e6269e38db9bc1732555e9969e3648" );
-        e.put( "--min_mapping_quality_score 26", "64be99183c100caed4aa5f8bad64c7e9" );
-        e.put( "--p_nonref_model GRID_SEARCH", "0592fe33f705ad8e2f13619fcf157805" );
+        e.put( "--min_base_quality_score 26", "5043c9a101e691602eb7a3f9704bdf20" );
+        e.put( "--min_mapping_quality_score 26", "71a833eb8fd93ee62ae0d5a430f27940" );
+        e.put( "--p_nonref_model GRID_SEARCH", "ddf443e9dcadef367476b26b4d52c134" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -153,9 +153,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testOutputParameter() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "-sites_only", "1483e637dc0279935a7f90d136d147bb" );
-        e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "adcd91bc7dae8020df8caf1a30060e98" );
-        e.put( "--output_mode EMIT_ALL_SITES", "b708acc2fa40f336bcd2d0c70091e07e" );
+        e.put( "-sites_only", "eaad6ceb71ab94290650a70bea5ab951" );
+        e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "05bf7db8a3d19ef4a3d14772c90b732f" );
+        e.put( "--output_mode EMIT_ALL_SITES", "e4b86740468d7369f0156550855586c7" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -169,12 +169,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testConfidence() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
-                Arrays.asList("64be99183c100caed4aa5f8bad64c7e9"));
+                Arrays.asList("71a833eb8fd93ee62ae0d5a430f27940"));
         executeTest("test confidence 1", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
-                Arrays.asList("e76ca54232d02f0d92730e1affeb804e"));
+                Arrays.asList("79968844dc3ddecb97748c1acf2984c7"));
         executeTest("test confidence 2", spec2);
     }
 
@@ -186,8 +186,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testHeterozyosity() {
         HashMap<Double, String> e = new HashMap<Double, String>();
-        e.put( 0.01, "18d37f7f107853b5e32c757b4e143205" );
-        e.put( 1.0 / 1850, "2bcb90ce2f7542bf590f7612018fae8e" );
+        e.put( 0.01, "4e878664f61d2d800146d3762303fde1" );
+        e.put( 1.0 / 1850, "9204caec095ff5e63ca21a10b6fab453" );
 
         for ( Map.Entry<Double, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -211,7 +211,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("825f05b31b5bb7e82231a15c7e4e2b0d"));
+                Arrays.asList("1a58ec52df545f946f80cc16c5736a91"));
 
         executeTest(String.format("test multiple technologies"), spec);
     }
@@ -230,7 +230,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -L 1:10,000,000-10,100,000" +
                         " -baq CALCULATE_AS_NECESSARY",
                 1,
-                Arrays.asList("0919ab7e513c377610e23a67d33608fa"));
+                Arrays.asList("62d0f6d9de344ce68ce121c13b1e78b1"));
 
         executeTest(String.format("test calling with BAQ"), spec);
     }
@@ -244,7 +244,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -L 1:10,000,000-10,100,000" +
                         " -baq OFF",
                 1,
-                Arrays.asList("825f05b31b5bb7e82231a15c7e4e2b0d"));
+                Arrays.asList("1a58ec52df545f946f80cc16c5736a91"));
 
         executeTest(String.format("test calling with BAQ OFF"), spec);
     }
@@ -263,7 +263,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("cb37348c41b8181be829912730f747e1"));
+                Arrays.asList("631ae1f1eb6bc4c1a4136b8495250536"));
 
         executeTest(String.format("test indel caller in SLX"), spec);
     }
@@ -278,7 +278,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -minIndelCnt 1" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("ca5b6a5fb53ae401b146cc3044f454f2"));
+                Arrays.asList("fd556585c79e2b892a5976668f45aa43"));
 
         executeTest(String.format("test indel caller in SLX witn low min allele count"), spec);
     }
@@ -291,7 +291,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                          " -o %s" +
                          " -L 1:10,000,000-10,500,000",
                  1,
-                 Arrays.asList("ca4343a4ab6d3cce94ce61d7d1910f81"));
+                 Arrays.asList("9cd56feedd2787919e571383889fde70"));
 
          executeTest(String.format("test indel calling, multiple technologies"), spec);
      }
@@ -301,14 +301,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("3f555b53e9dd14cf7cdf96c24e322364"));
+                Arrays.asList("315e1b78d7a403d7fcbcf0caa8c496b8"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf "
                         + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("1b9764b783acf7822edc58e6822eef5b"));
+                Arrays.asList("cf89e0c54f14482a23c105b73a333d8a"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java
index 3f87fc1a2..c88eac149 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java
@@ -23,7 +23,7 @@ public class MergeMNPsIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 1)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("e312b7d3854d5b2834a370659514a813"));
+                Arrays.asList("7f11f7f75d1526077f0173c7ed1fc6c4"));
         executeTest("Merge MNP sites within genomic distance of 1 [TEST ONE]", spec);
     }
 
@@ -33,7 +33,7 @@ public class MergeMNPsIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 10)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("681f50e45f1d697370d2c355df2e18bc"));
+                Arrays.asList("53dd312468296826bdd3c22387390c88"));
         executeTest("Merge MNP sites within genomic distance of 10 [TEST TWO]", spec);
     }
 
@@ -43,7 +43,7 @@ public class MergeMNPsIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 100)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("0bccb0ef928a108418246bec01098083"));
+                Arrays.asList("e26f92d2fb9f4eaeac7f9d8ee27410ee"));
         executeTest("Merge MNP sites within genomic distance of 100 [TEST THREE]", spec);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java
index 009048c10..f855c1dd3 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java
@@ -23,7 +23,7 @@ public class MergeSegregatingAlternateAllelesIntegrationTest extends WalkerTest
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 1)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("e16f957d888054ae0518e25660295241"));
+                Arrays.asList("af5e1370822551c0c6f50f23447dc627"));
         executeTest("Merge sites within genomic distance of 1 [TEST ONE]", spec);
     }
 
@@ -33,7 +33,7 @@ public class MergeSegregatingAlternateAllelesIntegrationTest extends WalkerTest
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 10)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("122a482090677c7619c2105d44e00d11"));
+                Arrays.asList("dd8c44ae1ef059a7fe85399467e102eb"));
         executeTest("Merge sites within genomic distance of 10 [TEST TWO]", spec);
     }
 
@@ -43,7 +43,7 @@ public class MergeSegregatingAlternateAllelesIntegrationTest extends WalkerTest
                 baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 100)
                         + " -L chr20:556259-756570",
                 1,
-                Arrays.asList("bc6a8c8a42bb2601db98e88e9ad74748"));
+                Arrays.asList("f81fd72ecaa57b3215406fcea860bcc5"));
         executeTest("Merge sites within genomic distance of 100 [TEST THREE]", spec);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
index 0ed16967a..1bf3e579f 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
@@ -26,7 +26,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("6020a68bbec97fcd87819c10cd4e2470"));
+                Arrays.asList("9568ba0b6624b97ac55a59bdee2d9150"));
         executeTest("MAX 10 het sites [TEST ONE]; require PQ >= 10", spec);
     }
 
@@ -36,7 +36,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:1232503-1332503",
                 1,
-                Arrays.asList("712c2145df4756c9a15758865d8007b5"));
+                Arrays.asList("ce65194c24fe83b0ec90faa6c8e6109a"));
         executeTest("MAX 10 het sites [TEST TWO]; require PQ >= 10", spec);
     }
 
@@ -46,7 +46,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 2, 30)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("297e0896e4761529d979f40f5ad694db"));
+                Arrays.asList("02d134fd544613b1e5dd7f7197fc3753"));
         executeTest("MAX 2 het sites [TEST THREE]; require PQ >= 30", spec);
     }
 
@@ -56,7 +56,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 5, 100)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("52a17f14692d726d3b726cf0ae7f2a09"));
+                Arrays.asList("2f7ec9904fc054c2ba1a7db05eb29334"));
         executeTest("MAX 5 het sites [TEST FOUR]; require PQ >= 100", spec);
     }
 
@@ -66,7 +66,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 1000, 7, 10)
                         + " -L chr20:332341-482503",
                 1,
-                Arrays.asList("af768f7958b8f4599c2374f1cc2fc613"));
+                Arrays.asList("da7a31725f229d1782dd3049848730aa"));
         executeTest("MAX 7 het sites [TEST FIVE]; require PQ >= 10; cacheWindow = 1000", spec);
     }
 
@@ -76,7 +76,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:652810-681757",
                 1,
-                Arrays.asList("3dd886672f59a47908b94136d0427bb0"));
+                Arrays.asList("e9d35cb88089fb0e8ae6678bfaeeac8c"));
         executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index b0f76229b..129161da3 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -19,9 +19,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     public void testCountCovariates1() {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "7b5832d4b2a23b8ef2bb639eb59bfa88" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "f4f8a49bb5764d2a8f61e055f64dcce4");
+        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "9c006f8e9fb5752b1c139f5a8cc7ea88");
         e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "e6f7b4ab9aa291022e0ba8b7dbe4c77e" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "570506533f079d738d70934dfe1c02cd" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "e6b98af01c5a08e4954b79ec42db6fc3" );
 
         for ( String parallelism : Arrays.asList("", " -nt 4")) {
             for ( Map.Entry<String, String> entry : e.entrySet() ) {
@@ -53,9 +53,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     public void testTableRecalibrator1() {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0278cce4cfdab869dc0c11d6852a984b" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "344d4252143df8c2cce6b568747553a5");
+        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "6797d7ffa4ef6c48413719ba32696ccf");
         e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "2bb3374dde131791d7638031ae3b3e10" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "064c4a7bdd23974c3a9c5f924540df76" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "1f9d8944b73169b367cb83b0d22e5432" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -107,7 +107,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testTableRecalibratorMaxQ70() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "344d4252143df8c2cce6b568747553a5" );
+        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0278cce4cfdab869dc0c11d6852a984b" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -133,12 +133,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
-
-
     @Test
     public void testCountCovariatesSolidIndelsRemoveRefBias() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "0a6cdb9611e5880ea6611205080aa267" );
+        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "c9ea5f995e1e2b7a5688533e678dcedc" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -164,7 +162,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testTableRecalibratorSolidIndelsRemoveRefBias() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "9bc7e1ad223ba759fe5e8ddb4c07369c" );
+        e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "993fae4270e7e1e15986f270acf247af" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -189,13 +187,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
-
-
-
     @Test
     public void testCountCovariatesVCF() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "3700eaf567e4937f442fc777a226d6ad");
+        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "170f0c3cc4b8d72c539136effeec9a16");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -219,7 +214,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesBED() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "6803891a3398821fc8a37e19ea8e5a00");
+        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "b460478d9683e827784e42bc352db8bb");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -243,7 +238,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testCountCovariatesVCFPlusDBsnp() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "f224c42fbc4026db973ccc91265ab5c7");
+        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "a3d892bd60d8f679affda3c1e3af96c1");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -268,69 +263,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
-    @Test
-    public void testCountCovariatesNoReadGroups() {
-        HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "c024e03f019aeceaf364fa58c8295ad8" );
-
-        for ( Map.Entry<String, String> entry : e.entrySet() ) {
-            String bam = entry.getKey();
-            String md5 = entry.getValue();
-
-            WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-R " + b36KGReference +
-                            " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
-                            " -T CountCovariates" +
-                            " -I " + bam +
-                            " -L 1:10,000,000-10,200,000" +
-                            " -cov ReadGroupCovariate" +
-                            " -cov QualityScoreCovariate" +
-                            " -cov CycleCovariate" +
-                            " -cov DinucCovariate" +
-                            " --default_read_group DefaultReadGroup" +
-                            " --default_platform illumina" +
-                            " --solid_recal_mode SET_Q_ZERO" +
-                            " -recalFile %s",
-                    1, // just one output file
-                    Arrays.asList(md5));
-            List<File> result = executeTest("testCountCovariatesNoReadGroups", spec).getFirst();
-            paramsFilesNoReadGroupTest.put(bam, result.get(0).getAbsolutePath());
-        }
-    }
-
-    @Test
-    public void testTableRecalibratorNoReadGroups() {
-        HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "1eefbe7ac0376fc1ed1392d85242171e" );
-
-        for ( Map.Entry<String, String> entry : e.entrySet() ) {
-            String bam = entry.getKey();
-            String md5 = entry.getValue();
-            String paramsFile = paramsFilesNoReadGroupTest.get(bam);
-            System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile);
-            if ( paramsFile != null ) {
-                WalkerTestSpec spec = new WalkerTestSpec(
-                        "-R " + b36KGReference +
-                                " -T TableRecalibration" +
-                                " -I " + bam +
-                                " -L 1:10,100,000-10,300,000" +
-                                " -o %s" +
-                                " --no_pg_tag" +
-                                " --solid_recal_mode SET_Q_ZERO" +
-                                " --default_read_group DefaultReadGroup" +
-                                " --default_platform illumina" +
-                                " -recalFile " + paramsFile,
-                        1, // just one output file
-                        Arrays.asList(md5));
-                executeTest("testTableRecalibratorNoReadGroups", spec);
-            }
-        }
-    }
-
     @Test
     public void testCountCovariatesNoIndex() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "cfc31bb6f51436d1c3b34f62bb801dc8" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "284ccac1f8fe485e52c86333cac7c2d4" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -356,7 +292,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testTableRecalibratorNoIndex() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "83b848a16034c2fb423d1bb0f5be7784" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "c167799c2d9cab815d7c9b23337f162e" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -380,11 +316,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
         }
     }
 
-
     @Test
     public void testCountCovariatesFailWithoutDBSNP() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "");
+        e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "");
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index 9600046da..2fec2e70f 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -27,7 +27,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf",
             "d33212a84368e821cbedecd4f59756d6",  // tranches
             "4652dca41222bebdf9d9fda343b2a835",  // recal file
-            "5350b1a4c1250cf3b77ca45327c04711"); // cut VCF
+            "243a397a33a935fcaccd5deb6d16f0c0"); // cut VCF
 
     @DataProvider(name = "VRTest")
     public Object[][] createData1() {
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
index 33a20f7b5..fb18c6c33 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
@@ -34,76 +34,76 @@ import java.util.Arrays;
  * Tests CombineVariants
  */
 public class CombineVariantsIntegrationTest extends WalkerTest {
-//    public static String baseTestString(String args) {
-//        return "-T CombineVariants -NO_HEADER -L 1:1-50,000,000 -o %s -R " + b36KGReference + args;
-//    }
-//
-//    public void test1InOut(String file, String md5, boolean vcf3) {
-//        test1InOut(file, md5, "", vcf3);
-//    }
-//
-//    public void test1InOut(String file, String md5, String args, boolean vcf3) {
-//         WalkerTestSpec spec = new WalkerTestSpec(
-//                 baseTestString(" -priority v1 -B:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file + args),
-//                 1,
-//                 Arrays.asList(md5));
-//         executeTest("testInOut1--" + file, spec);
-//    }
-//
-//    public void combine2(String file1, String file2, String args, String md5, boolean vcf3) {
-//         WalkerTestSpec spec = new WalkerTestSpec(
-//                 baseTestString(" -priority v1,v2 -B:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file1 + " -B:v2,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file2 + args),
-//                 1,
-//                 Arrays.asList(md5));
-//         executeTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
-//    }
-//
-//    public void combineSites(String args, String md5) {
-//        String file1 = "1000G_omni2.5.b37.sites.vcf";
-//        String file2 = "hapmap_3.3.b37.sites.vcf";
-//        WalkerTestSpec spec = new WalkerTestSpec(
-//                "-T CombineVariants -NO_HEADER -o %s -R " + b37KGReference
-//                        + " -L 1:1-10,000,000 -B:omni,VCF " + validationDataLocation + file1
-//                        + " -B:hm3,VCF " + validationDataLocation + file2 + args,
-//                1,
-//                Arrays.asList(md5));
-//        executeTest("combineSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
-//    }
-//
-//
-//    @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2117fff6e0d182cd20be508e9661829c", true); }
-//    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "2cfaf7af3dd119df08b8a9c1f72e2f93", " -setKey foo", true); }
-//    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "1474ac0fde2ce42a3c24f1c97eab333e", " -setKey null", true); }
-//    @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "7fc66df048a0ab08cf507906e1d4a308", false); } // official project VCF files in tabix format
-//
-//    @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "ec9715f53dbf4531570557c212822f12", false); }
-//    @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "f1072be5f5c6ee810276d9ca6537224d", false); }
-//
-//    @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "b77a1eec725201d9d8e74ee0c45638d3", false); } // official project VCF files in tabix format
-//    @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "802977fdfd2f4905b501bb06800f60af", false); } // official project VCF files in tabix format
-//    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "a67157287dd2b24b5cdf7ebf8fcbbe9a", false); }
-//
-//    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e1f4718a179f1196538a33863da04f53", false); }
-//
-//    @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "b3783384b7c8e877b971033e90beba48", true); }
-//
-//    @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "902e541c87caa72134db6293fc46f0ad"); }
-//    @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "f339ad4bb5863b58b9c919ce7d040bb9"); }
-//
-//    @Test public void threeWayWithRefs() {
-//        WalkerTestSpec spec = new WalkerTestSpec(
-//                baseTestString(" -B:NA19240_BGI,VCF "+validationDataLocation+"NA19240.BGI.RG.vcf" +
-//                        " -B:NA19240_ILLUMINA,VCF "+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" +
-//                        " -B:NA19240_WUGSC,VCF "+validationDataLocation+"NA19240.WUGSC.RG.vcf" +
-//                        " -B:denovoInfo,VCF "+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" +
-//                        " -setKey centerSet" +
-//                        " -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED" +
-//                        " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
-//                        " -genotypeMergeOptions UNIQUIFY -L 1"),
-//                1,
-//                Arrays.asList("a07995587b855f3214fb71940bf23c0f"));
-//        executeTest("threeWayWithRefs", spec);
-//    }
+    public static String baseTestString(String args) {
+        return "-T CombineVariants -NO_HEADER -L 1:1-50,000,000 -o %s -R " + b36KGReference + args;
+    }
+
+    public void test1InOut(String file, String md5, boolean vcf3) {
+        test1InOut(file, md5, "", vcf3);
+    }
+
+    public void test1InOut(String file, String md5, String args, boolean vcf3) {
+         WalkerTestSpec spec = new WalkerTestSpec(
+                 baseTestString(" -priority v1 -B:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file + args),
+                 1,
+                 Arrays.asList(md5));
+         executeTest("testInOut1--" + file, spec);
+    }
+
+    public void combine2(String file1, String file2, String args, String md5, boolean vcf3) {
+         WalkerTestSpec spec = new WalkerTestSpec(
+                 baseTestString(" -priority v1,v2 -B:v1,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file1 + " -B:v2,VCF" + (vcf3 ? "3 " : " ") + validationDataLocation + file2 + args),
+                 1,
+                 Arrays.asList(md5));
+         executeTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
+    }
+
+    public void combineSites(String args, String md5) {
+        String file1 = "1000G_omni2.5.b37.sites.vcf";
+        String file2 = "hapmap_3.3.b37.sites.vcf";
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T CombineVariants -NO_HEADER -o %s -R " + b37KGReference
+                        + " -L 1:1-10,000,000 -B:omni,VCF " + validationDataLocation + file1
+                        + " -B:hm3,VCF " + validationDataLocation + file2 + args,
+                1,
+                Arrays.asList(md5));
+        executeTest("combineSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
+    }
+
+
+    @Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "c608b9fc1e36dba6cebb4f259883f9f0", true); }
+    @Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "20caad94411d6ab48153b214de916df8", " -setKey foo", true); }
+    @Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "004f3065cb1bc2ce2f9afd695caf0b48", " -setKey null", true); }
+    @Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "c9c901ff9ef2a982624b203a8086dff0", false); } // official project VCF files in tabix format
+
+    @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "7593be578d4274d672fc22fced38012b", false); }
+    @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "1cd467863c4e948fadd970681552d57e", false); }
+
+    @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "1d5a021387a8a86554db45a29f66140f", false); } // official project VCF files in tabix format
+    @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "20163d60f18a46496f6da744ab5cc0f9", false); } // official project VCF files in tabix format
+    @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "5b82f37df1f5ba40f0474d71c94142ec", false); }
+
+    @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "c58dca482bf97069eac6d9f1a07a2cba", false); }
+
+    @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "89f55abea8f59e39d1effb908440548c", true); }
+
+    @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "4836086891f6cbdd40eebef3076d215a"); }
+    @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "6a34b5d743efda8b2f3b639f3a2f5de8"); }
+
+    @Test public void threeWayWithRefs() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(" -B:NA19240_BGI,VCF "+validationDataLocation+"NA19240.BGI.RG.vcf" +
+                        " -B:NA19240_ILLUMINA,VCF "+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" +
+                        " -B:NA19240_WUGSC,VCF "+validationDataLocation+"NA19240.WUGSC.RG.vcf" +
+                        " -B:denovoInfo,VCF "+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" +
+                        " -setKey centerSet" +
+                        " -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED" +
+                        " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
+                        " -genotypeMergeOptions UNIQUIFY -L 1"),
+                1,
+                Arrays.asList("8b78339ccf7a5a5a837f79e88a3a38e5"));
+        executeTest("threeWayWithRefs", spec);
+    }
 
 
     // complex examples with filtering, indels, and multiple alleles
@@ -120,7 +120,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
     }
 
     @Test public void complexTestFull() { combineComplexSites("", "64b991fd3850f83614518f7d71f0532f"); }
-    @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "0db9ef50fe54b60426474273d7c7fa99"); }
-    @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "d20acb3d53ba0a02ce92d540ebeda2a9"); }
-    @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "8d1b3d120515f8b56b5a0d10bc5da713"); }
+    @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "df96cb3beb2dbb5e02f80abec7d3571e"); }
+    @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "f72a178137e25dbe0b931934cdc0079d"); }
+    @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "f704caeaaaed6711943014b847fe381a"); }
 }
\ No newline at end of file
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
index d32ab6282..82c894c6f 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
@@ -40,7 +40,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
-                 Arrays.asList("37e23efd7d6471fc0f807b31ccafe0eb"));
+                 Arrays.asList("70aeaca5b74cc7ba8e2da7b71ff0fbfd"));
          executeTest("test b36 to hg19", spec);
     }
 
@@ -49,7 +49,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LiftoverVariants -o %s -R " + b36KGReference + " -B:variant,vcf3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.unsortedSamples.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
-                 Arrays.asList("b6ef4a2f026fd3843aeb9ed764a66921"));
+                 Arrays.asList("3fd7ec2dc4064ef410786276b0dc9d08"));
          executeTest("test b36 to hg19, unsorted samples", spec);
     }
 
@@ -58,7 +58,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
          WalkerTestSpec spec = new WalkerTestSpec(
                  "-T LiftoverVariants -o %s -R " + hg18Reference + " -B:variant,vcf " + validationDataLocation + "liftover_test.vcf -chain " + validationDataLocation + "hg18ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
-                 Arrays.asList("3275373b3c44ad14a270b50664b3f8a3"));
+                 Arrays.asList("ab2c6254225d7e2ecf52eee604d5673b"));
          executeTest("test hg18 to hg19, unsorted", spec);
     }
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index e18287a21..b5f41542e 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -18,7 +18,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
             baseTestString(" -sn A -se '[CDH]' -sf " + samplesFile + " -env -ef -select 'DP < 250' -B:variant,VCF3 " + testfile + " -NO_HEADER"),
             1,
-            Arrays.asList("1b9d551298dc048c7d36b60440ff4d50")
+            Arrays.asList("d18516c1963802e92cb9e425c0b75fd6")
         );
 
         executeTest("testComplexSelection--" + testfile, spec);
@@ -31,7 +31,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -sn A -sn B -sn C -B:variant,VCF3 " + testfile + " -NO_HEADER"),
                 1,
-                Arrays.asList("5ba7536a0819421b330350a160e4261a")
+                Arrays.asList("b74038779fe6485dbb8734ae48178356")
         );
 
         executeTest("testRepeatedLineSelection--" + testfile, spec);
@@ -44,7 +44,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -disc myvar -L 20:1012700-1020000 -B:variant,VCF " + b37hapmapGenotypes + " -B:myvar,VCF " + testFile + " -o %s -NO_HEADER",
                 1,
-                Arrays.asList("97621ae8f29955eedfc4e0be3515fcb9")
+                Arrays.asList("78e6842325f1f1bc9ab30d5e7737ee6e")
         );
 
         executeTest("testDiscordance--" + testFile, spec);
@@ -57,7 +57,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + hg19Reference + " -sn NA12878 -conc hapmap -L 20:1012700-1020000 -B:hapmap,VCF " + b37hapmapGenotypes + " -B:variant,VCF " + testFile + " -o %s -NO_HEADER",
                 1,
-                Arrays.asList("a0ae016fdffcbe7bfb99fd3dbc311407")
+                Arrays.asList("d2ba3ea30a810f6f0fbfb1b643292b6a")
         );
 
         executeTest("testConcordance--" + testFile, spec);
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
index cf0673ee6..d7efe4212 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
@@ -60,7 +60,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
                     " --NO_HEADER" +
                     " -o %s",
             1,
-            Arrays.asList("debbbf3e661b6857cc8d99ff7635bb1d")
+            Arrays.asList("658f580f7a294fd334bd897102616fed")
         );
 
         executeTest("testSimpleVCFStreaming", spec);
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
index 64d0db14b..8c96c1e11 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
@@ -20,7 +20,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testVariantsToVCFUsingGeliInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("bd15d98adc76b5798e3bbeff3f936feb");
+        md5.add("4accae035d271b35ee2ec58f403c68c6");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -38,7 +38,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingGeliInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("acd15d3f85bff5b545bc353e0e23cc6e");
+        md5.add("71e8c98d7c3a73b6287ecc339086fe03");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -56,7 +56,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingHapMapInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("6f34528569f8cf5941cb365fa77288c1");
+        md5.add("f343085305e80c7a2493422e4eaad983");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
@@ -73,7 +73,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
     @Test
     public void testGenotypesToVCFUsingVCFInput() {
         List<String> md5 = new ArrayList<String>();
-        md5.add("d8316fc1b9d8e954a58940354119a32e");
+        md5.add("86f02e2e764ba35854cff2aa05a1fdd8");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-R " + b36KGReference +
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
index 2f6b589f4..68a2ecf8d 100755
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
@@ -4,6 +4,7 @@ import org.broad.tribble.Tribble;
 import org.broad.tribble.index.*;
 import org.broad.tribble.iterators.CloseableTribbleIterator;
 import org.broad.tribble.source.BasicFeatureSource;
+import org.broadinstitute.sting.WalkerTest;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.testng.Assert;
 import org.testng.annotations.Test;
@@ -75,7 +76,7 @@ public class IndexFactoryUnitTest {
 
             // test that the input index is the same as the one created from the identical input file
             // test that the dynamic index is the same as the output index, which is equal to the input index
-            Assert.assertTrue(IndexFactory.onDiskIndexEqualToNewlyCreatedIndex(outputFile, outputFileIndex, new VCFCodec()));
+            WalkerTest.assertOnDiskIndexEqualToNewlyCreatedIndex(outputFileIndex, "unittest", outputFile);
         }
     }
 }
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
new file mode 100644
index 000000000..32ff25c7b
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
@@ -0,0 +1,28 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.List;
+
+public class VCFIntegrationTest extends WalkerTest {
+
+    @Test
+    public void testReadingAndWritingWitHNoChanges() {
+
+        String md5ofInputVCF = "a990ba187a69ca44cb9bc2bb44d00447";
+        String testVCF = validationDataLocation + "vcf4.1.example.vcf";
+
+        String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s ";
+
+        String test1 = baseCommand + "-T VariantAnnotator -BTI variant -B:variant,vcf " + testVCF;
+        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList(md5ofInputVCF));
+        List<File> result = executeTest("Test Variant Annotator with no changes", spec1).getFirst();
+
+        String test2 = baseCommand + "-T VariantsToVCF -B:variant,vcf " + result.get(0).getAbsolutePath();
+        WalkerTestSpec spec2 = new WalkerTestSpec(test2, 1, Arrays.asList(md5ofInputVCF));
+        executeTest("Test Variants To VCF from new output", spec2);
+    }
+}
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
index 5d42f8d0c..a344817a0 100755
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
@@ -49,7 +49,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
 
         WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -B:vcf,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s",
                 2, // just one output file
-                Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "e6673737acbb6bfabfcd92c4b2268241"));
+                Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "ff91731213fd0bbdc200ab6fd1c93e63"));
          executeTest("testToVCF", spec);
     }
 
diff --git a/public/packages/AnalyzeCovariates.xml b/public/packages/AnalyzeCovariates.xml
index 1862d6cbb..7e31934df 100644
--- a/public/packages/AnalyzeCovariates.xml
+++ b/public/packages/AnalyzeCovariates.xml
@@ -10,7 +10,6 @@
       <class name="org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate" />
       <class name="org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate" />
       <class name="org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate" />
-      <class name="org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate" />
     </dependencies>
   </executable>
   <resources>
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
index f9369ee3f..6a47d4b97 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -3,14 +3,15 @@ package org.broadinstitute.sting.queue.qscripts
 import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.function.ListWriterFunction
-
-import scala.io.Source._
-import collection.JavaConversions._
-import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
 import org.broadinstitute.sting.queue.extensions.picard._
-import net.sf.samtools.{SAMFileReader, SAMReadGroupRecord}
+import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
+import org.broadinstitute.sting.utils.baq.BAQ.CalculationMode
+
+import collection.JavaConversions._
+import net.sf.samtools.SAMFileReader
 import net.sf.samtools.SAMFileHeader.SortOrder
 
+import org.broadinstitute.sting.queue.util.QScriptUtils
 
 class DataProcessingPipeline extends QScript {
   qscript =>
@@ -29,7 +30,8 @@ class DataProcessingPipeline extends QScript {
   @Input(doc="Reference fasta file", fullName="reference", shortName="R", required=true)
   var reference: File = _
 
-
+  @Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=true)
+  var dbSNP: File = _
 
   /****************************************************************************
   * Optional Parameters
@@ -39,14 +41,12 @@ class DataProcessingPipeline extends QScript {
 //  @Input(doc="path to Picard's SortSam.jar (if re-aligning a previously processed BAM file)", fullName="path_to_sort_jar", shortName="sort", required=false)
 //  var sortSamJar: File = _
 //
-  @Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
-  var bwaPath: File = _
-
-  @Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=false)
-  var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
 
   @Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false)
-  var indels: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf")
+  var indels: File = _
+
+  @Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
+  var bwaPath: File = _
 
   @Input(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", fullName="project", shortName="p", required=false)
   var projectName: String = "project"
@@ -103,18 +103,6 @@ class DataProcessingPipeline extends QScript {
                    val ds: String)
   {}
 
-  // Utility function to check if there are multiple samples in a BAM file (currently we can't deal with that)
-  def hasMultipleSamples(readGroups: java.util.List[SAMReadGroupRecord]): Boolean = {
-    var sample: String = ""
-    for (r <- readGroups) {
-      if (sample.isEmpty)
-        sample = r.getSample
-      else if (sample != r.getSample)
-          return true;
-    }
-    return false
-  }
-
   // Utility function to merge all bam files of similar samples. Generates one BAM file per sample.
   // It uses the sample information on the header of the input BAM files.
   //
@@ -135,7 +123,7 @@ class DataProcessingPipeline extends QScript {
 
       // only allow one sample per file. Bam files with multiple samples would require pre-processing of the file
       // with PrintReads to separate the samples. Tell user to do it himself!
-      assert(!hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
+      assert(!QScriptUtils.hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
 
       // Fill out the sample table with the readgroups in this file
       for (rg <- readGroups) {
@@ -147,20 +135,23 @@ class DataProcessingPipeline extends QScript {
       }
     }
 
+    println("\n\n*** DEBUG ***\n")
     // Creating one file for each sample in the dataset
     val sampleBamFiles = scala.collection.mutable.Map.empty[String, File]
     for ((sample, flist) <- sampleTable) {
+
+      println(sample + ":")
+      for (f <- flist)
+        println (f)
+      println()
+
       val sampleFileName = new File(qscript.outputDir + qscript.projectName + "." + sample + ".bam")
       sampleBamFiles(sample) = sampleFileName
       add(joinBams(flist, sampleFileName))
     }
-    return sampleBamFiles.toMap
-  }
+    println("*** DEBUG ***\n\n")
 
-  // Checks how many contigs are in the dataset. Uses the BAM file header information.
-  def getNumberOfContigs(bamFile: File): Int = {
-    val samReader = new SAMFileReader(new File(bamFile))
-    return samReader.getFileHeader.getSequenceDictionary.getSequences.size()
+    return sampleBamFiles.toMap
   }
 
   // Rebuilds the Read Group string to give BWA
@@ -206,17 +197,6 @@ class DataProcessingPipeline extends QScript {
     return realignedBams
   }
 
-  // Reads a BAM LIST file and creates a scala list with all the files
-  def createListFromFile(in: File):List[File] = {
-    if (in.toString.endsWith("bam"))
-      return List(in)
-    var l: List[File] = List()
-    for (bam <- fromFile(in).getLines)
-      l :+= new File(bam)
-    return l
-  }
-
-
 
   /****************************************************************************
   * Main script
@@ -226,17 +206,14 @@ class DataProcessingPipeline extends QScript {
   def script = {
 
     // keep a record of the number of contigs in the first bam file in the list
-    val bams = createListFromFile(input)
-    nContigs = getNumberOfContigs(bams(0))
+    val bams = QScriptUtils.createListFromFile(input)
+    nContigs = QScriptUtils.getNumberOfContigs(bams(0))
 
     val realignedBams = if (useBWApe || useBWAse) {performAlignment(bams)} else {bams}
 
     // Generate a BAM file per sample joining all per lane files if necessary
     val sampleBamFiles: Map[String, File] = createSampleFiles(bams, realignedBams)
 
-
-    println("nContigs: " + nContigs)
-
     // Final output list of processed bam files
     var cohortList: List[File] = List()
 
@@ -244,6 +221,7 @@ class DataProcessingPipeline extends QScript {
     println("\nFound the following samples: ")
     for ((sample, file) <- sampleBamFiles)
       println("\t" + sample + " -> " + file)
+    println("\n")
 
     // If this is a 'knowns only' indel realignment run, do it only once for all samples.
     val globalIntervals = new File(outputDir + projectName + ".intervals")
@@ -310,7 +288,8 @@ class DataProcessingPipeline extends QScript {
     this.out = outIntervals
     this.mismatchFraction = 0.0
     this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
-    this.rodBind :+= RodBind("indels", "VCF", indels)
+    if (!indels.isEmpty)
+      this.rodBind :+= RodBind("indels", "VCF", indels)
     this.scatterCount = nContigs
     this.analysisName = queueLogDir + outIntervals + ".target"
     this.jobName = queueLogDir + outIntervals + ".target"
@@ -321,7 +300,8 @@ class DataProcessingPipeline extends QScript {
     this.targetIntervals = tIntervals
     this.out = outBam
     this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
-    this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
+    if (!indels.isEmpty)
+      this.rodBind :+= RodBind("indels", "VCF", indels)
     this.consensusDeterminationModel =  consensusDeterminationModel
     this.compress = 0
     this.scatterCount = nContigs
@@ -344,7 +324,7 @@ class DataProcessingPipeline extends QScript {
   case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
     this.input_file :+= inBam
     this.recal_file = inRecalFile
-    this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY
+    this.baq = CalculationMode.CALCULATE_AS_NECESSARY
     this.out = outBam
     if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
     else if (qscript.intervals != null) this.intervals :+= qscript.intervals
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
index 51de3a7ad..fca420816 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.queue.qscripts
 
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk._
-import net.sf.samtools.SAMFileReader
+import org.broadinstitute.sting.queue.util.QScriptUtils
 
 /**
  * Created by IntelliJ IDEA.
@@ -32,26 +32,25 @@ class RecalibrateBaseQualities extends QScript {
   val queueLogDir: String = ".qlog/"
   var nContigs: Int = 0
 
-  def getNumberOfContigs(bamFile: File): Int = {
-    val samReader = new SAMFileReader(new File(bamFile))
-    return samReader.getFileHeader.getSequenceDictionary.getSequences.size()
-  }
-
   def script = {
 
-    nContigs = getNumberOfContigs(input)
+    val bamList = QScriptUtils.createListFromFile(input)
+    nContigs = QScriptUtils.getNumberOfContigs(bamList(0))
 
-    val recalFile1: File = swapExt(input, ".bam", "recal1.csv")
-    val recalFile2: File = swapExt(input, ".bam", "recal2.csv")
-    val recalBam: File   = swapExt(input, ".bam", "recal.bam")
-    val path1: String    = "before"
-    val path2: String    = "after"
-    
-    add(cov(input, recalFile1),
-        recal(input, recalFile1, recalBam),
-        cov(recalBam, recalFile2),
-        analyzeCovariates(recalFile1, path1),
-        analyzeCovariates(recalFile2, path2))
+    for (bam <- bamList) {
+
+      val recalFile1: File = swapExt(bam, ".bam", ".recal1.csv")
+      val recalFile2: File = swapExt(bam, ".bam", ".recal2.csv")
+      val recalBam: File   = swapExt(bam, ".bam", ".recal.bam")
+      val path1: String    = bam + ".before"
+      val path2: String    = bam + ".after"
+
+      add(cov(bam, recalFile1),
+          recal(bam, recalFile1, recalBam),
+          cov(recalBam, recalFile2),
+          analyzeCovariates(recalFile1, path1),
+          analyzeCovariates(recalFile2, path2))
+    }
   }
 
   trait CommandLineGATKArgs extends CommandLineGATK {
@@ -84,7 +83,7 @@ class RecalibrateBaseQualities extends QScript {
   case class analyzeCovariates (inRecalFile: File, outPath: String) extends AnalyzeCovariates {
     this.resources = R
     this.recal_file = inRecalFile
-    this.output_dir = outPath.toString
+    this.output_dir = outPath
     this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
     this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
   }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
index bfcc4d48c..8ed3f84c1 100755
--- a/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
@@ -138,30 +138,32 @@ class QGraph extends Logging {
     validate()
 
     if (running && numMissingValues == 0) {
-      logger.info("Generating scatter gather jobs.")
       val scatterGathers = jobGraph.edgeSet.filter(edge => scatterGatherable(edge))
+      if (!scatterGathers.isEmpty) {
+        logger.info("Generating scatter gather jobs.")
 
-      var addedFunctions = List.empty[QFunction]
-      for (scatterGather <- scatterGathers) {
-        val functions = scatterGather.asInstanceOf[FunctionEdge]
-                .function.asInstanceOf[ScatterGatherableFunction]
-                .generateFunctions()
-        addedFunctions ++= functions
+        var addedFunctions = List.empty[QFunction]
+        for (scatterGather <- scatterGathers) {
+          val functions = scatterGather.asInstanceOf[FunctionEdge]
+                  .function.asInstanceOf[ScatterGatherableFunction]
+                  .generateFunctions()
+          addedFunctions ++= functions
+        }
+
+        logger.info("Removing original jobs.")
+        this.jobGraph.removeAllEdges(scatterGathers)
+        prune()
+
+        logger.info("Adding scatter gather jobs.")
+        addedFunctions.foreach(function => if (running) this.add(function))
+
+        logger.info("Regenerating graph.")
+        fill
+        val scatterGatherDotFile = if (settings.expandedDotFile != null) settings.expandedDotFile else settings.dotFile
+        if (scatterGatherDotFile != null)
+          renderToDot(scatterGatherDotFile)
+        validate()
       }
-
-      logger.info("Removing original jobs.")
-      this.jobGraph.removeAllEdges(scatterGathers)
-      prune()
-
-      logger.info("Adding scatter gather jobs.")
-      addedFunctions.foreach(function => if (running) this.add(function))
-
-      logger.info("Regenerating graph.")
-      fill
-      val scatterGatherDotFile = if (settings.expandedDotFile != null) settings.expandedDotFile else settings.dotFile
-      if (scatterGatherDotFile != null)
-        renderToDot(scatterGatherDotFile)
-      validate()
     }
   }
 
diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala b/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
index 57d133dfe..ac2f036b4 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
@@ -286,11 +286,11 @@ object Lsf706JobRunner extends Logging {
     // LSB_SHAREDIR/cluster_name/logdir/lsb.acct (man bacct)
     // LSB_SHAREDIR/cluster_name/logdir/lsb.events (man bhist)
     logger.debug("Job Id %s status / exitStatus / exitInfo: ??? / ??? / ???".format(runner.jobId))
-    val unknownStatusSeconds = (System.currentTimeMillis - runner.lastStatusUpdate)
-    if (unknownStatusSeconds > (unknownStatusMaxSeconds * 1000L)) {
+    val unknownStatusMillis = (System.currentTimeMillis - runner.lastStatusUpdate)
+    if (unknownStatusMillis > (unknownStatusMaxSeconds * 1000L)) {
       // Unknown status has been returned for a while now.
       runner.updateStatus(RunnerStatus.FAILED)
-      logger.error("Unable to read LSF status for %d minutes: job id %d: %s".format(unknownStatusSeconds/60, runner.jobId, runner.function.description))
+      logger.error("Unable to read LSF status for %0.2f minutes: job id %d: %s".format(unknownStatusMillis/(60 * 1000D), runner.jobId, runner.function.description))
     }
   }
 
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
new file mode 100644
index 000000000..99aaa9474
--- /dev/null
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
@@ -0,0 +1,60 @@
+package org.broadinstitute.sting.queue.util
+
+import java.io.File
+import io.Source._
+import net.sf.samtools.{SAMReadGroupRecord, SAMFileReader}
+
+import collection.JavaConversions._
+
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: carneiro
+ * Date: 7/14/11
+ * Time: 4:57 PM
+ * To change this template use File | Settings | File Templates.
+ */
+
+object QScriptUtils {
+
+  /**
+   * Takes a bam list file and produces a scala list with each file allowing the bam list
+   * to have empty lines and comment lines (lines starting with #).
+   */
+  def createListFromFile(in: File):List[File] = {
+    // If the file provided ends with .bam, it is not a bam list, we treat it as a single file.
+    // and return a list with only this file.
+    if (in.toString.endsWith(".bam"))
+      return List(in)
+
+    var list: List[File] = List()
+    for (bam <- fromFile(in).getLines)
+      if (!bam.startsWith("#") && !bam.isEmpty )
+        list :+= new File(bam.trim())
+    list.sortWith(_.compareTo(_) < 0)
+  }
+
+  /**
+   * Returns the number of contigs in the BAM file header.
+   */
+  def getNumberOfContigs(bamFile: File): Int = {
+    val samReader = new SAMFileReader(bamFile)
+    samReader.getFileHeader.getSequenceDictionary.getSequences.size()
+  }
+
+  /**
+   * Check if there are multiple samples in a BAM file
+   */
+  def hasMultipleSamples(readGroups: java.util.List[SAMReadGroupRecord]): Boolean = {
+    var sample: String = ""
+    for (r <- readGroups) {
+      if (sample.isEmpty)
+        sample = r.getSample
+      else if (sample != r.getSample)
+          return true;
+    }
+    false
+  }
+
+
+}
\ No newline at end of file
diff --git a/public/testdata/diffTestMaster.vcf b/public/testdata/diffTestMaster.vcf
new file mode 100644
index 000000000..549f54345
--- /dev/null
+++ b/public/testdata/diffTestMaster.vcf
@@ -0,0 +1,11 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	
+chr1	2646	rs62635284	G	A	0.15	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:53,75:3:-12.40,-0.90,-0.00:9.03
+chr1	2979	rs62635286	T	G	83.67	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:31,32:9:-33.61,-2.71,-0.00:27.09
+chr1	2981	rs62028691	A	G	14.69	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:31,33:9:-32.12,-2.71,-0.00:27.08
+chr1	4536	rs11582131	G	C	0.18	PASS	AC=1;AF=0.50;AN=2	GT:AD:DP:GL:GQ	0/1:42,33:16:-41.67,-4.82,-26.29:99
+chr1	4562	rs11490464	C	G	0.14	PASS	AC=1;AF=0.50;AN=2	GT:AD:DP:GL:GQ	0/1:26,30:9:-19.64,-2.72,-14.87:99
+chr1	4770	rs6682375	A	G	0.32	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:9,111:84:-306.27,-28.58,-3.46:99
+chr1	4793	rs6682385	A	G	0.15	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:4,115:109:-350.74,-32.88,-0.10:99
+chr1	5074	rs11586607	T	G	0.01	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:29,97:39:-130.41,-11.75,-3.82:79.31
+chr1	5137	rs62636497	A	T	140.49	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:0,74:39:-148.99,-11.75,-0.01:99
diff --git a/public/testdata/diffTestTest.vcf b/public/testdata/diffTestTest.vcf
new file mode 100644
index 000000000..8699ab253
--- /dev/null
+++ b/public/testdata/diffTestTest.vcf
@@ -0,0 +1,11 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	
+chr1	2646	rs62635284	G	A	0.15	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:53,75:3:-12.40,-0.90,-0.00:9.03
+chr1	2979	rs62635286	T	G	83.67	CHANGED_FILTER	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:31,32:9:-33.61,-2.71,-0.00:27.09
+chr1	2981	rs62028691	A	G	14.69	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:31,33:9:-32.12,-2.71,-0.00:27.08
+chr1	4536	rs11582131	G	C	0.18	PASS	AC=2;AF=0.50;AN=2	GT:AD:DP:GL:GQ	0/1:42,33:16:-41.67,-4.82,-26.29:99
+chr1	4562	rs11490464	C	G	0.14	PASS	AC=1;AF=0.50;AN=2	GT:AD:DP:GL:GQ	1/1:26,30:9:-19.64,-2.72,-14.87:99
+chr1	4770	rs6682375	A	G	0.32	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	0/1:9,111:84:-306.27,-28.58,-3.46:99
+chr1	4793	rs6682385	A	G	0.15	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:4,114:109:-350.74,-32.88,-0.10:99
+chr1	5074	rs11586607	T	G	0.01	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:29,97:39:-130.41,-11.74,-3.82:79.31
+chr1	5137	rs62636497	A	T	140.49	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:0,74:39:-148.99,-11.75,-0.01:9
diff --git a/settings/ivysettings.xml b/settings/ivysettings.xml
index 2c8fc388f..2b4a081d4 100644
--- a/settings/ivysettings.xml
+++ b/settings/ivysettings.xml
@@ -26,5 +26,6 @@
     <module organisation="net.java.dev.jna" resolver="maven2-repository.dev.java.net" />
     <module organisation="com.google.code.caliper" resolver="projects" />
     <module organisation="net.sf.gridscheduler" resolver="projects" />
+    <module organisation="com.google.code.cofoja" resolver="projects" />
   </modules>
 </ivysettings>
diff --git a/settings/repository/com.google/cofoja-1.0-20110609.jar b/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar
similarity index 100%
rename from settings/repository/com.google/cofoja-1.0-20110609.jar
rename to settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar
diff --git a/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml b/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml
new file mode 100644
index 000000000..38d4e88f1
--- /dev/null
+++ b/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="com.google.code.cofoja" module="cofoja" revision="1.0-20110609" status="integration" publication="20110609114800" />
+</ivy-module>
diff --git a/settings/repository/org.broad/tribble-3.jar b/settings/repository/org.broad/tribble-16.jar
similarity index 67%
rename from settings/repository/org.broad/tribble-3.jar
rename to settings/repository/org.broad/tribble-16.jar
index f0ab44a05..331f28ec3 100644
Binary files a/settings/repository/org.broad/tribble-3.jar and b/settings/repository/org.broad/tribble-16.jar differ
diff --git a/settings/repository/org.broad/tribble-3.xml b/settings/repository/org.broad/tribble-16.xml
similarity index 57%
rename from settings/repository/org.broad/tribble-3.xml
rename to settings/repository/org.broad/tribble-16.xml
index c35358331..e23eec339 100644
--- a/settings/repository/org.broad/tribble-3.xml
+++ b/settings/repository/org.broad/tribble-16.xml
@@ -1,4 +1,4 @@
 <ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="3" 
+    <info organisation="org.broad" module="tribble" revision="15" 
           status="integration" publication="" />
 </ivy-module>