diff --git a/build.xml b/build.xml
index 068c69316..fe4c7a3f4 100644
--- a/build.xml
+++ b/build.xml
@@ -780,6 +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">
@@ -814,6 +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                             ********* -->
     <!-- ***************************************************************************** -->
diff --git a/public/java/src/org/broadinstitute/sting/alignment/Aligner.java b/public/java/src/org/broadinstitute/sting/alignment/Aligner.java
index 9ffe5f857..4bf05cb75 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/Aligner.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/Aligner.java
@@ -1,10 +1,7 @@
 package org.broadinstitute.sting.alignment;
 
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
-
-import java.util.List;
-import java.util.Iterator;
+import net.sf.samtools.SAMRecord;
 
 /**
  * Create perfect alignments from the read to the genome represented by the given BWT / suffix array. 
diff --git a/public/java/src/org/broadinstitute/sting/alignment/Alignment.java b/public/java/src/org/broadinstitute/sting/alignment/Alignment.java
index ebbc8c1b8..c63f5615f 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/Alignment.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/Alignment.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.alignment;
 
 import net.sf.samtools.*;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 /**
  * Represents an alignment of a read to a site in the reference genome.
diff --git a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
index 16e713bf6..c6755e878 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
@@ -25,16 +25,16 @@
 
 package org.broadinstitute.sting.alignment;
 
-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.BaseUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
-import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
+import org.broadinstitute.sting.commandline.Argument;
+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.utils.BaseUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.Iterator;
 
diff --git a/public/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java b/public/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
index e97d7a56f..7064e637f 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
@@ -25,21 +25,22 @@
 
 package org.broadinstitute.sting.alignment;
 
-import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.walkers.WalkerName;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
+import net.sf.picard.reference.ReferenceSequenceFileFactory;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMSequenceDictionary;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
-import net.sf.samtools.*;
-import net.sf.picard.reference.ReferenceSequenceFileFactory;
+import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
+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;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.WalkerName;
 
 import java.io.File;
-import java.io.PrintStream;
 
 /**
  * Aligns reads to a given reference using Heng Li's BWA aligner, presenting the resulting alignments in SAM or BAM format.
diff --git a/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java b/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
index 1a1e1197d..57d92319f 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
@@ -25,18 +25,21 @@
 
 package org.broadinstitute.sting.alignment;
 
-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.alignment.bwa.BWTFiles;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
+import org.broadinstitute.sting.alignment.bwa.BWTFiles;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
-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 java.util.*;
 import java.io.PrintStream;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
 
 /**
  * Counts the number of best alignments as presented by BWA and outputs a histogram of number of placements vs. the
diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java b/public/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java
index cd7800900..a0589ac84 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java
@@ -1,21 +1,15 @@
 package org.broadinstitute.sting.alignment.bwa;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
-import org.broadinstitute.sting.alignment.reference.bwt.BWT;
-import org.broadinstitute.sting.alignment.reference.bwt.BWTWriter;
-import org.broadinstitute.sting.alignment.reference.bwt.SuffixArray;
-import org.broadinstitute.sting.alignment.reference.bwt.SuffixArrayWriter;
-import org.broadinstitute.sting.alignment.reference.bwt.ANNWriter;
-import org.broadinstitute.sting.alignment.reference.bwt.AMBWriter;
-
-import java.io.File;
-import java.io.IOException;
-
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
 import net.sf.samtools.util.StringUtil;
+import org.broadinstitute.sting.alignment.reference.bwt.*;
+import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+import java.io.File;
+import java.io.IOException;
 
 /**
  * Support files for BWT.
diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java b/public/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
index 8631c42d8..165314259 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
@@ -1,14 +1,15 @@
 package org.broadinstitute.sting.alignment.bwa.c;
 
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.alignment.Alignment;
+import org.broadinstitute.sting.alignment.bwa.BWAAligner;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
-import org.broadinstitute.sting.alignment.bwa.BWAAligner;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.Iterator;
 
 /**
  * An aligner using the BWA/C implementation.
diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
index ae6e22221..2d568a96a 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
@@ -1,16 +1,15 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.samtools.*;
 import org.broadinstitute.sting.alignment.Aligner;
 import org.broadinstitute.sting.alignment.Alignment;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 import java.io.FileNotFoundException;
 
-import net.sf.samtools.*;
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-
 /**
  * A test harness to ensure that the perfect aligner works.
  *
diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java
index 879ecb5fb..f1e3c31b6 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java
@@ -1,14 +1,13 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-
-import java.util.Deque;
-import java.util.ArrayDeque;
-import java.util.Iterator;
-
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+import java.util.ArrayDeque;
+import java.util.Deque;
+import java.util.Iterator;
 
 /**
  * Represents a sequence of matches.
diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java
index c59546bbb..f3b515dba 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
+import net.sf.samtools.Cigar;
 import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import net.sf.samtools.Cigar;
 
 /**
  * An alignment object to be used incrementally as the BWA aligner
diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java
index 81186c53e..fbeac9192 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java
@@ -1,17 +1,18 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
-import org.broadinstitute.sting.alignment.reference.bwt.*;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.alignment.bwa.BWAAligner;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
-import org.broadinstitute.sting.alignment.Alignment;
+import org.broadinstitute.sting.alignment.reference.bwt.*;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 
 import java.io.File;
-import java.util.*;
-
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMFileHeader;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.PriorityQueue;
 
 /**
  * Create imperfect alignments from the read to the genome represented by the given BWT / suffix array. 
diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java
index 3784643c0..be7514255 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java
@@ -1,10 +1,10 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
-import java.util.List;
-import java.util.ArrayList;
-
 import org.broadinstitute.sting.alignment.reference.bwt.BWT;
 
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * At any point along the given read, what is a good lower bound for the
  * total number of differences?
diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java
index 1d97fec79..ec10415dd 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java
@@ -3,10 +3,10 @@ package org.broadinstitute.sting.alignment.reference.bwt;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
 
-import java.io.PrintStream;
 import java.io.File;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.io.PrintStream;
 
 /**
  * Writes .amb files - a file indicating where 'holes' (indeterminant bases)
diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java
index 17296c31c..8d692a9e7 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java
@@ -3,10 +3,10 @@ package org.broadinstitute.sting.alignment.reference.bwt;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
 
-import java.io.PrintStream;
 import java.io.File;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.io.PrintStream;
 
 /**
  * Writes .ann files - an alternate sequence dictionary format
diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java
index 64a595419..5c4f6d39d 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java
@@ -1,11 +1,14 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.BasePackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
+import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.io.*;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.nio.ByteOrder;
 /**
  * Reads a BWT from a given file.
diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java
index f24baf766..3370f79c8 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import net.sf.picard.reference.ReferenceSequenceFileFactory;
 import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.picard.reference.ReferenceSequenceFileFactory;
 import net.sf.samtools.SAMSequenceDictionary;
 
 import java.io.File;
diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java
index b3867ebfe..a813cdc9a 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
 import org.broadinstitute.sting.alignment.reference.packing.BasePackedOutputStream;
+import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.*;
 import java.nio.ByteOrder;
diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
index 92bb713f0..801ab3a0b 100755
--- a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
@@ -25,14 +25,14 @@
 
 package org.broadinstitute.sting.alignment.reference.bwt;
 
+import net.sf.picard.reference.ReferenceSequence;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFileFactory;
-import net.sf.picard.reference.ReferenceSequence;
-
-import java.io.*;
-
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+import java.io.File;
+import java.io.IOException;
 
 /**
  * Create a suffix array data structure.
diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
index dba3633d1..49af98bb9 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
@@ -1,12 +1,11 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
+import net.sf.samtools.util.StringUtil;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.Comparator;
 import java.util.TreeSet;
 
-import net.sf.samtools.util.StringUtil;
-
 /**
  * An in-memory representation of a suffix array.
  *
diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java
index c10984145..b48e4c69c 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java
@@ -1,10 +1,13 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
+import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.io.*;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.nio.ByteOrder;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java
index 972fc2a15..b6f79be2f 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.*;
 import java.nio.ByteOrder;
diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java b/public/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
index 6681e37ec..174a9853b 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
@@ -2,9 +2,12 @@ package org.broadinstitute.sting.alignment.reference.packing;
 
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
-import java.io.*;
-import java.nio.ByteOrder;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
 import java.nio.channels.FileChannel;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java b/public/java/src/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java
index 8211c97d8..561535e29 100755
--- a/public/java/src/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java
@@ -25,12 +25,12 @@
 
 package org.broadinstitute.sting.alignment.reference.packing;
 
+import net.sf.picard.reference.ReferenceSequence;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFileFactory;
-import net.sf.picard.reference.ReferenceSequence;
 
-import java.io.*;
-import java.nio.ByteOrder;
+import java.io.File;
+import java.io.IOException;
 
 /**
  * Generate a .PAC file from a given reference.
diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java b/public/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java
index beed21b49..972e31cf0 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java
@@ -3,9 +3,9 @@ package org.broadinstitute.sting.alignment.reference.packing;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.OutputStream;
-import java.io.FileOutputStream;
 import java.nio.ByteOrder;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedInputStream.java b/public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedInputStream.java
index c07766ee1..999e54451 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedInputStream.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedInputStream.java
@@ -1,6 +1,8 @@
 package org.broadinstitute.sting.alignment.reference.packing;
 
-import java.io.*;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.nio.channels.FileChannel;
diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedOutputStream.java b/public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedOutputStream.java
index 9d7853695..b02024366 100755
--- a/public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedOutputStream.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedOutputStream.java
@@ -25,7 +25,10 @@
 
 package org.broadinstitute.sting.alignment.reference.packing;
 
-import java.io.*;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 
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/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java
index cecbedda8..1afec36d1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableReadFilter.java
@@ -24,7 +24,6 @@
 
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.picard.util.QualityUtil;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.QualityUtils;
 
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
index 6f0a712bf..ab1ac59d8 100755
--- 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
index 4b4ebe450..ca73ee960 100755
--- 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
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/report/GATKReport.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
index f4c565318..59d496828 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
@@ -100,7 +100,11 @@ public class GATKReport {
      * @param tableDescription  the description of the table
      */
     public void addTable(String tableName, String tableDescription) {
-        GATKReportTable table = new GATKReportTable(tableName, tableDescription);
+        addTable(tableName, tableDescription, true);
+    }
+
+    public void addTable(String tableName, String tableDescription, boolean sortByPrimaryKey) {
+        GATKReportTable table = new GATKReportTable(tableName, tableDescription, sortByPrimaryKey);
         tables.put(tableName, table);
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
index 0e503f92a..f7ea25696 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
@@ -3,9 +3,7 @@ package org.broadinstitute.sting.gatk.report;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.PrintStream;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.TreeSet;
+import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -96,8 +94,9 @@ public class GATKReportTable {
     private String tableDescription;
 
     private String primaryKeyName;
-    private TreeSet<Object> primaryKeyColumn;
+    private Collection<Object> primaryKeyColumn;
     private boolean primaryKeyDisplay;
+    boolean sortByPrimaryKey = true;
 
     private LinkedHashMap<String, GATKReportColumn> columns;
 
@@ -121,12 +120,17 @@ public class GATKReportTable {
      * @param tableDescription  the description of the table
      */
     public GATKReportTable(String tableName, String tableDescription) {
-        if (!isValidName(tableName)) {
+        this(tableName, tableDescription, true);
+    }
+
+    public GATKReportTable(String tableName, String tableDescription, boolean sortByPrimaryKey) {
+         if (!isValidName(tableName)) {
             throw new ReviewedStingException("Attempted to set a GATKReportTable name of '" + tableName + "'.  GATKReportTable names must be purely alphanumeric - no spaces or special characters are allowed.");
         }
 
         this.tableName = tableName;
         this.tableDescription = tableDescription;
+        this.sortByPrimaryKey = sortByPrimaryKey;
 
         columns = new LinkedHashMap<String, GATKReportColumn>();
     }
@@ -137,20 +141,14 @@ public class GATKReportTable {
      * @param primaryKeyName  the name of the primary key column
      */
     public void addPrimaryKey(String primaryKeyName) {
-        if (!isValidName(primaryKeyName)) {
-            throw new ReviewedStingException("Attempted to set a GATKReportTable primary key name of '" + primaryKeyName + "'.  GATKReportTable primary key names must be purely alphanumeric - no spaces or special characters are allowed.");
-        }
-
-        this.primaryKeyName = primaryKeyName;
-
-        primaryKeyColumn = new TreeSet<Object>();
-        primaryKeyDisplay = true;
+        addPrimaryKey(primaryKeyName, true);
     }
 
     /**
      * Add an optionally visible primary key column.  This becomes the unique identifier for every column in the table, and will always be printed as the first column.
      *
      * @param primaryKeyName  the name of the primary key column
+     * @param display should this primary key be displayed?
      */
     public void addPrimaryKey(String primaryKeyName, boolean display) {
         if (!isValidName(primaryKeyName)) {
@@ -159,7 +157,7 @@ public class GATKReportTable {
 
         this.primaryKeyName = primaryKeyName;
 
-        primaryKeyColumn = new TreeSet<Object>();
+        primaryKeyColumn = sortByPrimaryKey ? new TreeSet<Object>() : new LinkedList<Object>();
         primaryKeyDisplay = display;
     }
 
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..57ea5166a 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 +28,18 @@ 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.utils.SampleUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 
-import java.io.PrintStream;
+import java.io.File;
+import java.util.Collection;
+import java.util.Set;
+import java.util.TreeSet;
 
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 /**
  * 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
@@ -54,6 +58,13 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
     String platform = null; // E.g. ILLUMINA, 454
     @Argument(fullName = "number", shortName = "n", doc="Print the first n reads from the file, discarding the rest", required = false)
     int nReadsToPrint = -1;
+    @Argument(fullName="sample_file", shortName="sf", doc="File containing a list of samples (one per line). Can be specified multiple times", required=false)
+    public Set<File> sampleFiles;
+    @Argument(fullName="sample_name", shortName="sn", doc="Sample name to be included in the analysis. Can be specified multiple times.", required=false)
+    public Set<String> sampleNames;
+
+    private TreeSet<String> samplesToChoose = new TreeSet<String>();
+    private boolean NO_SAMPLES_SPECIFIED = false;
 
     /**
      * The initialize function.
@@ -61,6 +72,17 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
     public void initialize() {
         if  ( platform != null )
             platform = platform.toUpperCase();
+
+        Collection<String> samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles);
+        samplesToChoose.addAll(samplesFromFile);
+
+        if (sampleNames != null)
+            samplesToChoose.addAll(sampleNames);
+
+        if(samplesToChoose.isEmpty()) {
+            NO_SAMPLES_SPECIFIED = true;
+        }
+
     }
 
     /**
@@ -87,6 +109,22 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
             if ( readPlatformAttr == null || !readPlatformAttr.toString().toUpperCase().contains(platform))
                 return false;
         }
+        if (!NO_SAMPLES_SPECIFIED )  {
+            // user specified samples to select
+            String readSample = read.getReadGroup().getSample();
+            boolean  found = false;
+            for (String sampleSelected : samplesToChoose) {
+                if (readSample.equalsIgnoreCase(sampleSelected)) {
+                    found = true;
+                    break;
+                }
+
+            }
+
+            if (!found)
+                return false;
+        }
+
 
         // check if we've reached the output limit
         if ( nReadsToPrint == 0 ) {
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 51d290763..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.*;
 
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 f3ec2b1df..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
@@ -25,18 +25,22 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
-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 {
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 ee66b50ee..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
@@ -1,21 +1,20 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
-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;
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..2fd62ddf3 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.*;
 
@@ -24,11 +24,27 @@ public class IndelType implements InfoFieldAnnotation, ExperimentalAnnotation {
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
 
          int run;
-        if ( vc.isIndel() && vc.isBiallelic() ) {
+        if (vc.isMixed()) {
+            Map<String, Object> map = new HashMap<String, Object>();
+            map.put(getKeyNames().get(0), String.format("%s", "MIXED"));
+            return map;
+
+        }
+        else if ( vc.isIndel() ) {
             String type="";
-            ArrayList<Integer> inds = IndelUtils.findEventClassificationIndex(vc, ref);
-            for (int k : inds) {
-                type = type+ IndelUtils.getIndelClassificationName(k)+".";
+            if (!vc.isBiallelic())
+                type = "MULTIALLELIC_INDEL";
+            else {
+                if (vc.isInsertion())
+                    type = "INS.";
+                else if (vc.isDeletion())
+                    type = "DEL.";
+                else
+                    type = "OTHER.";
+                ArrayList<Integer> inds = IndelUtils.findEventClassificationIndex(vc, ref);
+                for (int k : inds) {
+                    type = type+ IndelUtils.getIndelClassificationName(k)+".";
+                }
             }
             Map<String, Object> map = new HashMap<String, Object>();
             map.put(getKeyNames().get(0), String.format("%s", type));
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 8260a5a81..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
@@ -1,17 +1,17 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
 import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 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 {
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 3b64abfff..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;
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 1ef7ccd0b..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
@@ -1,20 +1,23 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.QualityUtils;
-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 {
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 f00abd6a1..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;
 
 
 
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 a670532af..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
@@ -26,25 +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.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.pileup.ReadBackedPileup;
+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.
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 e2fd2a3d4..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
@@ -25,15 +25,15 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
-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;
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
index a5ebf27bb..a1c043365 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
@@ -24,22 +24,13 @@
 
 package org.broadinstitute.sting.gatk.walkers.diffengine;
 
-import net.sf.samtools.*;
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMRecordIterator;
 import net.sf.samtools.util.BlockCompressedInputStream;
-import org.broad.tribble.readers.AsciiLineReader;
-import org.broad.tribble.readers.LineReader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.io.DataInputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
+import java.io.*;
 import java.util.Arrays;
-import java.util.Map;
-import java.util.zip.GZIPInputStream;
 
 
 /**
@@ -109,8 +100,10 @@ public class BAMDiffableReader implements DiffableReader {
         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);
+            InputStream fstream = new BufferedInputStream(new FileInputStream(file));
+            if ( !BlockCompressedInputStream.isValidFile(fstream) )
+                return false;
+            new BlockCompressedInputStream(fstream).read(buffer, 0, BAM_MAGIC.length);
             return Arrays.equals(buffer, BAM_MAGIC);
         } catch ( IOException 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
index 4c3f7bd95..eb8a71c2c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
@@ -24,7 +24,9 @@
 
 package org.broadinstitute.sting.gatk.walkers.diffengine;
 
-import com.google.java.contract.*;
+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;
 
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
index 6d85df71d..89e20dad1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
@@ -58,7 +58,7 @@ public class DiffEngine {
     //
     // --------------------------------------------------------------------------------
 
-    public List<SpecificDifference> diff(DiffElement master, DiffElement test) {
+    public List<Difference> diff(DiffElement master, DiffElement test) {
         DiffValue masterValue = master.getValue();
         DiffValue testValue = test.getValue();
 
@@ -68,14 +68,14 @@ public class DiffEngine {
             return diff(masterValue, testValue);
         } else {
             // structural difference in types.  one is node, other is leaf
-            return Arrays.asList(new SpecificDifference(master, test));
+            return Arrays.asList(new Difference(master, test));
         }
     }
 
-    public List<SpecificDifference> diff(DiffNode master, DiffNode test) {
+    public List<Difference> diff(DiffNode master, DiffNode test) {
         Set<String> allNames = new HashSet<String>(master.getElementNames());
         allNames.addAll(test.getElementNames());
-        List<SpecificDifference> diffs = new ArrayList<SpecificDifference>();
+        List<Difference> diffs = new ArrayList<Difference>();
 
         for ( String name : allNames ) {
             DiffElement masterElt = master.getElement(name);
@@ -84,7 +84,7 @@ public class DiffEngine {
                 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));
+                diffs.add(new Difference(masterElt, testElt));
             } else {
                 diffs.addAll(diff(masterElt, testElt));
             }
@@ -93,11 +93,11 @@ public class DiffEngine {
         return diffs;
     }
 
-    public List<SpecificDifference> diff(DiffValue master, DiffValue test) {
+    public List<Difference> diff(DiffValue master, DiffValue test) {
         if ( master.getValue().equals(test.getValue()) ) {
             return Collections.emptyList();
         } else {
-            return Arrays.asList(new SpecificDifference(master.getBinding(), test.getBinding()));
+            return Arrays.asList(new Difference(master.getBinding(), test.getBinding()));
         }
     }
 
@@ -143,13 +143,13 @@ public class DiffEngine {
      * Not that only pairs of the same length are considered as potentially equivalent
      *
      * @param params determines how we display the items
-     * @param diffs
+     * @param diffs the list of differences to summarize
      */
-    public void reportSummarizedDifferences(List<SpecificDifference> diffs, SummaryReportParams params ) {
+    public void reportSummarizedDifferences(List<Difference> diffs, SummaryReportParams params ) {
         printSummaryReport(summarizeDifferences(diffs), params );
     }
 
-    public List<Difference> summarizeDifferences(List<SpecificDifference> diffs) {
+    public List<Difference> summarizeDifferences(List<Difference> diffs) {
         return summarizedDifferencesOfPaths(diffs);
     }
 
@@ -177,8 +177,12 @@ public class DiffEngine {
                 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);
+                    String path = diffPath2.getPath();
+                    if ( lcp != 0 && lcp != diffPath1.length() )
+                        path = summarizedPath(diffPath2.getParts(), lcp);
+                    Difference sumDiff = new Difference(path, diffPath2.getMaster(), diffPath2.getTest());
+                    sumDiff.setCount(0);
+                    addSummaryIfMissing(summaries, sumDiff);
                 }
             }
         }
@@ -187,7 +191,7 @@ public class DiffEngine {
         for ( Difference diffPath : singletonDiffs ) {
             for ( Difference sumDiff : summaries.values() ) {
                 if ( sumDiff.matches(diffPath.getParts()) )
-                    addSummary(summaries, sumDiff.getPath(), false);
+                    sumDiff.incCount();
             }
         }
 
@@ -196,24 +200,14 @@ public class DiffEngine {
         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 addSummaryIfMissing(Map<String, Difference> summaries, Difference diff) {
+        if ( ! summaries.containsKey(diff.getPath()) ) {
+            summaries.put(diff.getPath(), diff);
         }
     }
 
     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/DiffObjectsWalker_and_SummarizedDifferences for more information");
-        GATKReportTable table = report.getTable(tableName);
-        table.addPrimaryKey("Difference", true);
-        table.addColumn("NumberOfOccurrences", 0);
-
+        List<Difference> toShow = new ArrayList<Difference>();
         int count = 0, count1 = 0;
         for ( Difference diff : sortedSummaries ) {
             if ( diff.getCount() < params.minSumDiffToShow )
@@ -229,9 +223,26 @@ public class DiffEngine {
                     break;
             }
 
-            table.set(diff.getPath(), "NumberOfOccurrences", diff.getCount());
+            toShow.add(diff);
         }
 
+        // if we want it in descending order, reverse the list
+        if ( ! params.descending ) {
+            Collections.reverse(toShow);
+        }
+
+        // now that we have a specific list of values we want to show, display them
+        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", false);
+        GATKReportTable table = report.getTable(tableName);
+        table.addPrimaryKey("Difference", true);
+        table.addColumn("NumberOfOccurrences", 0);
+        table.addColumn("ExampleDifference", 0);
+        for ( Difference diff : toShow ) {
+            table.set(diff.getPath(), "NumberOfOccurrences", diff.getCount());
+            table.set(diff.getPath(), "ExampleDifference", diff.valueDiffString());
+        }
         table.write(params.out);
     }
 
@@ -250,7 +261,7 @@ public class DiffEngine {
      * commonPostfixLength: how many parts are shared at the end, suppose its 2
      * We want to create a string *.*.C.D
      *
-     * @param parts
+     * @param parts the separated path values [above without .]
      * @param commonPostfixLength
      * @return
      */
@@ -336,7 +347,7 @@ public class 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);
+            List<Difference> diffs = diffEngine.diff(master, test);
             diffEngine.reportSummarizedDifferences(diffs, params);
             return true;
         } else {
@@ -349,6 +360,7 @@ public class DiffEngine {
         int maxItemsToDisplay = 0;
         int maxCountOneItems = 0;
         int minSumDiffToShow = 0;
+        boolean descending = true;
 
         public SummaryReportParams(PrintStream out, int maxItemsToDisplay, int maxCountOneItems, int minSumDiffToShow) {
             this.out = out;
@@ -356,5 +368,9 @@ public class DiffEngine {
             this.maxCountOneItems = maxCountOneItems;
             this.minSumDiffToShow = minSumDiffToShow;
         }
+
+        public void setDescending(boolean descending) {
+            this.descending = descending;
+        }
     }
 }
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
index ecb836af9..fba6549fb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
@@ -104,14 +104,15 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
 //        out.printf("Test diff objects%n");
 //        out.println(test.toString());
 
-        List<SpecificDifference> diffs = diffEngine.diff(master, test);
+        List<Difference> diffs = diffEngine.diff(master, test);
         if ( showItemizedDifferences ) {
             out.printf("Itemized results%n");
-            for ( SpecificDifference diff : diffs )
+            for ( Difference diff : diffs )
                 out.printf("DIFF: %s%n", diff.toString());
         }
 
         DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out, MAX_DIFFS, MAX_COUNT1_DIFFS, minCountForDiff);
+        params.setDescending(false);
         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
index 3750496a1..963191446 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
@@ -24,8 +24,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.diffengine;
 
-import org.broadinstitute.sting.utils.Utils;
-
 /**
  * Created by IntelliJ IDEA.
  * User: depristo
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
index af5771c55..a117206f1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
@@ -39,12 +39,27 @@ import java.io.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
index efc6ef160..81b6f7e0e 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
@@ -27,13 +27,24 @@ 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;
+    int count = 1;
+    DiffElement master = null , test = null;
 
     public Difference(String path) {
         this.path = path;
         this.parts = DiffEngine.diffNameToPath(path);
     }
 
+    public Difference(DiffElement master, DiffElement test) {
+        this(createPath(master, test), master, test);
+    }
+
+    public Difference(String path, DiffElement master, DiffElement test) {
+        this(path);
+        this.master = master;
+        this.test = test;
+    }
+
     public String[] getParts() {
         return parts;
     }
@@ -44,6 +55,10 @@ public class Difference implements Comparable<Difference> {
         return count;
     }
 
+    public void setCount(int count) {
+        this.count = count;
+    }
+
     /**
      * The fully qualified path object A.B.C etc
      * @return
@@ -81,7 +96,7 @@ public class Difference implements Comparable<Difference> {
 
     @Override
     public String toString() {
-        return String.format("%s:%d", getPath(), getCount());
+        return String.format("%s:%d:%s", getPath(), getCount(), valueDiffString());
     }
 
     @Override
@@ -91,5 +106,31 @@ public class Difference implements Comparable<Difference> {
         return countCmp != 0 ? -1 * countCmp : path.compareTo(other.path);
     }
 
+    public String valueDiffString() {
+        if ( hasSpecificDifference() ) {
+            return String.format("%s!=%s", getOneLineString(master), getOneLineString(test));
+        } else {
+            return "N/A";
+        }
+    }
 
+    private static String createPath(DiffElement master, DiffElement test) {
+        return (master == null ? test : master).fullyQualifiedName();
+    }
+
+    private static String getOneLineString(DiffElement elt) {
+        return elt == null ? "MISSING" : elt.getValue().toOneLineString();
+    }
+
+    public boolean hasSpecificDifference() {
+        return master != null || test != null;
+    }
+
+    public DiffElement getMaster() {
+        return master;
+    }
+
+    public DiffElement getTest() {
+        return test;
+    }
 }
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
deleted file mode 100644
index 2fe9b47f8..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/SpecificDifference.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * 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
index 06d14366f..77a992ce0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
@@ -26,16 +26,15 @@ 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.VCFCodec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.io.*;
-import java.util.Arrays;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
 import java.util.Map;
-import java.util.zip.GZIPInputStream;
 
 
 /**
@@ -54,20 +53,38 @@ public class VCFDiffableReader implements DiffableReader {
     public DiffElement readFromFile(File file, int maxElementsToRead) {
         DiffNode root = DiffNode.rooted(file.getName());
         try {
+            // read the version line from the file
             LineReader lineReader = new AsciiLineReader(new FileInputStream(file));
+            final String version = lineReader.readLine();
+            root.add("VERSION", version);
+            lineReader.close();
+
+            lineReader = new AsciiLineReader(new FileInputStream(file));
             VCFCodec vcfCodec = new VCFCodec();
 
             // must be read as state is stored in reader itself
-            vcfCodec.readHeader(lineReader);
+            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;
+            int count = 0, nRecordsAtPos = 1;
+            String prevName = "";
             while ( line != null ) {
                 if ( count++ > maxElementsToRead && maxElementsToRead != -1)
                     break;
 
                 VariantContext vc = (VariantContext)vcfCodec.decode(line);
                 String name = vc.getChr() + ":" + vc.getStart();
+                if ( name.equals(prevName) ) {
+                    name += "_" + ++nRecordsAtPos;
+                } else {
+                    prevName = name;
+                }
                 DiffNode vcRoot = DiffNode.empty(name, root);
 
                 // add fields
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 fc8a5819a..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.gatk.filters.MappingQualityUnavailableReadFilter;
-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.*;
 
-import java.util.*;
 import java.io.PrintStream;
+import java.util.*;
 
 
 /**
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 6fc972b5d..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.*;
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 df1f4f908..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
@@ -1,11 +1,13 @@
 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;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.*;
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 3b94989aa..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
@@ -25,27 +25,27 @@
 
 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.MappingQualityZeroReadFilter;
 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.
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 1f05ddaf0..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.*;
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/MergeAndMatchHaplotypes.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java
new file mode 100644
index 000000000..298d8d6c8
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java
@@ -0,0 +1,110 @@
+package org.broadinstitute.sting.gatk.walkers.phasing;
+
+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.SampleUtils;
+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.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.*;
+
+/**
+ * Merges read-back-phased and phase-by-transmission files.
+ */
+public class MergeAndMatchHaplotypes extends RodWalker<Integer, Integer> {
+    @Output
+    protected VCFWriter vcfWriter = null;
+
+    private Map<String, Genotype> pbtCache = new HashMap<String, Genotype>();
+    private Map<String, Genotype> rbpCache = new HashMap<String, Genotype>();
+
+    private final String SOURCE_NAME = "MergeReadBackedAndTransmissionPhasedVariants";
+
+    public void initialize() {
+        ArrayList<String> rodNames = new ArrayList<String>();
+        rodNames.add("pbt");
+
+        Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
+        Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
+        Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
+        headerLines.addAll(VCFUtils.getHeaderFields(this.getToolkit()));
+
+        vcfWriter.writeHeader(new VCFHeader(headerLines, vcfSamples));
+    }
+
+    @Override
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if (tracker != null) {
+            Collection<VariantContext> pbts = tracker.getVariantContexts(ref, "pbt", null, ref.getLocus(), true, true);
+            Collection<VariantContext> rbps = tracker.getVariantContexts(ref, "rbp", null, ref.getLocus(), true, true);
+
+            VariantContext pbt = pbts.iterator().hasNext() ? pbts.iterator().next() : null;
+            VariantContext rbp = rbps.iterator().hasNext() ? rbps.iterator().next() : null;
+
+            if (pbt != null && rbp != null) {
+                Map<String, Genotype> genotypes = pbt.getGenotypes();
+
+                if (!rbp.isFiltered()) {
+                    for (String sample : rbp.getSampleNames()) {
+                        Genotype rbpg = rbp.getGenotype(sample);
+                        Genotype pbtg = pbt.getGenotype(sample);
+
+                        // Propagate read-backed phasing information to genotypes unphased by transmission
+                        //if (!pbtg.isPhased() && rbpCache.containsKey(sample)) {
+                        if (!pbtg.isPhased() && rbpg.isPhased() && rbpCache.containsKey(sample)) {
+                            boolean orientationMatches = rbpCache.get(sample).sameGenotype(pbtCache.get(sample), false);
+
+                            if (orientationMatches) {
+                                pbtg = rbpg;
+                            } else {
+                                List<Allele> fwdAlleles = rbpg.getAlleles();
+                                List<Allele> revAlleles = new ArrayList<Allele>();
+
+                                for (int i = fwdAlleles.size() - 1; i >= 0; i--) {
+                                    revAlleles.add(fwdAlleles.get(i));
+                                }
+
+                                pbtg = new Genotype(sample, revAlleles, rbpg.getNegLog10PError(), rbpg.getFilters(), rbpg.getAttributes(), rbpg.isPhased());
+                            }
+                        }
+
+                        genotypes.put(sample, pbtg);
+
+                        // Update the cache
+                        if (/*rbpg.isPhased() &&*/ rbpg.isHet()) {
+                            rbpCache.put(sample, rbpg);
+                            pbtCache.put(sample, pbtg);
+                        } else if (!rbpg.isPhased()) {
+                            rbpCache.remove(sample);
+                            pbtCache.remove(sample);
+                        }
+                    }
+                }
+
+                VariantContext newvc = new VariantContext(SOURCE_NAME, pbt.getChr(), pbt.getStart(), pbt.getStart(), pbt.getAlleles(), genotypes, pbt.getNegLog10PError(), pbt.getFilters(), pbt.getAttributes());
+                vcfWriter.add(newvc, ref.getBase());
+            }
+        }
+
+        return null;
+    }
+
+    @Override
+    public Integer reduceInit() {
+        return null;
+    }
+
+    @Override
+    public Integer reduce(Integer value, Integer sum) {
+        return null;
+    }
+}
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/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
new file mode 100755
index 000000000..b24437c4a
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
@@ -0,0 +1,320 @@
+package org.broadinstitute.sting.gatk.walkers.phasing;
+
+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.MathUtils;
+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.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.*;
+
+/**
+ * Phases a trio VCF (child phased by transmission, implied phase carried over to parents).  Given genotypes for a trio,
+ * this walker modifies the genotypes (if necessary) to reflect the most likely configuration given the genotype
+ * likelihoods and inheritance constraints, phases child by transmission and carries over implied phase to the parents
+ * (their alleles in their genotypes are ordered as transmitted|untransmitted).  Computes probability that the
+ * determined phase is correct given that the genotype configuration is correct (useful if you want to use this to
+ * compare phasing accuracy, but want to break that comparison down by phasing confidence in the truth set).  Optionally
+ * filters out sites where the phasing is indeterminate (site has no-calls), ambiguous (everyone is heterozygous), or
+ * the genotypes exhibit a Mendelian violation.  This walker assumes there are only three samples in the VCF file to
+ * begin.
+ */
+public class PhaseByTransmission extends RodWalker<Integer, Integer> {
+    @Argument(shortName="f", fullName="familyPattern", required=true, doc="Pattern for the family structure (usage: mom+dad=child)")
+    public String familyStr = null;
+
+    @Argument(shortName="nofilters", fullName="disableFilters", required=false, doc="Disable filters for sites where the phase can't be determined, where the parental origin of the alleles is ambiguous (i.e. everyone is heterozygous), or Mendelian violations")
+    public Boolean noFilters = false;
+
+    @Output
+    protected VCFWriter vcfWriter = null;
+
+    private String SAMPLE_NAME_MOM;
+    private String SAMPLE_NAME_DAD;
+    private String SAMPLE_NAME_CHILD;
+
+    private final String ROD_NAME = "variant";
+    private final String AMBIGUOUS_ALLELE_ORIGIN_FILTER_NAME = "AmbiguousAlleleOrigin";
+    private final String INSUFFICIENT_DATA_FILTER_NAME = "InsufficientInformation";
+    private final String MENDELIAN_VIOLATION_FILTER_NAME = "MendelianViolation";
+    private final String TRANSMISSION_PROBABILITY_TAG_NAME = "TP";
+    private final String SOURCE_NAME = "PhaseByTransmission";
+
+    private final Double MENDELIAN_VIOLATION_PRIOR = 1e-8;
+
+    /**
+     * Parse the familial relationship specification, and initialize VCF writer
+     */
+    public void initialize() {
+        String[] pieces = familyStr.split("[\\+\\=]");
+
+        SAMPLE_NAME_MOM = pieces[0];
+        SAMPLE_NAME_DAD = pieces[1];
+        SAMPLE_NAME_CHILD = pieces[2];
+
+        ArrayList<String> rodNames = new ArrayList<String>();
+        rodNames.add(ROD_NAME);
+
+        Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
+        Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
+
+        if (vcfSamples.size() != 3) {
+            throw new UserException("File to phase by transmission contains more than three samples.  This walker only" +
+                                    "accepts VCFs with three samples, so that the meaning of the applied filters is" +
+                                    "unambiguous.");
+        }
+
+        if (!vcfSamples.contains(SAMPLE_NAME_MOM) || !vcfSamples.contains(SAMPLE_NAME_DAD) || !vcfSamples.contains(SAMPLE_NAME_CHILD)) {
+            throw new UserException("One or more of the samples specified in the familyPattern argument is not present" +
+                                    "in this file.  Please supply a VCF file that contains only three samples: the" +
+                                    "mother, the father, and the child");
+        }
+
+        Set<String> samples = new TreeSet<String>();
+        samples.add(SAMPLE_NAME_MOM);
+        samples.add(SAMPLE_NAME_DAD);
+        samples.add(SAMPLE_NAME_CHILD);
+
+        Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
+        headerLines.addAll(VCFUtils.getHeaderFields(this.getToolkit()));
+
+        if (!noFilters) {
+            headerLines.add(new VCFFilterHeaderLine(AMBIGUOUS_ALLELE_ORIGIN_FILTER_NAME, "The parental origin of each of the child's allele cannot be determined (ie everyone is heterozygous)"));
+            headerLines.add(new VCFFilterHeaderLine(INSUFFICIENT_DATA_FILTER_NAME, "The phase of the child's genotype cannot be determined (ie someone is a no-call)"));
+            headerLines.add(new VCFFilterHeaderLine(MENDELIAN_VIOLATION_FILTER_NAME, "No combination of the parents' alleles can yield the child's genotype (ie a possible Mendelian violation)"));
+        }
+
+        headerLines.add(new VCFInfoHeaderLine(TRANSMISSION_PROBABILITY_TAG_NAME, 1, VCFHeaderLineType.Float, "Probability that the phase is correct given that the genotypes are correct"));
+        vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
+    }
+
+    private double computeTransmissionLikelihoodOfGenotypeConfiguration(Genotype mom, Genotype dad, Genotype child) {
+        double[] momLikelihoods = MathUtils.normalizeFromLog10(mom.getLikelihoods().getAsVector());
+        double[] dadLikelihoods = MathUtils.normalizeFromLog10(dad.getLikelihoods().getAsVector());
+        double[] childLikelihoods = MathUtils.normalizeFromLog10(child.getLikelihoods().getAsVector());
+
+        int momIndex = mom.getType().ordinal() - 1;
+        int dadIndex = dad.getType().ordinal() - 1;
+        int childIndex = child.getType().ordinal() - 1;
+
+        return momLikelihoods[momIndex]*dadLikelihoods[dadIndex]*childLikelihoods[childIndex];
+    }
+
+    private ArrayList<Genotype> createAllThreeGenotypes(Allele refAllele, Allele altAllele, Genotype g) {
+        List<Allele> homRefAlleles = new ArrayList<Allele>();
+        homRefAlleles.add(refAllele);
+        homRefAlleles.add(refAllele);
+        Genotype homRef = new Genotype(g.getSampleName(), homRefAlleles, g.getNegLog10PError(), null, g.getAttributes(), false);
+
+        List<Allele> hetAlleles = new ArrayList<Allele>();
+        hetAlleles.add(refAllele);
+        hetAlleles.add(altAllele);
+        Genotype het = new Genotype(g.getSampleName(), hetAlleles, g.getNegLog10PError(), null, g.getAttributes(), false);
+
+        List<Allele> homVarAlleles = new ArrayList<Allele>();
+        homVarAlleles.add(altAllele);
+        homVarAlleles.add(altAllele);
+        Genotype homVar = new Genotype(g.getSampleName(), homVarAlleles, g.getNegLog10PError(), null, g.getAttributes(), false);
+
+        ArrayList<Genotype> genotypes = new ArrayList<Genotype>();
+        genotypes.add(homRef);
+        genotypes.add(het);
+        genotypes.add(homVar);
+
+        return genotypes;
+    }
+
+    private int getNumberOfMatchingAlleles(Allele alleleToMatch, Genotype g) {
+        List<Allele> alleles = g.getAlleles();
+        int matchingAlleles = 0;
+
+        for (Allele a : alleles) {
+            if (!alleleToMatch.equals(a)) {
+                matchingAlleles++;
+            }
+        }
+
+        return matchingAlleles;
+    }
+
+    private boolean isMendelianViolation(Allele refAllele, Allele altAllele, Genotype mom, Genotype dad, Genotype child) {
+        int numMomRefAlleles = getNumberOfMatchingAlleles(refAllele, mom) > 0 ? 1 : 0;
+        int numMomAltAlleles = getNumberOfMatchingAlleles(altAllele, mom) > 0 ? 1 : 0;
+
+        int numDadRefAlleles = getNumberOfMatchingAlleles(refAllele, dad) > 0 ? 1 : 0;
+        int numDadAltAlleles = getNumberOfMatchingAlleles(altAllele, dad) > 0 ? 1 : 0;
+
+        int numChildRefAlleles = getNumberOfMatchingAlleles(refAllele, child);
+        int numChildAltAlleles = getNumberOfMatchingAlleles(altAllele, child);
+
+        return (numMomRefAlleles + numDadRefAlleles < numChildRefAlleles || numMomAltAlleles + numDadAltAlleles < numChildAltAlleles);
+    }
+
+    private ArrayList<Genotype> getPhasedGenotypes(Genotype mom, Genotype dad, Genotype child) {
+        Set<Genotype> possiblePhasedChildGenotypes = new HashSet<Genotype>();
+
+        for (Allele momAllele : mom.getAlleles()) {
+            for (Allele dadAllele : dad.getAlleles()) {
+                ArrayList<Allele> possiblePhasedChildAlleles = new ArrayList<Allele>();
+                possiblePhasedChildAlleles.add(momAllele);
+                possiblePhasedChildAlleles.add(dadAllele);
+
+                Genotype possiblePhasedChildGenotype = new Genotype(child.getSampleName(), possiblePhasedChildAlleles, child.getNegLog10PError(), child.getFilters(), child.getAttributes(), true);
+
+                possiblePhasedChildGenotypes.add(possiblePhasedChildGenotype);
+            }
+        }
+
+        ArrayList<Genotype> finalGenotypes = new ArrayList<Genotype>();
+
+        for (Genotype phasedChildGenotype : possiblePhasedChildGenotypes) {
+            if (child.sameGenotype(phasedChildGenotype, true)) {
+                Allele momTransmittedAllele = phasedChildGenotype.getAllele(0);
+                Allele momUntransmittedAllele = mom.getAllele(0) != momTransmittedAllele ? mom.getAllele(0) : mom.getAllele(1);
+
+                ArrayList<Allele> phasedMomAlleles = new ArrayList<Allele>();
+                phasedMomAlleles.add(momTransmittedAllele);
+                phasedMomAlleles.add(momUntransmittedAllele);
+
+                Genotype phasedMomGenotype = new Genotype(mom.getSampleName(), phasedMomAlleles, mom.getNegLog10PError(), mom.getFilters(), mom.getAttributes(), true);
+
+                Allele dadTransmittedAllele = phasedChildGenotype.getAllele(1);
+                Allele dadUntransmittedAllele = dad.getAllele(0) != dadTransmittedAllele ? dad.getAllele(0) : dad.getAllele(1);
+
+                ArrayList<Allele> phasedDadAlleles = new ArrayList<Allele>();
+                phasedDadAlleles.add(dadTransmittedAllele);
+                phasedDadAlleles.add(dadUntransmittedAllele);
+
+                Genotype phasedDadGenotype = new Genotype(dad.getSampleName(), phasedDadAlleles, dad.getNegLog10PError(), dad.getFilters(), dad.getAttributes(), true);
+
+                finalGenotypes.add(phasedMomGenotype);
+                finalGenotypes.add(phasedDadGenotype);
+                finalGenotypes.add(phasedChildGenotype);
+
+                return finalGenotypes;
+            }
+        }
+
+        finalGenotypes.add(mom);
+        finalGenotypes.add(dad);
+        finalGenotypes.add(child);
+
+        return finalGenotypes;
+    }
+
+    private VariantContext phaseTrioGenotypes(VariantContext vc) {
+        Genotype mom = vc.getGenotype(SAMPLE_NAME_MOM);
+        Genotype dad = vc.getGenotype(SAMPLE_NAME_DAD);
+        Genotype child = vc.getGenotype(SAMPLE_NAME_CHILD);
+
+        Set<String> filters = new HashSet<String>();
+        filters.addAll(vc.getFilters());
+
+        Map<String, Object> attributes = new HashMap<String, Object>();
+        attributes.putAll(vc.getAttributes());
+        attributes.put(TRANSMISSION_PROBABILITY_TAG_NAME, 0.0);
+
+        ArrayList<Genotype> finalGenotypes = new ArrayList<Genotype>();
+        finalGenotypes.add(mom);
+        finalGenotypes.add(dad);
+        finalGenotypes.add(child);
+
+        if (!mom.isCalled() || !dad.isCalled() || !child.isCalled()) {
+            filters.add(INSUFFICIENT_DATA_FILTER_NAME);
+        } else {
+            ArrayList<Genotype> possibleMomGenotypes = createAllThreeGenotypes(vc.getReference(), vc.getAlternateAllele(0), mom);
+            ArrayList<Genotype> possibleDadGenotypes = createAllThreeGenotypes(vc.getReference(), vc.getAlternateAllele(0), dad);
+            ArrayList<Genotype> possibleChildGenotypes = createAllThreeGenotypes(vc.getReference(), vc.getAlternateAllele(0), child);
+
+            double bestConfigurationLikelihood = 0.0;
+            double bestPrior = 0.0;
+            Genotype bestMomGenotype = mom;
+            Genotype bestDadGenotype = dad;
+            Genotype bestChildGenotype = child;
+
+            double norm = 0.0;
+
+            for (Genotype momGenotype : possibleMomGenotypes) {
+                for (Genotype dadGenotype : possibleDadGenotypes) {
+                    for (Genotype childGenotype : possibleChildGenotypes) {
+                        double prior = isMendelianViolation(vc.getReference(), vc.getAlternateAllele(0), momGenotype, dadGenotype, childGenotype) ? MENDELIAN_VIOLATION_PRIOR : 1.0 - 12*MENDELIAN_VIOLATION_PRIOR;
+                        double configurationLikelihood = computeTransmissionLikelihoodOfGenotypeConfiguration(momGenotype, dadGenotype, childGenotype);
+                        norm += prior*configurationLikelihood;
+
+                        if (prior*configurationLikelihood > bestPrior*bestConfigurationLikelihood) {
+                            bestConfigurationLikelihood = configurationLikelihood;
+                            bestPrior = prior;
+                            bestMomGenotype = momGenotype;
+                            bestDadGenotype = dadGenotype;
+                            bestChildGenotype = childGenotype;
+                        }
+                    }
+                }
+            }
+
+            if (isMendelianViolation(vc.getReference(), vc.getAlternateAllele(0), bestMomGenotype, bestDadGenotype, bestChildGenotype)) {
+                filters.add(MENDELIAN_VIOLATION_FILTER_NAME);
+            } else if (bestMomGenotype.isHet() && bestDadGenotype.isHet() && bestChildGenotype.isHet()) {
+                filters.add(AMBIGUOUS_ALLELE_ORIGIN_FILTER_NAME);
+            } else {
+                finalGenotypes = getPhasedGenotypes(bestMomGenotype, bestDadGenotype, bestChildGenotype);
+
+                attributes.put(TRANSMISSION_PROBABILITY_TAG_NAME, bestPrior*bestConfigurationLikelihood / norm);
+            }
+        }
+
+        return new VariantContext(SOURCE_NAME, vc.getChr(), vc.getStart(), vc.getStart(), vc.getAlleles(), finalGenotypes, vc.getNegLog10PError(), noFilters ? vc.getFilters() : filters, attributes);
+    }
+
+    /**
+     * For each variant in the file, determine the phasing for the child and replace the child's genotype with the trio's genotype
+     *
+     * @param tracker  the reference meta-data tracker
+     * @param ref      the reference context
+     * @param context  the alignment context
+     * @return null
+     */
+    @Override
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if (tracker != null) {
+            Collection<VariantContext> vcs = tracker.getVariantContexts(ref, ROD_NAME, null, context.getLocation(), true, true);
+
+            for (VariantContext vc : vcs) {
+                vcfWriter.add(phaseTrioGenotypes(vc), ref.getBase());
+            }
+        }
+
+        return null;
+    }
+
+    /**
+     * Provide an initial value for reduce computations.
+     *
+     * @return Initial value of reduce.
+     */
+    @Override
+    public Integer reduceInit() {
+        return null;
+    }
+
+    /**
+     * Reduces a single map with the accumulator provided as the ReduceType.
+     *
+     * @param value result of the map.
+     * @param sum   accumulator for the reduce.
+     * @return accumulator with result of the map taken into account.
+     */
+    @Override
+    public Integer reduce(Integer value, Integer sum) {
+        return null;
+    }
+}
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 4833a6cad..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.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.*;
@@ -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 c21f548b3..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
@@ -27,24 +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.gatk.filters.MappingQualityUnavailableReadFilter;
-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.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;
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/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
index 466c1aee3..14d462518 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
@@ -8,16 +8,19 @@ import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.commandline.Argument;
-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.refdata.features.table.TableFeature;
-import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+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.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
 import java.io.PrintStream;
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 2cbc66e31..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;
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/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 ddeda1699..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
@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
 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;
@@ -34,9 +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.
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 2d0355d7d..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;
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..9c2a520ef 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 +25,13 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.apache.poi.hpsf.Variant;
+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 +39,10 @@ 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.*;
 
@@ -150,7 +150,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
 
         // get all of the vcf rods at this locus
         // Need to provide reference bases to simpleMerge starting at current locus
-        Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, null,context.getLocation(), true, false);
+        Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, null, context.getLocation(), true, false);
 
         if ( sitesOnlyVCF ) {
             vcs = VariantContextUtils.sitesOnlyVariantContexts(vcs);
@@ -173,17 +173,25 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
         if (minimumN > 1 && (vcs.size() - numFilteredRecords < minimumN))
             return 0;
         
-        VariantContext mergedVC;
+        List<VariantContext> mergedVCs = new ArrayList<VariantContext>();
         if ( master ) {
-             mergedVC = VariantContextUtils.masterMerge(vcs, "master");
+            mergedVCs.add(VariantContextUtils.masterMerge(vcs, "master"));
         } else {
-            mergedVC = VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(),vcs, priority, filteredRecordsMergeType,
-                    genotypeMergeOption, true, printComplexMerges, ref.getBase(), SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC);
+            Map<VariantContext.Type, List<VariantContext>> VCsByType = VariantContextUtils.separateVariantContextsByType(vcs);
+            // iterate over the types so that it's deterministic
+            for ( VariantContext.Type type : VariantContext.Type.values() ) {
+                if ( VCsByType.containsKey(type) )
+                    mergedVCs.add(VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), VCsByType.get(type),
+                            priority, filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges,
+                            ref.getBase(), SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC));
+            }
         }
 
-        //out.printf("   merged => %s%nannotated => %s%n", mergedVC, annotatedMergedVC);
+        for ( VariantContext mergedVC : mergedVCs ) {
+            // only operate at the start of events
+            if ( mergedVC == null )
+                continue;
 
-        if ( mergedVC != null ) { // only operate at the start of events
             HashMap<String, Object> attributes = new HashMap<String, Object>(mergedVC.getAttributes());
             // re-compute chromosome counts
             VariantContextUtils.calculateChromosomeCounts(mergedVC, attributes, false);
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..ac6797609 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
@@ -25,25 +25,37 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.text.XReadLines;
 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.io.FileNotFoundException;
+import java.io.PrintStream;
 import java.lang.annotation.AnnotationFormatError;
 import java.util.*;
 
@@ -92,6 +104,13 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
     @Argument(fullName="keepAFSpectrum", shortName="keepAF", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false)
     private boolean KEEP_AF_SPECTRUM = false;
 
+    @Hidden
+    @Argument(fullName="afFile", shortName="afFile", doc="The output recal file used by ApplyRecalibration", required=false)
+    private File AF_FILE = new File("");
+
+    @Hidden
+    @Argument(fullName="family_structure_file", shortName="familyFile", doc="USE YAML FILE INSTEAD (-SM) !!! string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false)
+    private File FAMILY_STRUCTURE_FILE = null;
 
     @Argument(fullName="family_structure", shortName="family", doc="USE YAML FILE INSTEAD (-SM) !!! string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false)
     private String FAMILY_STRUCTURE = "";
@@ -114,6 +133,9 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
     @Argument(fullName="selectIndels", shortName="indels", doc="Select only Indels.", required=false)
     private boolean SELECT_INDELS = false;
 
+    @Hidden
+     @Argument(fullName="outMVFile", shortName="outMVFile", doc="USE YAML FILE INSTEAD (-SM) !!! string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false)
+      private String outMVFile = null;
 
     /* Private class used to store the intermediate variants in the integer random selection process */
     private class RandomVariantStructure {
@@ -141,7 +163,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
     private boolean DISCORDANCE_ONLY = false;
     private boolean CONCORDANCE_ONLY = false;
 
-    private MendelianViolation mv;
+    private Set<MendelianViolation> mvSet = new HashSet<MendelianViolation>();
 
     /* default name for the variant dataset (VCF) */
     private final String variantRodName = "variant";
@@ -156,8 +178,14 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
     private RandomVariantStructure [] variantArray;
 
 
+    /* Variables used for random selection with AF boosting */
+    private ArrayList<Double> afBreakpoints = null;
+    private ArrayList<Double> afBoosts = null;
+    double bkDelta = 0.0;
 
 
+        private PrintStream outMVFileStream = null;
+
 
     /**
      * Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher
@@ -213,10 +241,29 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
         CONCORDANCE_ONLY = concordanceRodName.length() > 0;
         if (CONCORDANCE_ONLY) logger.info("Selecting only variants concordant with the track: " + concordanceRodName);
 
-        if (MENDELIAN_VIOLATIONS)
-            mv = new MendelianViolation(getToolkit(), MENDELIAN_VIOLATION_QUAL_THRESHOLD);
+        if (MENDELIAN_VIOLATIONS) {
+            if ( FAMILY_STRUCTURE_FILE != null) {
+                try {
+                    for ( final String line : new XReadLines( FAMILY_STRUCTURE_FILE ) ) {
+                        MendelianViolation mv = new MendelianViolation(line, MENDELIAN_VIOLATION_QUAL_THRESHOLD);
+                        if (samples.contains(mv.getSampleChild()) &&  samples.contains(mv.getSampleDad()) && samples.contains(mv.getSampleMom()))
+                            mvSet.add(mv);
+                    }
+                } catch ( FileNotFoundException e ) {
+                    throw new UserException.CouldNotReadInputFile(AF_FILE, e);
+                }
+                if (outMVFile != null)
+                    try {
+                        outMVFileStream = new PrintStream(outMVFile);
+                    }
+                    catch (FileNotFoundException e) {
+                        throw new UserException.CouldNotCreateOutputFile(outMVFile, "Can't open output file", e);   }
+            }
+            else
+                mvSet.add(new MendelianViolation(getToolkit(), MENDELIAN_VIOLATION_QUAL_THRESHOLD));
+        }
         else if (!FAMILY_STRUCTURE.isEmpty()) {
-            mv = new MendelianViolation(FAMILY_STRUCTURE, MENDELIAN_VIOLATION_QUAL_THRESHOLD);
+            mvSet.add(new MendelianViolation(FAMILY_STRUCTURE, MENDELIAN_VIOLATION_QUAL_THRESHOLD));
             MENDELIAN_VIOLATIONS = true;
         }
 
@@ -228,6 +275,33 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
 
         SELECT_RANDOM_FRACTION = fractionRandom > 0;
         if (SELECT_RANDOM_FRACTION) logger.info("Selecting approximately " + fractionRandom + "% of the variants at random from the variant track");
+
+
+        if (KEEP_AF_SPECTRUM) {
+            try {
+                afBreakpoints = new ArrayList<Double>();
+                afBoosts = new ArrayList<Double>();
+                logger.info("Reading in AF boost table...");
+                boolean firstLine = false;
+                for ( final String line : new XReadLines( AF_FILE ) ) {
+                    if (!firstLine) {
+                        firstLine = true;
+                        continue;
+                    }
+                    final String[] vals = line.split(" ");
+
+                    double bkp = Double.valueOf(vals[0]);
+                    double afb = Double.valueOf(vals[1]);
+                    afBreakpoints.add(bkp);
+                    afBoosts.add(afb);
+
+                }
+                bkDelta = afBreakpoints.get(0);
+            } catch ( FileNotFoundException e ) {
+                throw new UserException.CouldNotReadInputFile(AF_FILE, e);
+            }
+
+        }
     }
 
     /**
@@ -251,9 +325,24 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
 
         for (VariantContext vc : vcs) {
             if (MENDELIAN_VIOLATIONS) {
-                if (!mv.isViolation(vc)) {
-                    break;
+                boolean foundMV = false;
+                for (MendelianViolation mv : mvSet) {
+                    if (mv.isViolation(vc)) {
+                        foundMV = true;
+                        //System.out.println(vc.toString());
+                        if (outMVFile != null)
+                            outMVFileStream.format("MV@%s:%d. REF=%s, ALT=%s, AC=%d, momID=%s, dadID=%s, childID=%s, momG=%s, momGL=%s, dadG=%s, dadGL=%s, " +
+                                "childG=%s childGL=%s\n",vc.getChr(), vc.getStart(),
+                                vc.getReference().getDisplayString(), vc.getAlternateAllele(0).getDisplayString(),  vc.getChromosomeCount(vc.getAlternateAllele(0)),
+                                mv.getSampleMom(), mv.getSampleDad(), mv.getSampleChild(),
+                                vc.getGenotype(mv.getSampleMom()).toBriefString(), vc.getGenotype(mv.getSampleMom()).getLikelihoods().getAsString(),
+                                vc.getGenotype(mv.getSampleDad()).toBriefString(), vc.getGenotype(mv.getSampleMom()).getLikelihoods().getAsString(),
+                                vc.getGenotype(mv.getSampleChild()).toBriefString(),vc.getGenotype(mv.getSampleChild()).getLikelihoods().getAsString()  );
+                    }
                 }
+
+                if (!foundMV)
+                    break;
             }
             if (DISCORDANCE_ONLY) {
                 Collection<VariantContext> compVCs = tracker.getVariantContexts(ref, discordanceRodName, null, context.getLocation(), true, false);
@@ -284,46 +373,59 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
                 if (SELECT_RANDOM_NUMBER) {
                     randomlyAddVariant(++variantNumber, sub, ref.getBase());
                 }
-                else if (!SELECT_RANDOM_FRACTION || GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom) {
+                else if (!SELECT_RANDOM_FRACTION || (!KEEP_AF_SPECTRUM && GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) {
                     vcfWriter.add(sub, ref.getBase());
                 }
                 else {
                     if (SELECT_RANDOM_FRACTION && KEEP_AF_SPECTRUM ) {
-                        Collection<VariantContext> compVCs = tracker.getVariantContexts(ref, inputAFRodName, null, context.getLocation(), true, false);
-                        if (compVCs.isEmpty())
-                            return 0;
-
                         // ok we have a comp VC and we need to match the AF spectrum of inputAFRodName.
                         // We then pick a variant with probablity AF*desiredFraction
-                        for (VariantContext compVC : compVCs) {
-                            if ( compVC.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) )  {
-                                String afo = compVC.getAttributeAsString(VCFConstants.ALLELE_FREQUENCY_KEY);
+                        if ( sub.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) )  {
+                            String afo = sub.getAttributeAsString(VCFConstants.ALLELE_FREQUENCY_KEY);
 
-                                double af;
-                                if (afo.contains(",")) {
-                                    String[] afs = afo.split(",");
-                                    afs[0] = afs[0].substring(1,afs[0].length());
-                                    afs[afs.length-1] = afs[afs.length-1].substring(0,afs[afs.length-1].length()-1);
+                            double af;
+                            double afBoost = 1.0;
+                            if (afo.contains(",")) {
+                                String[] afs = afo.split(",");
+                                afs[0] = afs[0].substring(1,afs[0].length());
+                                afs[afs.length-1] = afs[afs.length-1].substring(0,afs[afs.length-1].length()-1);
 
-                                    double[] afd = new double[afs.length];
+                                double[] afd = new double[afs.length];
 
-                                    for (int k=0; k < afd.length; k++)
-                                        afd[k] = Double.valueOf(afs[k]);
+                                for (int k=0; k < afd.length; k++)
+                                    afd[k] = Double.valueOf(afs[k]);
 
-                                    af = MathUtils.arrayMax(afd);
-                                    //af = Double.valueOf(afs[0]);
+                                af = MathUtils.arrayMax(afd);
+                                //af = Double.valueOf(afs[0]);
 
-                                }
-                                else
-                                    af = Double.valueOf(afo);
-
-                                //System.out.format("%s .. %4.4f\n",afo.toString(), af);
-                                if (GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom * af)
-                                    vcfWriter.add(sub, ref.getBase());
                             }
-                            break; // do only one vc
+                            else
+                                af = Double.valueOf(afo);
+
+                            // now boost af by table read from file if desired
+                            //double bkpt = 0.0;
+                            int bkidx = 0;
+                            if (!afBreakpoints.isEmpty()) {
+                                for ( Double bkpt : afBreakpoints) {
+                                    if (af < bkpt + bkDelta)
+                                        break;
+                                    else bkidx++;
+                                }
+                                if (bkidx >=afBoosts.size())
+                                    bkidx = afBoosts.size()-1;
+                                afBoost = afBoosts.get(bkidx);
+                                //System.out.formatPrin("af:%f bkidx:%d afboost:%f\n",af,bkidx,afBoost);
+
+
+
+                            }
+
+                            //System.out.format("%s .. %4.4f\n",afo.toString(), af);
+                            if (GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom * afBoost *   afBoost)
+                                vcfWriter.add(sub, ref.getBase());
                         }
 
+
                     }
                 }
             }
@@ -407,8 +509,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
 
     private boolean haveSameGenotypes(Genotype g1, Genotype g2) {
         if ((g1.isCalled() && g2.isFiltered()) ||
-            (g2.isCalled() && g1.isFiltered()) ||
-            (g1.isFiltered() && g2.isFiltered() && EXCLUDE_FILTERED))
+                (g2.isCalled() && g1.isFiltered()) ||
+                (g1.isFiltered() && g2.isFiltered() && EXCLUDE_FILTERED))
             return false;
 
         List<Allele> a1s = g1.getAlleles();
@@ -441,7 +543,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
      * @param vc       the VariantContext record to subset
      * @param samples  the samples to extract
      * @return the subsetted VariantContext
-     */                                                             
+     */
     private VariantContext subsetRecord(VariantContext vc, Set<String> samples) {
         if ( samples == null || samples.isEmpty() )
             return vc;
@@ -451,7 +553,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
             if ( samples.contains(genotypePair.getKey()) )
                 genotypes.add(genotypePair.getValue());
         }
-        
+
         VariantContext sub = vc.subContextFromGenotypes(genotypes, vc.getAlleles());
 
         HashMap<String, Object> attributes = new HashMap<String, Object>(sub.getAttributes());
@@ -461,7 +563,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
             Genotype g = sub.getGenotype(sample);
 
             if (g.isNotFiltered() && g.isCalled()) {
-                
+
                 String dp = (String) g.getAttribute("DP");
                 if (dp != null && ! dp.equals(VCFConstants.MISSING_DEPTH_v3) && ! dp.equals(VCFConstants.MISSING_VALUE_v4) ) {
                     depth += Integer.valueOf(dp);
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..39358dad5 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 +24,18 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
+import org.broadinstitute.sting.utils.MathUtils;
 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.VariantContextUtils;
 
 import java.io.PrintStream;
 import java.util.*;
@@ -75,17 +75,29 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
         // #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
         getters.put("CHROM", new Getter() { public String get(VariantContext vc) { return vc.getChr(); } });
         getters.put("POS", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getStart()); } });
-        getters.put("REF", new Getter() { public String get(VariantContext vc) { return vc.getReference().toString(); } });
+        getters.put("REF", new Getter() {
+            public String get(VariantContext vc) {
+                String x = "";
+                if (vc.hasAttribute(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY)) {
+                    Byte refByte = (Byte)(vc.getAttribute(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY));
+                    x=x+new String(new byte[]{refByte});
+                }
+                return x+vc.getReference().getDisplayString();
+            }
+        });
         getters.put("ALT", new Getter() {
             public String get(VariantContext vc) {
                 StringBuilder x = new StringBuilder();
                 int n = vc.getAlternateAlleles().size();
-
                 if ( n == 0 ) return ".";
+                if (vc.hasAttribute(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY)) {
+                    Byte refByte = (Byte)(vc.getAttribute(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY));
+                    x.append(new String(new byte[]{refByte}));                    
+                }
 
                 for ( int i = 0; i < n; i++ ) {
                     if ( i != 0 ) x.append(",");
-                    x.append(vc.getAlternateAllele(i).toString());
+                    x.append(vc.getAlternateAllele(i).getDisplayString());
                 }
                 return x.toString();
             }
@@ -169,6 +181,31 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
                 throw new UserException(String.format("Missing field %s in vc %s at %s", field, vc.getSource(), vc));
             }
 
+            if (field.equals("AF") || field.equals("AC")) {
+                     String afo = val;
+
+                     double af=0;
+                     if (afo.contains(",")) {
+                         String[] afs = afo.split(",");
+                         afs[0] = afs[0].substring(1,afs[0].length());
+                         afs[afs.length-1] = afs[afs.length-1].substring(0,afs[afs.length-1].length()-1);
+
+                         double[] afd = new double[afs.length];
+
+                         for (int k=0; k < afd.length; k++)
+                             afd[k] = Double.valueOf(afs[k]);
+
+                         af = MathUtils.arrayMax(afd);
+                         //af = Double.valueOf(afs[0]);
+
+                     }
+                     else
+                         if (!afo.equals("NA"))
+                             af = Double.valueOf(afo);
+
+                val = Double.toString(af);
+
+            }
             vals.add(val);
         }
 
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/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 01344a117..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);
     }
 
     /**
@@ -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
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 a8bf74707..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
@@ -300,10 +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);
@@ -387,16 +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;
 
@@ -440,9 +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));
             }
         }
     }
@@ -488,10 +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())
@@ -504,7 +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/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/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/VCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
index 4037f75b9..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.*;
 
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 31791e805..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;
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 901de6fae..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
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 da80a3431..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.*;
@@ -1206,9 +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);
+                }
             }
         }
     }
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..212600360 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 {
@@ -284,8 +289,8 @@ public class VariantContextUtils {
 
     /**
      * Returns a newly allocated VC that is the same as VC, but without genotypes
-     * @param vc
-     * @return
+     * @param vc  variant context
+     * @return  new VC without genotypes
      */
     @Requires("vc != null")
     @Ensures("result != null")
@@ -298,8 +303,8 @@ public class VariantContextUtils {
 
     /**
      * Returns a newly allocated list of VC, where each VC is the same as the input VCs, but without genotypes
-     * @param vcs
-     * @return
+     * @param vcs  collection of VCs
+     * @return new VCs without genotypes
      */
     @Requires("vcs != null")
     @Ensures("result != null")
@@ -357,9 +362,9 @@ public class VariantContextUtils {
      * information per genotype.  The master merge will add the PQ information from each genotype record, where
      * appropriate, to the master VC.
      *
-     * @param unsortedVCs
-     * @param masterName
-     * @return
+     * @param unsortedVCs   collection of VCs
+     * @param masterName    name of master VC
+     * @return  master-merged VC
      */
     public static VariantContext masterMerge(Collection<VariantContext> unsortedVCs, String masterName) {
         VariantContext master = findMaster(unsortedVCs, masterName);
@@ -430,11 +435,15 @@ public class VariantContextUtils {
      * If uniqifySamples is true, the priority order is ignored and names are created by concatenating the VC name with
      * the sample name
      *
-     * @param unsortedVCs
-     * @param priorityListOfVCs
-     * @param filteredRecordMergeType
-     * @param genotypeMergeOptions
-     * @return
+     * @param genomeLocParser           loc parser
+     * @param unsortedVCs               collection of unsorted VCs
+     * @param priorityListOfVCs         priority list detailing the order in which we should grab the VCs
+     * @param filteredRecordMergeType   merge type for filtered records
+     * @param genotypeMergeOptions      merge option for genotypes
+     * @param annotateOrigin            should we annotate the set it came from?
+     * @param printMessages             should we print messages?
+     * @param inputRefBase              the ref base
+     * @return new VariantContext
      */
     public static VariantContext simpleMerge(GenomeLocParser genomeLocParser, Collection<VariantContext> unsortedVCs, List<String> priorityListOfVCs,
                                              FilteredRecordMergeType filteredRecordMergeType, GenotypeMergeType genotypeMergeOptions,
@@ -443,6 +452,24 @@ public class VariantContextUtils {
         return simpleMerge(genomeLocParser, unsortedVCs, priorityListOfVCs, filteredRecordMergeType, genotypeMergeOptions, annotateOrigin, printMessages, inputRefBase, "set", false, false);
     }
 
+    /**
+     * Merges VariantContexts into a single hybrid.  Takes genotypes for common samples in priority order, if provided.
+     * If uniqifySamples is true, the priority order is ignored and names are created by concatenating the VC name with
+     * the sample name
+     *
+     * @param genomeLocParser           loc parser
+     * @param unsortedVCs               collection of unsorted VCs
+     * @param priorityListOfVCs         priority list detailing the order in which we should grab the VCs
+     * @param filteredRecordMergeType   merge type for filtered records
+     * @param genotypeMergeOptions      merge option for genotypes
+     * @param annotateOrigin            should we annotate the set it came from?
+     * @param printMessages             should we print messages?
+     * @param inputRefBase              the ref base
+     * @param setKey                    the key name of the set
+     * @param filteredAreUncalled       are filtered records uncalled?
+     * @param mergeInfoWithMaxAC        should we merge in info from the VC with maximum allele count?
+     * @return new VariantContext
+     */
     public static VariantContext simpleMerge(GenomeLocParser genomeLocParser, Collection<VariantContext> unsortedVCs, List<String> priorityListOfVCs,
                                              FilteredRecordMergeType filteredRecordMergeType, GenotypeMergeType genotypeMergeOptions,
                                              boolean annotateOrigin, boolean printMessages, byte inputRefBase, String setKey,
@@ -465,7 +492,7 @@ public class VariantContextUtils {
             if ( ! filteredAreUncalled || vc.isNotFiltered() )
                 VCs.add(VariantContext.createVariantContextWithPaddedAlleles(vc,inputRefBase,false));
         }
-        if ( VCs.size() == 0 ) // everything is filtered out and we're filteredareUncalled
+        if ( VCs.size() == 0 ) // everything is filtered out and we're filteredAreUncalled
             return null;
 
         // establish the baseline info from the first VC
@@ -610,6 +637,17 @@ public class VariantContextUtils {
         return merged;
     }
 
+    public static Map<VariantContext.Type, List<VariantContext>> separateVariantContextsByType(Collection<VariantContext> VCs) {
+        HashMap<VariantContext.Type, List<VariantContext>> mappedVCs = new HashMap<VariantContext.Type, List<VariantContext>>();
+        for ( VariantContext vc : VCs ) {
+            if ( !mappedVCs.containsKey(vc.getType()) )
+                mappedVCs.put(vc.getType(), new ArrayList<VariantContext>());
+            mappedVCs.get(vc.getType()).add(vc);
+        }
+
+        return mappedVCs;
+    }
+
     private static class AlleleMapper {
         private VariantContext vc = null;
         private Map<Allele, Allele> map = null;
@@ -829,6 +867,7 @@ public class VariantContextUtils {
 
     /**
      * create a genome location, given a variant context
+     * @param genomeLocParser parser
      * @param vc the variant context
      * @return the genomeLoc
      */
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 b3e422ba9..ef46d4bff 100755
--- a/public/java/test/org/broadinstitute/sting/BaseTest.java
+++ b/public/java/test/org/broadinstitute/sting/BaseTest.java
@@ -13,10 +13,7 @@ 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;
+import java.util.*;
 
 /**
  *
@@ -83,11 +80,6 @@ public abstract class BaseTest {
     public static final String networkTempDir = "/broad/shptmp/";
     public static final File networkTempDirFile = new File(networkTempDir);
 
-    /**
-     * Subdirectory under the ant build directory where we store integration test md5 results
-     */
-    public static final String MD5_FILE_DB_SUBDIR = "integrationtests";
-
     public static final String testDir = "public/testdata/";
 
     /** before the class starts up */
@@ -129,7 +121,7 @@ public abstract class BaseTest {
      * 2: Create instances of your subclass.  Return from it the call to getTests, providing
      * the class type of your test
      *
-     * @DataProvider(name = "summaries")
+     * @DataProvider(name = "summaries"
      * public Object[][] createSummaries() {
      *   new SummarizeDifferenceTest().addDiff("A", "A").addSummary("A:2");
      *   new SummarizeDifferenceTest().addDiff("A", "B").addSummary("A:1", "B:1");
@@ -206,200 +198,6 @@ public abstract class BaseTest {
         }
     }
 
-    /**
-     * a little utility function for all tests to md5sum a file
-     * Shameless taken from:
-     *
-     * http://www.javalobby.org/java/forums/t84420.html
-     *
-     * @param file the file
-     * @return a string
-     */
-    public static String md5SumFile(File file) {
-        MessageDigest digest;
-        try {
-            digest = MessageDigest.getInstance("MD5");
-        } catch (NoSuchAlgorithmException e) {
-            throw new ReviewedStingException("Unable to find MD5 digest");
-        }
-        InputStream is;
-        try {
-            is = new FileInputStream(file);
-        } catch (FileNotFoundException e) {
-            throw new ReviewedStingException("Unable to open file " + file);
-        }
-        byte[] buffer = new byte[8192];
-        int read;
-        try {
-            while ((read = is.read(buffer)) > 0) {
-                digest.update(buffer, 0, read);
-            }
-            byte[] md5sum = digest.digest();
-            BigInteger bigInt = new BigInteger(1, md5sum);
-            return bigInt.toString(16);
-
-        }
-        catch (IOException e) {
-            throw new ReviewedStingException("Unable to process file for MD5", e);
-        }
-        finally {
-            try {
-                is.close();
-            }
-            catch (IOException e) {
-                throw new ReviewedStingException("Unable to close input stream for MD5 calculation", e);
-            }
-        }
-    }
-
-    protected static void ensureMd5DbDirectory() {
-        // todo -- make path
-        File dir = new File(MD5_FILE_DB_SUBDIR);
-        if ( ! dir.exists() ) {
-            System.out.printf("##### Creating MD5 db %s%n", MD5_FILE_DB_SUBDIR);
-            if ( ! dir.mkdir() ) {
-                throw new ReviewedStingException("Infrastructure failure: failed to create md5 directory " + MD5_FILE_DB_SUBDIR);
-            }
-        }
-    }
-
-    protected static File getFileForMD5(final String md5) {
-        final String basename = String.format("%s.integrationtest", md5);
-        return new File(MD5_FILE_DB_SUBDIR + "/" + basename);
-    }
-
-    private static void updateMD5Db(final String md5, final File resultsFile) {
-        // todo -- copy results file to DB dir if needed under filename for md5
-        final File dbFile = getFileForMD5(md5);
-        if ( ! dbFile.exists() ) {
-            // the file isn't already in the db, copy it over
-            System.out.printf("##### Updating MD5 file: %s%n", dbFile.getPath());
-            try {
-                FileUtils.copyFile(resultsFile, dbFile);
-            } catch ( IOException e ) {
-                throw new ReviewedStingException(e.getMessage());
-            }
-        } else {
-            System.out.printf("##### MD5 file is up to date: %s%n", dbFile.getPath());
-
-        }
-    }
-
-    private static String getMD5Path(final String md5, final String valueIfNotFound) {
-        // todo -- look up the result in the directory and return the path if it exists
-        final File dbFile = getFileForMD5(md5);
-        return dbFile.exists() ? dbFile.getPath() : valueIfNotFound;
-    }
-
-    public static byte[] getBytesFromFile(File file) throws IOException {
-        InputStream is = new FileInputStream(file);
-
-        // Get the size of the file
-        long length = file.length();
-
-        if (length > Integer.MAX_VALUE) {
-            // File is too large
-        }
-
-        // Create the byte array to hold the data
-        byte[] bytes = new byte[(int) length];
-
-        // Read in the bytes
-        int offset = 0;
-        int numRead = 0;
-        while (offset < bytes.length
-                && (numRead = is.read(bytes, offset, bytes.length - offset)) >= 0) {
-            offset += numRead;
-        }
-
-        // Ensure all the bytes have been read in
-        if (offset < bytes.length) {
-            throw new IOException("Could not completely read file " + file.getName());
-        }
-
-        // Close the input stream and return bytes
-        is.close();
-        return bytes;
-    }
-
-    /**
-     * Tests a file MD5 against an expected value, returning the MD5.  NOTE: This function WILL throw an exception if the MD5s are different.
-     * @param name Name of the test.
-     * @param resultsFile File to MD5.
-     * @param expectedMD5 Expected MD5 value.
-     * @param parameterize If true or if expectedMD5 is an empty string, will print out the calculated MD5 instead of error text.
-     * @return The calculated MD5.
-     */
-    public static String assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5, final boolean parameterize) {
-        String filemd5sum = testFileMD5(name, resultsFile, expectedMD5, parameterize);
-        
-        if (parameterize || expectedMD5.equals("")) {
-            // Don't assert
-        } 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;
-    }
-
-
-    /**
-     * Tests a file MD5 against an expected value, returning the MD5.  NOTE: This function WILL NOT throw an exception if the MD5s are different.
-     * @param name Name of the test.
-     * @param resultsFile File to MD5.
-     * @param expectedMD5 Expected MD5 value.
-     * @param parameterize If true or if expectedMD5 is an empty string, will print out the calculated MD5 instead of error text.
-     * @return The calculated MD5.
-     */
-    public static String testFileMD5(final String name, final File resultsFile, final String expectedMD5, final boolean parameterize) {
-        try {
-            byte[] bytesOfMessage = getBytesFromFile(resultsFile);
-            byte[] thedigest = MessageDigest.getInstance("MD5").digest(bytesOfMessage);
-            BigInteger bigInt = new BigInteger(1, thedigest);
-            String filemd5sum = bigInt.toString(16);
-            while (filemd5sum.length() < 32) filemd5sum = "0" + filemd5sum; // pad to length 32
-
-            //
-            // copy md5 to integrationtests
-            //
-            updateMD5Db(filemd5sum, resultsFile);
-
-            if (parameterize || expectedMD5.equals("")) {
-                System.out.println(String.format("PARAMETERIZATION[%s]: file %s has md5 = %s, stated expectation is %s, equal? = %b",
-                                                 name, resultsFile, filemd5sum, expectedMD5, filemd5sum.equals(expectedMD5)));
-            } else {
-                System.out.println(String.format("Checking MD5 for %s [calculated=%s, expected=%s]", resultsFile, filemd5sum, expectedMD5));
-                System.out.flush();
-
-                if ( ! expectedMD5.equals(filemd5sum) ) {
-                    // we are going to fail for real in assertEquals (so we are counted by the testing framework).
-                    // prepare ourselves for the comparison
-                    System.out.printf("##### Test %s is going fail #####%n", name);
-                    String pathToExpectedMD5File = getMD5Path(expectedMD5, "[No DB file found]");
-                    String pathToFileMD5File = getMD5Path(filemd5sum, "[No DB file found]");
-                    System.out.printf("##### Path to expected   file (MD5=%s): %s%n", expectedMD5, pathToExpectedMD5File);
-                    System.out.printf("##### Path to calculated file (MD5=%s): %s%n", filemd5sum, pathToFileMD5File);
-                    System.out.printf("##### Diff command: diff %s %s%n", pathToExpectedMD5File, pathToFileMD5File);
-
-                    // 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);
-                }
-            }
-
-            return filemd5sum;
-        } catch (Exception e) {
-            throw new RuntimeException("Failed to read bytes from calls file: " + resultsFile, e);
-        }
-    }
-
     /**
      * Creates a temp file that will be deleted on exit after tests are complete.
      * @param name Prefix of the file.
diff --git a/public/java/test/org/broadinstitute/sting/MD5DB.java b/public/java/test/org/broadinstitute/sting/MD5DB.java
new file mode 100644
index 000000000..bea9eaec5
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/MD5DB.java
@@ -0,0 +1,247 @@
+/*
+ * 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;
+
+import org.apache.commons.io.FileUtils;
+import org.broadinstitute.sting.gatk.walkers.diffengine.DiffEngine;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.testng.Assert;
+
+import java.io.*;
+import java.math.BigInteger;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import java.util.Arrays;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: depristo
+ * Date: 7/18/11
+ * Time: 9:10 AM
+ *
+ * Utilities for manipulating the MD5 database of previous results
+ */
+public class MD5DB {
+    /**
+     * Subdirectory under the ant build directory where we store integration test md5 results
+     */
+    public static final String LOCAL_MD5_DB_DIR = "integrationtests";
+    public static final String GLOBAL_MD5_DB_DIR = "/humgen/gsa-hpprojects/GATK/data/integrationtests";
+
+    // ----------------------------------------------------------------------
+    //
+    // MD5 DB stuff
+    //
+    // ----------------------------------------------------------------------
+
+    /**
+     * Create the MD5 file directories if necessary
+     */
+    protected static void ensureMd5DbDirectory() {
+        File dir = new File(LOCAL_MD5_DB_DIR);
+        if ( ! dir.exists() ) {
+            System.out.printf("##### Creating MD5 db %s%n", LOCAL_MD5_DB_DIR);
+            if ( ! dir.mkdir() ) {
+                throw new ReviewedStingException("Infrastructure failure: failed to create md5 directory " + LOCAL_MD5_DB_DIR);
+            }
+        }
+    }
+
+    /**
+     * Returns the path to an already existing file with the md5 contents, or valueIfNotFound
+     * if no such file exists in the db.
+     *
+     * @param md5
+     * @param valueIfNotFound
+     * @return
+     */
+    public static String getMD5FilePath(final String md5, final String valueIfNotFound) {
+        // we prefer the local db to the global DB, so match it first
+        for ( String dir : Arrays.asList(LOCAL_MD5_DB_DIR, GLOBAL_MD5_DB_DIR)) {
+            File f = getFileForMD5(md5, dir);
+            if ( f.exists() && f.canRead() )
+                return f.getPath();
+        }
+
+        return valueIfNotFound;
+    }
+
+    /**
+     * Utility function that given a file's md5 value and the path to the md5 db,
+     * returns the canonical name of the file. For example, if md5 is XXX and db is YYY,
+     * this will return YYY/XXX.integrationtest
+     *
+     * @param md5
+     * @param dbPath
+     * @return
+     */
+    private static File getFileForMD5(final String md5, final String dbPath) {
+        final String basename = String.format("%s.integrationtest", md5);
+        return new File(dbPath + "/" + basename);
+    }
+
+    /**
+     * Copies the results file with md5 value to its canonical file name and db places
+     *
+     * @param md5
+     * @param resultsFile
+     */
+    private static void updateMD5Db(final String md5, final File resultsFile) {
+        copyFileToDB(getFileForMD5(md5, LOCAL_MD5_DB_DIR), resultsFile);
+        copyFileToDB(getFileForMD5(md5, GLOBAL_MD5_DB_DIR), resultsFile);
+    }
+
+    /**
+     * Low-level utility routine that copies resultsFile to dbFile
+     * @param dbFile
+     * @param resultsFile
+     */
+    private static void copyFileToDB(File dbFile, final File resultsFile) {
+        if ( ! dbFile.exists() ) {
+            // the file isn't already in the db, copy it over
+            System.out.printf("##### Updating MD5 file: %s%n", dbFile.getPath());
+            try {
+                FileUtils.copyFile(resultsFile, dbFile);
+            } catch ( IOException e ) {
+                System.out.printf("##### Skipping update, cannot write file %s%n", dbFile);
+            }
+        } else {
+            System.out.printf("##### MD5 file is up to date: %s%n", dbFile.getPath());
+        }
+    }
+
+    /**
+     * Returns the byte[] of the entire contents of file, for md5 calculations
+     * @param file
+     * @return
+     * @throws IOException
+     */
+    private static byte[] getBytesFromFile(File file) throws IOException {
+        InputStream is = new FileInputStream(file);
+
+        // Get the size of the file
+        long length = file.length();
+
+        if (length > Integer.MAX_VALUE) {
+            // File is too large
+        }
+
+        // Create the byte array to hold the data
+        byte[] bytes = new byte[(int) length];
+
+        // Read in the bytes
+        int offset = 0;
+        int numRead = 0;
+        while (offset < bytes.length
+                && (numRead = is.read(bytes, offset, bytes.length - offset)) >= 0) {
+            offset += numRead;
+        }
+
+        // Ensure all the bytes have been read in
+        if (offset < bytes.length) {
+            throw new IOException("Could not completely read file " + file.getName());
+        }
+
+        // Close the input stream and return bytes
+        is.close();
+        return bytes;
+    }
+
+    /**
+     * Tests a file MD5 against an expected value, returning the MD5.  NOTE: This function WILL throw an exception if the MD5s are different.
+     * @param name Name of the test.
+     * @param resultsFile File to MD5.
+     * @param expectedMD5 Expected MD5 value.
+     * @param parameterize If true or if expectedMD5 is an empty string, will print out the calculated MD5 instead of error text.
+     * @return The calculated MD5.
+     */
+    public static String assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5, final boolean parameterize) {
+        String filemd5sum = testFileMD5(name, resultsFile, expectedMD5, parameterize);
+
+        if (parameterize || expectedMD5.equals("")) {
+            // Don't assert
+        } 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;
+    }
+
+
+    /**
+     * Tests a file MD5 against an expected value, returning the MD5.  NOTE: This function WILL NOT throw an exception if the MD5s are different.
+     * @param name Name of the test.
+     * @param resultsFile File to MD5.
+     * @param expectedMD5 Expected MD5 value.
+     * @param parameterize If true or if expectedMD5 is an empty string, will print out the calculated MD5 instead of error text.
+     * @return The calculated MD5.
+     */
+    public static String testFileMD5(final String name, final File resultsFile, final String expectedMD5, final boolean parameterize) {
+        try {
+            byte[] bytesOfMessage = getBytesFromFile(resultsFile);
+            byte[] thedigest = MessageDigest.getInstance("MD5").digest(bytesOfMessage);
+            BigInteger bigInt = new BigInteger(1, thedigest);
+            String filemd5sum = bigInt.toString(16);
+            while (filemd5sum.length() < 32) filemd5sum = "0" + filemd5sum; // pad to length 32
+
+            //
+            // copy md5 to integrationtests
+            //
+            updateMD5Db(filemd5sum, resultsFile);
+
+            if (parameterize || expectedMD5.equals("")) {
+                System.out.println(String.format("PARAMETERIZATION[%s]: file %s has md5 = %s, stated expectation is %s, equal? = %b",
+                        name, resultsFile, filemd5sum, expectedMD5, filemd5sum.equals(expectedMD5)));
+            } else {
+                System.out.println(String.format("Checking MD5 for %s [calculated=%s, expected=%s]", resultsFile, filemd5sum, expectedMD5));
+                System.out.flush();
+
+                if ( ! expectedMD5.equals(filemd5sum) ) {
+                    // we are going to fail for real in assertEquals (so we are counted by the testing framework).
+                    // prepare ourselves for the comparison
+                    System.out.printf("##### Test %s is going fail #####%n", name);
+                    String pathToExpectedMD5File = getMD5FilePath(expectedMD5, "[No DB file found]");
+                    String pathToFileMD5File = getMD5FilePath(filemd5sum, "[No DB file found]");
+                    System.out.printf("##### Path to expected   file (MD5=%s): %s%n", expectedMD5, pathToExpectedMD5File);
+                    System.out.printf("##### Path to calculated file (MD5=%s): %s%n", filemd5sum, pathToFileMD5File);
+                    System.out.printf("##### Diff command: diff %s %s%n", pathToExpectedMD5File, pathToFileMD5File);
+
+                    // 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);
+                }
+            }
+
+            return filemd5sum;
+        } catch (Exception e) {
+            throw new RuntimeException("Failed to read bytes from calls file: " + resultsFile, e);
+        }
+    }
+}
diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java
index dacaf2738..386c17659 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;
@@ -51,7 +53,7 @@ public class WalkerTest extends BaseTest {
     }
 
     public String assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5) {
-        return assertMatchingMD5(name, resultsFile, expectedMD5, parameterize());
+        return MD5DB.assertMatchingMD5(name, resultsFile, expectedMD5, parameterize());
     }
 
     public void maybeValidateSupplementaryFile(final String name, final File resultFile) {
@@ -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()));
         }
     }
 
@@ -177,7 +191,7 @@ public class WalkerTest extends BaseTest {
     }
 
     protected Pair<List<File>, List<String>> executeTest(final String name, WalkerTestSpec spec) {
-        ensureMd5DbDirectory(); // ensure the md5 directory exists
+        MD5DB.ensureMd5DbDirectory(); // ensure the md5 directory exists
 
         List<File> tmpFiles = new ArrayList<File>();
         for (int i = 0; i < spec.nOutputFiles; i++) {
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
index 96dfec6e8..2ae19264e 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java
@@ -99,7 +99,7 @@ public class DiffEngineUnitTest extends BaseTest {
         logger.warn("Test tree1: " + test.tree1.toOneLineString());
         logger.warn("Test tree2: " + test.tree2.toOneLineString());
 
-        List<SpecificDifference> diffs = engine.diff(test.tree1, test.tree2);
+        List<Difference> diffs = engine.diff(test.tree1, test.tree2);
         logger.warn("Test expected diff : " + test.differences);
         logger.warn("Observed diffs     : " + diffs);
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java
new file mode 100644
index 000000000..77159d9c2
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java
@@ -0,0 +1,71 @@
+/*
+ * 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.WalkerTest;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+public class DiffObjectsIntegrationTest extends WalkerTest {
+    private class TestParams extends TestDataProvider {
+        public File master, test;
+        public String MD5;
+
+        private TestParams(String master, String test, String MD5) {
+            super(TestParams.class);
+            this.master = new File(master);
+            this.test = new File(test);
+            this.MD5 = MD5;
+        }
+
+        public String toString() {
+            return String.format("master=%s,test=%s,md5=%s", master, test, MD5);
+        }
+    }
+
+    @DataProvider(name = "data")
+    public Object[][] createData() {
+        new TestParams(testDir + "diffTestMaster.vcf", testDir + "diffTestTest.vcf", "4d9f4636de05b93c354d05011264546e");
+        new TestParams(testDir + "exampleBAM.bam", testDir + "exampleBAM.simple.bam", "37e6efd833b5cd6d860a9df3df9713fc");
+        return TestParams.getTests(TestParams.class);
+    }
+
+    @Test(enabled = true, dataProvider = "data")
+    public void testDiffs(TestParams params) {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T DiffObjects -R public/testdata/exampleFASTA.fasta "
+                        + " -m " + params.master
+                        + " -t " + params.test
+                        + " -o %s",
+                Arrays.asList(params.MD5));
+        executeTest("testDiffObjects:"+params, spec).getFirst();
+    }
+}
+
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
index baa2f0383..dee7bbd88 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
@@ -87,7 +87,7 @@ public class DiffableReaderUnitTest extends BaseTest {
         Assert.assertSame(diff.getParent(), DiffElement.ROOT);
 
         DiffNode node = diff.getValueAsNode();
-        Assert.assertEquals(node.getElements().size(), 9);
+        Assert.assertEquals(node.getElements().size(), 11);
 
         // 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();
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
index 64579a01b..4e4080bc7 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java
@@ -75,10 +75,10 @@ public class DifferenceUnitTest extends BaseTest {
 
     @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");
+        new DifferenceTest("A=X", "A=Y", "A:1:X!=Y");
+        new DifferenceTest("A=Y", "A=X", "A:1:Y!=X");
+        new DifferenceTest(DiffNode.fromString("A=X"), null, "A:1:X!=MISSING");
+        new DifferenceTest(null, DiffNode.fromString("A=X"), "A:1:MISSING!=X");
         return DifferenceTest.getTests(DifferenceTest.class);
     }
 
@@ -87,7 +87,7 @@ public class DifferenceUnitTest extends BaseTest {
         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);
+        Difference diff = new Difference(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 );
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java
new file mode 100644
index 000000000..21435dd7d
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java
@@ -0,0 +1,28 @@
+package org.broadinstitute.sting.gatk.walkers.phasing;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+
+public class MergeAndMatchHaplotypesIntegrationTest extends WalkerTest {
+    private static String mergeAndMatchHaplotypesTestDataRoot = validationDataLocation + "/MergeAndMatchHaplotypes";
+    private static String fundamentalTestPBTVCF = mergeAndMatchHaplotypesTestDataRoot + "/" + "FundamentalsTest.pbt.vcf";
+    private static String fundamentalTestRBPVCF = mergeAndMatchHaplotypesTestDataRoot + "/" + "FundamentalsTest.pbt.rbp.vcf";
+
+    @Test
+    public void testBasicFunctionality() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                buildCommandLine(
+                        "-T MergeAndMatchHaplotypes",
+                        "-R " + b37KGReference,
+                        "-B:pbt,VCF " + fundamentalTestPBTVCF,
+                        "-B:rbp,VCF " + fundamentalTestRBPVCF,
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("")
+        );
+        executeTest("testBasicMergeAndMatchHaplotypesFunctionality", spec);
+    }
+}
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/PhaseByTransmissionIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
new file mode 100644
index 000000000..9f59adeb6
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
@@ -0,0 +1,44 @@
+package org.broadinstitute.sting.gatk.walkers.phasing;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+
+public class PhaseByTransmissionIntegrationTest extends WalkerTest {
+    private static String phaseByTransmissionTestDataRoot = validationDataLocation + "/PhaseByTransmission";
+    private static String fundamentalTestVCF = phaseByTransmissionTestDataRoot + "/" + "FundamentalsTest.unfiltered.vcf";
+
+    @Test
+    public void testBasicFunctionalityWithoutFilters() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                buildCommandLine(
+                        "-T PhaseByTransmission",
+                        "-R " + b37KGReference,
+                        "-B:variant,VCF " + fundamentalTestVCF,
+                        "-f NA12892+NA12891=NA12878",
+                        "-nofilters",
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("416a483e87358cdcb0b09a496e3254c0")
+        );
+        executeTest("testBasicFunctionalityWithoutFilters", spec);
+    }
+
+    @Test
+    public void testBasicFunctionalityWithFilters() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                buildCommandLine(
+                        "-T PhaseByTransmission",
+                        "-R " + b37KGReference,
+                        "-B:variant,VCF " + fundamentalTestVCF,
+                        "-f NA12892+NA12891=NA12878",
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("8c5db343567e90e97993912c7e541d0d")
+        );
+        executeTest("testBasicFunctionalityWithFilters", spec);
+    }
+}
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 2fec2e70f..057053a1c 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
@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 
+import org.broadinstitute.sting.MD5DB;
 import org.broadinstitute.sting.WalkerTest;
 import org.testng.annotations.Test;
 import org.testng.annotations.DataProvider;
@@ -65,8 +66,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
                         " -NO_HEADER" +
                         " -B:input,VCF " + params.inVCF +
                         " -o %s" +
-                        " -tranchesFile " + getFileForMD5(params.tranchesMD5) +
-                        " -recalFile " + getFileForMD5(params.recalMD5),
+                        " -tranchesFile " + MD5DB.getMD5FilePath(params.tranchesMD5, null) +
+                        " -recalFile " + MD5DB.getMD5FilePath(params.recalMD5, null),
                 Arrays.asList(params.cutVCFMD5));
         executeTest("testApplyRecalibration-"+params.inVCF, spec);
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java
deleted file mode 100755
index 7e1d86105..000000000
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/BatchMergeIntegrationTest.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright (c) 2010, 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.variantutils;
-
-import org.broadinstitute.sting.WalkerTest;
-import org.testng.annotations.Test;
-
-import java.io.File;
-import java.util.Arrays;
-
-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);
-    }
-}
\ No newline at end of file
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 daaab9425..904a5b29b 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
@@ -70,7 +70,6 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
         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); }
@@ -81,9 +80,9 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
 
     @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 combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "f1cf095c2fe9641b7ca1f8ee2c46fd4a", 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 combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e144b6283765494bfe8189ac59965083", false); }
 
     @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "89f55abea8f59e39d1effb908440548c", true); }
 
@@ -101,7 +100,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
                         " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
                         " -genotypeMergeOptions UNIQUIFY -L 1"),
                 1,
-                Arrays.asList("8b78339ccf7a5a5a837f79e88a3a38e5"));
+                Arrays.asList("1de95f91ca15d2a8856de35dee0ce33e"));
         executeTest("threeWayWithRefs", spec);
     }
 
@@ -119,7 +118,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
         executeTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);
     }
 
-//    @Test public void complexTestFull() { combineComplexSites("", "64b991fd3850f83614518f7d71f0532f"); }
+    @Test public void complexTestFull() { combineComplexSites("", "b5a53ee92bdaacd2bb3327e9004ae058"); }
     @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "df96cb3beb2dbb5e02f80abec7d3571e"); }
     @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "f72a178137e25dbe0b931934cdc0079d"); }
     @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "f704caeaaaed6711943014b847fe381a"); }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java
old mode 100644
new mode 100755
index 72647c8e1..1db712353
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java
@@ -44,7 +44,7 @@ public class VariantsToTableIntegrationTest extends WalkerTest {
     @Test(enabled = true)
     public void testComplexVariantsToTable() {
         WalkerTestSpec spec = new WalkerTestSpec(variantsToTableCmd(" -AMD"),
-                Arrays.asList("b2a3712c1bfad8f1383ffada8b5017ba"));
+                Arrays.asList("e8f771995127b727fb433da91dd4ee98"));
         executeTest("testComplexVariantsToTable", spec).getFirst();
     }
 
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 8421076c9..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("815b82fff92aab41c209eedce2d7e7d9");
+        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("22336ee9c12aa222ce29c3c5babca7d0");
+        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("9bedaa7670b86a07be5191898c3727cf");
+        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("cc215edec9ca28e5c79ab1b67506f9f7");
+        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/genotype/vcf/VCFHeaderUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java
index c4ca6a551..14e63191d 100644
--- a/public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java
@@ -2,15 +2,16 @@ package org.broadinstitute.sting.utils.genotype.vcf;
 
 import org.broad.tribble.readers.AsciiLineReader;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
 
 import org.testng.annotations.Test;
 
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.io.StringBufferInputStream;
+import java.io.*;
+import java.math.BigInteger;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
 
 /**
  * Created by IntelliJ IDEA.
@@ -40,6 +41,52 @@ public class VCFHeaderUnitTest extends BaseTest {
         checkMD5ofHeaderFile(header, "ad8c4cf85e868b0261ab49ee2c613088");
     }
 
+        /**
+     * a little utility function for all tests to md5sum a file
+     * Shameless taken from:
+     *
+     * http://www.javalobby.org/java/forums/t84420.html
+     *
+     * @param file the file
+     * @return a string
+     */
+    private static String md5SumFile(File file) {
+        MessageDigest digest;
+        try {
+            digest = MessageDigest.getInstance("MD5");
+        } catch (NoSuchAlgorithmException e) {
+            throw new ReviewedStingException("Unable to find MD5 digest");
+        }
+        InputStream is;
+        try {
+            is = new FileInputStream(file);
+        } catch (FileNotFoundException e) {
+            throw new ReviewedStingException("Unable to open file " + file);
+        }
+        byte[] buffer = new byte[8192];
+        int read;
+        try {
+            while ((read = is.read(buffer)) > 0) {
+                digest.update(buffer, 0, read);
+            }
+            byte[] md5sum = digest.digest();
+            BigInteger bigInt = new BigInteger(1, md5sum);
+            return bigInt.toString(16);
+
+        }
+        catch (IOException e) {
+            throw new ReviewedStingException("Unable to process file for MD5", e);
+        }
+        finally {
+            try {
+                is.close();
+            }
+            catch (IOException e) {
+                throw new ReviewedStingException("Unable to close input stream for MD5 calculation", e);
+            }
+        }
+    }
+
     private void checkMD5ofHeaderFile(VCFHeader header, String md5sum) {
         File myTempFile = null;
         PrintWriter pw = null;
diff --git a/public/packages/PicardPrivate.xml b/public/packages/PicardPrivate.xml
index 110b41d3f..581c47979 100644
--- a/public/packages/PicardPrivate.xml
+++ b/public/packages/PicardPrivate.xml
@@ -7,6 +7,8 @@
       <class name="edu.mit.broad.picard.genotype.geli.GeliFileWriter" />
       <class name="edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods" />
       <class name="edu.mit.broad.picard.util.PasteParser" />
+      <class name="edu.mit.broad.picard.util.PicardAggregationFsUtil" />
+      <class name="edu.mit.broad.picard.util.PicardFileSystemUtil" />
       <class name="edu.mit.broad.picard.variation.KnownVariantCodecV2" />
       <class name="edu.mit.broad.picard.variation.KnownVariantCodec" />
       <class name="edu.mit.broad.picard.variation.KnownVariantFileHeader" />
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..1f4f79993 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"
@@ -72,6 +72,9 @@ class DataProcessingPipeline extends QScript {
   @Input(doc="Number of threads BWA should use", fullName="bwa_threads", shortName="bt", required=false)
   var bwaThreads: Int = 1
 
+  @Input(doc="Dont perform validation on the BAM files", fullName="no_validation", shortName="nv", required=false)
+  var noValidation: Boolean = false
+
 
   /****************************************************************************
   * Global Variables
@@ -103,18 +106,6 @@ 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 +126,7 @@ 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 +138,23 @@ class DataProcessingPipeline extends QScript {
       }
     }
 
+    println("\n\n*** INPUT FILES ***\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("*** INPUT FILES ***\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 +200,6 @@ 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 +209,14 @@ 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 +224,7 @@ 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")
@@ -268,7 +249,12 @@ class DataProcessingPipeline extends QScript {
       val preValidateLog  = swapExt(bam, ".bam", ".pre.validation")
       val postValidateLog = swapExt(bam, ".bam", ".post.validation")
 
-      add(validate(bam, preValidateLog))
+      // Validation is an optional step for the BAM file generated after
+      // alignment and the final bam file of the pipeline.
+      if (!noValidation) {
+        add(validate(bam, preValidateLog),
+            validate(recalBam, postValidateLog))
+      }
 
       if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY)
         add(target(bam, targetIntervals))
@@ -279,8 +265,8 @@ class DataProcessingPipeline extends QScript {
           recal(dedupedBam, preRecalFile, recalBam),
           cov(recalBam, postRecalFile),
           analyzeCovariates(preRecalFile, preOutPath),
-          analyzeCovariates(postRecalFile, postOutPath),
-          validate(recalBam, postValidateLog))
+          analyzeCovariates(postRecalFile, postOutPath))
+
 
       cohortList :+= recalBam
     }
@@ -304,13 +290,21 @@ class DataProcessingPipeline extends QScript {
     this.isIntermediate = true
   }
 
+  // General arguments to non-GATK tools
+  trait ExternalCommonArgs extends CommandLineFunction {
+    this.memoryLimit = 4
+    this.isIntermediate = true
+  }
+
+
   case class target (inBams: File, outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs {
     if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY)
       this.input_file :+= inBams
     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 +315,8 @@ class DataProcessingPipeline extends QScript {
     this.targetIntervals = tIntervals
     this.out = outBam
     this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
-    this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
+    if (!qscript.indels.isEmpty)
+      this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
     this.consensusDeterminationModel =  consensusDeterminationModel
     this.compress = 0
     this.scatterCount = nContigs
@@ -344,7 +339,7 @@ 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
@@ -352,7 +347,6 @@ class DataProcessingPipeline extends QScript {
     this.isIntermediate = false
     this.analysisName = queueLogDir + outBam + ".recalibration"
     this.jobName = queueLogDir + outBam + ".recalibration"
-
   }
 
 
@@ -370,48 +364,41 @@ class DataProcessingPipeline extends QScript {
     this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
   }
 
-  case class dedup (inBam: File, outBam: File, metricsFile: File) extends MarkDuplicates {
+  case class dedup (inBam: File, outBam: File, metricsFile: File) extends MarkDuplicates with ExternalCommonArgs {
     this.input = List(inBam)
     this.output = outBam
     this.metrics = metricsFile
-    this.memoryLimit = 6
-    this.isIntermediate = true
     this.analysisName = queueLogDir + outBam + ".dedup"
     this.jobName = queueLogDir + outBam + ".dedup"
   }
 
-  case class joinBams (inBams: List[File], outBam: File) extends MergeSamFiles {
+  case class joinBams (inBams: List[File], outBam: File) extends MergeSamFiles with ExternalCommonArgs {
     this.input = inBams
     this.output = outBam
-    this.memoryLimit = 4
-    this.isIntermediate = true
     this.analysisName = queueLogDir + outBam + ".joinBams"
     this.jobName = queueLogDir + outBam + ".joinBams"
   }
 
-  case class sortSam (inSam: File, outBam: File, sortOrderP: SortOrder) extends SortSam {
+  case class sortSam (inSam: File, outBam: File, sortOrderP: SortOrder) extends SortSam with ExternalCommonArgs {
     this.input = List(inSam)
     this.output = outBam
     this.sortOrder = sortOrderP
-    this.memoryLimit = 4
-    this.isIntermediate = true
     this.analysisName = queueLogDir + outBam + ".sortSam"
     this.jobName = queueLogDir + outBam + ".sortSam"
   }
 
-  case class validate (inBam: File, outLog: File) extends ValidateSamFile {
+  case class validate (inBam: File, outLog: File) extends ValidateSamFile with ExternalCommonArgs {
     this.input = List(inBam)
     this.output = outLog
     this.maxRecordsInRam = 100000
     this.REFERENCE_SEQUENCE = qscript.reference
-    this.memoryLimit = 4
     this.isIntermediate = false
     this.analysisName = queueLogDir + outLog + ".validate"
     this.jobName = queueLogDir + outLog + ".validate"
   }
 
 
-  case class addReadGroup (inBam: File, outBam: File, readGroup: ReadGroup) extends AddOrReplaceReadGroups {
+  case class addReadGroup (inBam: File, outBam: File, readGroup: ReadGroup) extends AddOrReplaceReadGroups with ExternalCommonArgs {
     this.input = List(inBam)
     this.output = outBam
     this.RGID = readGroup.id
@@ -427,12 +414,7 @@ class DataProcessingPipeline extends QScript {
     this.jobName = queueLogDir + outBam + ".rg"
   }
 
-  trait BWACommonArgs extends CommandLineFunction {
-    this.memoryLimit = 4
-    this.isIntermediate = true
-  }
-
-  case class bwa_aln_se (inBam: File, outSai: File) extends CommandLineFunction with BWACommonArgs {
+  case class bwa_aln_se (inBam: File, outSai: File) extends CommandLineFunction with ExternalCommonArgs {
     @Input(doc="bam file to be aligned") var bam = inBam
     @Output(doc="output sai file") var sai = outSai
     def commandLine = bwaPath + " aln -t " + bwaThreads + " -q 5 " + reference + " -b " + bam + " > " + sai
@@ -440,7 +422,7 @@ class DataProcessingPipeline extends QScript {
     this.jobName = queueLogDir + outSai + ".bwa_aln_se"
   }
 
-  case class bwa_aln_pe (inBam: File, outSai1: File, index: Int) extends CommandLineFunction with BWACommonArgs {
+  case class bwa_aln_pe (inBam: File, outSai1: File, index: Int) extends CommandLineFunction with ExternalCommonArgs {
     @Input(doc="bam file to be aligned") var bam = inBam
     @Output(doc="output sai file for 1st mating pair") var sai = outSai1
     def commandLine = bwaPath + " aln -t " + bwaThreads + " -q 5 " + reference + " -b" + index + " " + bam + " > " + sai
@@ -448,7 +430,7 @@ class DataProcessingPipeline extends QScript {
     this.jobName = queueLogDir + outSai1 + ".bwa_aln_pe1"
   }
 
-  case class bwa_sam_se (inBam: File, inSai: File, outBam: File) extends CommandLineFunction with BWACommonArgs {
+  case class bwa_sam_se (inBam: File, inSai: File, outBam: File) extends CommandLineFunction with ExternalCommonArgs {
     @Input(doc="bam file to be aligned") var bam = inBam
     @Input(doc="bwa alignment index file") var sai = inSai
     @Output(doc="output aligned bam file") var alignedBam = outBam
@@ -457,7 +439,7 @@ class DataProcessingPipeline extends QScript {
     this.jobName = queueLogDir + outBam + ".bwa_sam_se"
   }
 
-  case class bwa_sam_pe (inBam: File, inSai1: File, inSai2:File, outBam: File) extends CommandLineFunction with BWACommonArgs {
+  case class bwa_sam_pe (inBam: File, inSai1: File, inSai2:File, outBam: File) extends CommandLineFunction with ExternalCommonArgs {
     @Input(doc="bam file to be aligned") var bam = inBam
     @Input(doc="bwa alignment index file for 1st mating pair") var sai1 = inSai1
     @Input(doc="bwa alignment index file for 2nd mating pair") var sai2 = inSai2
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..f8218148e 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.
@@ -20,38 +20,37 @@ class RecalibrateBaseQualities extends QScript {
   @Input(doc="input BAM file - or list of BAM files", shortName="i", required=true)
   var input: File = _
 
-  @Input(doc="path to R resources folder inside the Sting repository", fullName="path_to_r", shortName="r", required=false)
-  var R: String = new File("/humgen/gsa-scr1/carneiro/stable/R")
+  @Input(doc="path to R resources folder inside the Sting repository", fullName="path_to_r", shortName="r", required=true)
+  var R: String = _
 
-  @Input(doc="Reference fasta file", shortName="R", required=false)
-  var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
+  @Input(doc="Reference fasta file", shortName="R", required=true)
+  var reference: File = _ // new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
 
-  @Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=false)
-  var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
+  @Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=true)
+  var dbSNP: File = _     // new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
 
   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/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/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
index dc3cfd9d4..c2c956118 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
@@ -31,6 +31,7 @@ import org.broadinstitute.sting.commandline.CommandLineProgram
 import java.util.Date
 import java.text.SimpleDateFormat
 import org.broadinstitute.sting.BaseTest
+import org.broadinstitute.sting.MD5DB
 import org.broadinstitute.sting.queue.QCommandLine
 import org.broadinstitute.sting.queue.util.{Logging, ProcessController}
 import java.io.{FileNotFoundException, File}
@@ -105,7 +106,7 @@ object PipelineTest extends BaseTest with Logging {
   private def assertMatchingMD5s(name: String, fileMD5s: Traversable[(File, String)], parameterize: Boolean) {
     var failed = 0
     for ((file, expectedMD5) <- fileMD5s) {
-      val calculatedMD5 = BaseTest.testFileMD5(name, file, expectedMD5, parameterize)
+      val calculatedMD5 = MD5DB.testFileMD5(name, file, expectedMD5, parameterize)
       if (!parameterize && expectedMD5 != "" && expectedMD5 != calculatedMD5)
         failed += 1
     }
diff --git a/public/testdata/exampleBAM.simple.bai b/public/testdata/exampleBAM.simple.bai
new file mode 100644
index 000000000..2d8268b1d
Binary files /dev/null and b/public/testdata/exampleBAM.simple.bai differ
diff --git a/public/testdata/exampleBAM.simple.bam b/public/testdata/exampleBAM.simple.bam
new file mode 100644
index 000000000..c3eb7ae7b
Binary files /dev/null and b/public/testdata/exampleBAM.simple.bam differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1941.jar b/settings/repository/edu.mit.broad/picard-private-parts-1941.jar
deleted file mode 100644
index 760db5cb8..000000000
Binary files a/settings/repository/edu.mit.broad/picard-private-parts-1941.jar and /dev/null differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1959.jar b/settings/repository/edu.mit.broad/picard-private-parts-1959.jar
new file mode 100644
index 000000000..ae11e636b
Binary files /dev/null and b/settings/repository/edu.mit.broad/picard-private-parts-1959.jar differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1941.xml b/settings/repository/edu.mit.broad/picard-private-parts-1959.xml
similarity index 58%
rename from settings/repository/edu.mit.broad/picard-private-parts-1941.xml
rename to settings/repository/edu.mit.broad/picard-private-parts-1959.xml
index 07d51ae53..e7c7e3a21 100644
--- a/settings/repository/edu.mit.broad/picard-private-parts-1941.xml
+++ b/settings/repository/edu.mit.broad/picard-private-parts-1959.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1941" status="integration" publication="20110614114100" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1959" status="integration" publication="20110718185300" />
 </ivy-module>
diff --git a/settings/repository/net.sf/picard-1.47.869.xml b/settings/repository/net.sf/picard-1.47.869.xml
deleted file mode 100644
index 86d07d4fa..000000000
--- a/settings/repository/net.sf/picard-1.47.869.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.47.869" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.47.869.jar b/settings/repository/net.sf/picard-1.49.895.jar
similarity index 87%
rename from settings/repository/net.sf/picard-1.47.869.jar
rename to settings/repository/net.sf/picard-1.49.895.jar
index d277fd217..3ee1f2090 100644
Binary files a/settings/repository/net.sf/picard-1.47.869.jar and b/settings/repository/net.sf/picard-1.49.895.jar differ
diff --git a/settings/repository/net.sf/picard-1.49.895.xml b/settings/repository/net.sf/picard-1.49.895.xml
new file mode 100644
index 000000000..52d4900c5
--- /dev/null
+++ b/settings/repository/net.sf/picard-1.49.895.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.49.895" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.47.869.xml b/settings/repository/net.sf/sam-1.47.869.xml
deleted file mode 100644
index 1b76fe2f9..000000000
--- a/settings/repository/net.sf/sam-1.47.869.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.47.869" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.47.869.jar b/settings/repository/net.sf/sam-1.49.895.jar
similarity index 91%
rename from settings/repository/net.sf/sam-1.47.869.jar
rename to settings/repository/net.sf/sam-1.49.895.jar
index 933b9cfd6..c55ab0b72 100644
Binary files a/settings/repository/net.sf/sam-1.47.869.jar and b/settings/repository/net.sf/sam-1.49.895.jar differ
diff --git a/settings/repository/net.sf/sam-1.49.895.xml b/settings/repository/net.sf/sam-1.49.895.xml
new file mode 100644
index 000000000..0436ce881
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.49.895.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.49.895" status="release" />
+</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>