diff --git a/java/src/org/broadinstitute/sting/alignment/Alignment.java b/java/src/org/broadinstitute/sting/alignment/Alignment.java
index e2ce1fab7..6fa1cb1c4 100644
--- a/java/src/org/broadinstitute/sting/alignment/Alignment.java
+++ b/java/src/org/broadinstitute/sting/alignment/Alignment.java
@@ -2,7 +2,6 @@ package org.broadinstitute.sting.alignment;
 
 import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 
diff --git a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
index aad9dd6b5..9a0545c02 100644
--- a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
@@ -30,7 +30,6 @@ 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.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/BWAConfiguration.java b/java/src/org/broadinstitute/sting/alignment/bwa/BWAConfiguration.java
index fb8000aa2..73441cb6a 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/BWAConfiguration.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/BWAConfiguration.java
@@ -1,7 +1,5 @@
 package org.broadinstitute.sting.alignment.bwa;
 
-import org.broadinstitute.sting.utils.StingException;
-
 /**
  * Configuration for the BWA/C aligner.
  *
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java b/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java
index 43d0b6ca3..ade0856e0 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java
@@ -1,8 +1,6 @@
 package org.broadinstitute.sting.alignment.bwa;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 import org.broadinstitute.sting.alignment.reference.bwt.BWT;
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java b/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
index 01c4672e9..75207f474 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
@@ -3,7 +3,6 @@ package org.broadinstitute.sting.alignment.bwa.c;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
index f8bb35f08..44f9894d7 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
@@ -3,7 +3,6 @@ package org.broadinstitute.sting.alignment.bwa.java;
 import org.broadinstitute.sting.alignment.Aligner;
 import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 
 import java.io.File;
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java
index b91c18416..8f32b20cd 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java
@@ -1,8 +1,6 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
-import org.broadinstitute.sting.alignment.bwa.java.AlignmentState;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Deque;
 import java.util.ArrayDeque;
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java
index eed0edaac..8129b4dac 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java
@@ -1,11 +1,7 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
 import org.broadinstitute.sting.alignment.Alignment;
-import org.broadinstitute.sting.alignment.bwa.java.BWAJavaAligner;
-import org.broadinstitute.sting.alignment.bwa.java.AlignmentMatchSequence;
-import org.broadinstitute.sting.alignment.bwa.java.AlignmentState;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import net.sf.samtools.Cigar;
 
 /**
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java
index f84385cca..c47642faa 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java
@@ -2,7 +2,6 @@ package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 /**
  * Represents the Burrows-Wheeler Transform of a reference sequence.
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java
index 7c4119295..7ec3da734 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.BasePackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java
index d1d9f0de0..901e1878a 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
 import org.broadinstitute.sting.alignment.reference.packing.BasePackedOutputStream;
 
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java
index 47e0cba8b..86653912f 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java
index 3dc2d794f..31868a165 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.HashMap;
 import java.util.Map;
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
index dbed5145e..a5f99792d 100755
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
@@ -32,7 +32,6 @@ import net.sf.picard.reference.ReferenceSequence;
 import java.io.*;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 
 /**
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
index e19c35374..4344a31b0 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Comparator;
 import java.util.TreeSet;
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java
index e9a95d66f..17ded2297 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java
index 6baf79cf1..da6b0d41d 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
 
 import java.io.*;
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
index 85cd9f47a..151fd0ebb 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.packing;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
 import java.nio.ByteOrder;
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java
index fd0eac58a..828ba52af 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.packing;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
 import java.nio.ByteBuffer;
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java
index 75dd6bd31..6ff2bf938 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.packing;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
 import java.io.IOException;
diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java
index 1139c1f55..a5647ec0f 100644
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java
@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 
 import java.lang.annotation.Annotation;
diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
index 4ae6f7803..58d985a2f 100644
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.List;
 import java.util.Collections;
diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
index 2d161ce5a..d4b774acd 100755
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Set;
 import java.util.HashSet;
diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java b/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java
index daa2ea5d6..93cabf0e3 100644
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java
@@ -25,7 +25,6 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.lang.annotation.Annotation;
 
diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java b/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
index 8c2c149cb..9fa9677c9 100644
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
@@ -26,10 +26,8 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.lang.reflect.Field;
-import java.lang.annotation.Annotation;
 import java.util.Arrays;
 import java.util.List;
 
diff --git a/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java b/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
index 6d1d07c85..29991bc72 100644
--- a/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
+++ b/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
@@ -26,8 +26,6 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java b/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
index 766b769b2..81555540f 100644
--- a/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
+++ b/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
@@ -29,14 +29,8 @@ import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.PrintStream;
 import java.util.*;
 
 import net.sf.picard.filter.SamRecordFilter;
diff --git a/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java b/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
index a790c9188..f9198a2ce 100755
--- a/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
+++ b/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
@@ -31,7 +31,6 @@ import java.util.HashMap;
 import java.util.Collections;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 /**
  * Holds a bunch of basic information about the traversal.
diff --git a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
index 4474eafe9..523fd4e88 100755
--- a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
@@ -32,7 +32,6 @@ import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.help.DescriptionTaglet;
 import org.broadinstitute.sting.utils.help.DisplayNameTaglet;
diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index d54757d4e..00a076d69 100755
--- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -28,7 +28,6 @@ package org.broadinstitute.sting.gatk.arguments;
 import net.sf.samtools.SAMFileReader;
 import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Input;
@@ -77,7 +76,7 @@ public class GATKArgumentCollection {
 
     @Element(required = false)
     @Argument(fullName = "phone_home", shortName = "et", doc="What kind of GATK run report should we generate?  Standard is the default, can be verbose or NO_ET so nothing is posted to the run repository", required = false)
-    public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.NO_ET;
+    public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.STANDARD;
 
     @ElementList(required = false)
     @Argument(fullName = "read_filter", shortName = "rf", doc = "Specify filtration criteria to apply to each read individually.", required = false)
diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
index 8005dc64e..49ea45901 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
@@ -28,10 +28,8 @@ package org.broadinstitute.sting.gatk.contexts;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
index 2bb02493e..c550b04bd 100644
--- a/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
@@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.contexts;
 
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 import net.sf.samtools.util.StringUtil;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java b/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java
index a6933918b..14e90ba95 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 /**
  * User: aaron
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
index 92ef09376..2801e2b8b 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
@@ -3,15 +3,11 @@ package org.broadinstitute.sting.gatk.datasources.providers;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.StingException;
 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 net.sf.samtools.util.StringUtil;
-
-import java.util.List;
 /*
  * Copyright (c) 2009 The Broad Institute
  *
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
index 7b52d3711..98582ce41 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
@@ -1,11 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
 import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMSequenceRecord;
-import net.sf.samtools.util.StringUtil;
-import net.sf.picard.reference.ReferenceSequence;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
index 68d9007f9..6df5f7a26 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
@@ -3,7 +3,6 @@ package org.broadinstitute.sting.gatk.datasources.providers;
 import org.broadinstitute.sting.gatk.datasources.shards.Shard;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java
index 1dd4f61d1..0ec3eead2 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.shards;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.gatk.ReadMetrics;
 import org.broadinstitute.sting.gatk.ReadProperties;
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShardStrategy.java
index e34f3cf12..010a6d815 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShardStrategy.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShardStrategy.java
@@ -1,16 +1,12 @@
 package org.broadinstitute.sting.gatk.datasources.shards;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
 
 import java.util.Iterator;
 import java.util.NoSuchElementException;
 import java.util.List;
 
-import net.sf.samtools.SAMSequenceDictionary;
-
 /**
  * Create a giant shard representing all the data in the input BAM(s).
  *
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java
index 344f55d69..db6d4d0da 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java
@@ -3,7 +3,6 @@ package org.broadinstitute.sting.gatk.datasources.shards;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java
index 70a5713dd..2308bc5d4 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java
@@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.List;
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java
index 314ad8eb7..4446e90d2 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 /**
  *
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java
index 819fa04c4..62826007f 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java
@@ -3,7 +3,6 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 
 /*
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java b/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java
index 101a0c464..e0448cd13 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java
@@ -28,7 +28,6 @@ package org.broadinstitute.sting.gatk.datasources.utilities;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.instrumentation.Sizeof;
 
 import java.io.File;
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java b/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
index 4776b12f3..1a23eb2bf 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
@@ -33,7 +33,6 @@ import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
index f5020bef7..6e83e6b46 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
@@ -8,9 +8,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.io.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.ReadMetrics;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
 
 import javax.management.MBeanServer;
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
index cd2fea839..4b1678f32 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
@@ -9,7 +9,6 @@ import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.concurrent.Callable;
 /**
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java b/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
index 99470f19a..47b8a048a 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
@@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.executive;
 
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.concurrent.Callable;
 import java.util.concurrent.Future;
diff --git a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
index 25641c12f..bb6d762fa 100755
--- a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
@@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.io;
 
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.ArgumentSource;
 import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
 import org.broadinstitute.sting.gatk.walkers.Walker;
@@ -36,7 +35,6 @@ 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.io.storage.OutputStreamStorage;
 
 import java.io.*;
 import java.lang.reflect.Field;
diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java b/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
index 56000f49f..0edeb0eb6 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
@@ -30,7 +30,6 @@ import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
index 166d4fbed..553d655b5 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java
@@ -26,16 +26,12 @@
 package org.broadinstitute.sting.gatk.io.stubs;
 
 import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 
 import java.io.OutputStream;
 import java.io.File;
 import java.lang.reflect.Constructor;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Field;
 
 /**
  * Insert an OutputStreamStub instead of a full-fledged concrete OutputStream implementations.
diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java
index cb4dd76d5..ce583ff57 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java
@@ -29,11 +29,9 @@ import net.sf.samtools.util.CloseableIterator;
 
 import java.util.Queue;
 import java.util.LinkedList;
-import java.util.Iterator;
 import java.util.NoSuchElementException;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 /**
  * Buffers access to a large stream of reads, replenishing the buffer only when the reads  
diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java b/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java
index 3bec57cd6..40febd06e 100755
--- a/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java
@@ -5,9 +5,6 @@ import net.sf.samtools.util.CloseableIterator;
 
 import java.util.Iterator;
 
-import org.broadinstitute.sting.gatk.ReadProperties;
-import org.broadinstitute.sting.utils.StingException;
-
 /**
  *
  * User: aaron
diff --git a/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
index ce3748a58..998b69bb0 100644
--- a/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
+++ b/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
@@ -31,7 +31,6 @@ 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.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.simpleframework.xml.Element;
 import org.simpleframework.xml.ElementList;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java b/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java
index 9afbba9f6..e95d394f0 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java
@@ -2,9 +2,7 @@ package org.broadinstitute.sting.gatk.refdata;
 
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 
-import java.util.Iterator;
 import java.io.File;
 import java.io.IOException;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java b/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java
index ace6300b8..e19b220b2 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java
@@ -4,7 +4,6 @@ import org.broad.tribble.util.variantcontext.Allele;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java b/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
index c983e2a34..96312d84c 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
@@ -4,7 +4,6 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
index a0c303408..3a6dbd291 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
@@ -7,7 +7,6 @@ import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java
index 0b29f10c3..48d5af0da 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java
@@ -24,7 +24,6 @@
 package org.broadinstitute.sting.gatk.refdata.tracks;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 
 /**
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java
index aa0dce51e..4f9191ed1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Comparator;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
index 854396e39..3e86408ef 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.fasta;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.PrintStream;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
index 1f958e89d..f62898643 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.gatk.walkers.filters;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
index 0430c604e..6abdf7fef 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
@@ -4,7 +4,6 @@ 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.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileWriter;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java
index 3fba72c49..173745552 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java
@@ -8,7 +8,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 
 @Analysis(name = "Count Variants", description = "Counts different classes of variants in the sample")
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java
index a8faf7c74..1b463cd6f 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java
@@ -8,7 +8,6 @@ import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.playground.utils.report.utils.TableType;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 /**
  * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java
index cb707a084..51dc5a5d2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java
@@ -9,7 +9,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.List;
 import java.util.Arrays;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java
index c64c5c070..cb840cda0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java
@@ -9,7 +9,6 @@ import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.playground.utils.report.utils.TableType;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.ArrayList;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
index 712bda9d6..4e23d4d62 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
@@ -25,22 +25,14 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broad.tribble.util.variantcontext.VariantContext;
-import org.broad.tribble.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.gatk.contexts.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-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.annotator.VariantAnnotatorEngine;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.vcf.VCFUtils;
 
 import java.io.PrintStream;
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
index 1164c54c4..0774584a0 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
@@ -37,7 +37,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.PrintStream;
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java
index 72ac5ff7f..33252ed58 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java
@@ -10,7 +10,6 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Output;
 
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java
index ac154bca4..23dace679 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java
@@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
 
 import java.util.ArrayList;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
index 1e9fc2bdc..043ad838c 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
@@ -13,7 +13,6 @@ import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 
 import java.io.File;
diff --git a/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java b/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java
index 350f37228..6bbb8f0aa 100644
--- a/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java
+++ b/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java
@@ -29,7 +29,6 @@ import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.PathUtils;
 import org.broadinstitute.sting.playground.utils.ProcessUtils;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
index fd6fbe4c5..1cb818349 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
@@ -40,7 +40,6 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java
index 4619b33e5..eabc9181b 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java
@@ -36,7 +36,6 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java
index b6355b1e0..0277b4c80 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java
@@ -26,7 +26,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.phasing;
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
+
 import java.util.ArrayList;
 import java.util.List;
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java
index 9804c58fd..97d36ad0e 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java
@@ -27,7 +27,6 @@ import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 public class BialleleSNP extends Biallele {
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java
index 470ab5d88..6ad907481 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java
@@ -11,7 +11,6 @@ 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.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
 import java.math.BigInteger;
diff --git a/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java b/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java
index 166d6ece7..111fe5ccc 100644
--- a/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java
@@ -27,7 +27,6 @@ package org.broadinstitute.sting.playground.utils;
 
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.StingException;
 import org.apache.log4j.Logger;
 
 /**
diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java b/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java
index fde4f31b3..71a6f310f 100644
--- a/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java
@@ -27,11 +27,9 @@ import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.playground.utils.report.tags.Param;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.lang.annotation.Annotation;
 import java.lang.reflect.Field;
-import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.Map;
 
diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java b/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java
index 9904db5ac..f947e7d36 100644
--- a/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java
@@ -28,7 +28,6 @@ import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat;
 import org.broadinstitute.sting.playground.utils.report.utils.ComplexDataUtils;
 import org.broadinstitute.sting.playground.utils.report.utils.Node;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
 import java.lang.reflect.Field;
diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java b/java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java
index b72bce656..b77ca24be 100644
--- a/java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java
@@ -2,7 +2,6 @@ package org.broadinstitute.sting.playground.utils.report;
 
 import org.broadinstitute.sting.playground.utils.report.templates.*;
 import org.broadinstitute.sting.playground.utils.report.utils.Node;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 
 import java.io.*;
diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/utils/Node.java b/java/src/org/broadinstitute/sting/playground/utils/report/utils/Node.java
index 7ebf09eaf..e597300fb 100644
--- a/java/src/org/broadinstitute/sting/playground/utils/report/utils/Node.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/report/utils/Node.java
@@ -1,7 +1,5 @@
 package org.broadinstitute.sting.playground.utils.report.utils;
 
-import org.broadinstitute.sting.utils.StingException;
-
 import java.util.*;
 
 /**
diff --git a/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java b/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
index 6adb4d371..8d59b7665 100644
--- a/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
+++ b/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
@@ -40,7 +40,6 @@ import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescripto
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackManager;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
 import java.io.IOException;
diff --git a/java/src/org/broadinstitute/sting/utils/GATKException.java b/java/src/org/broadinstitute/sting/utils/GATKException.java
index 883dba7ab..291e50f39 100644
--- a/java/src/org/broadinstitute/sting/utils/GATKException.java
+++ b/java/src/org/broadinstitute/sting/utils/GATKException.java
@@ -24,6 +24,8 @@
 
 package org.broadinstitute.sting.utils;
 
+import org.broadinstitute.sting.utils.exceptions.StingException;
+
 /**
  * Temp class to track split from Sting exception to UserException
  */
diff --git a/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java b/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
index 62dc3f237..acb873515 100755
--- a/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.utils.classloader;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.lang.reflect.Modifier;
 import java.lang.reflect.Field;
@@ -34,7 +33,6 @@ import java.io.File;
 import java.io.IOException;
 import java.util.List;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.Arrays;
 
 /**
diff --git a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java
index 0997f560e..c146c50f6 100755
--- a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java
@@ -27,9 +27,7 @@ package org.broadinstitute.sting.utils.classloader;
 
 import ch.qos.logback.classic.Level;
 import ch.qos.logback.classic.Logger;
-import ch.qos.logback.classic.LoggerContext;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.reflections.Reflections;
 import org.reflections.scanners.SubTypesScanner;
diff --git a/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java b/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java
index 69bc5fd8d..54c33d447 100644
--- a/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java
+++ b/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java
@@ -26,8 +26,6 @@
 package org.broadinstitute.sting.utils.classloader;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.classloader.PackageUtils;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 
 import java.util.HashMap;
diff --git a/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java b/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java
index 6272d1873..93a442da8 100644
--- a/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java
+++ b/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java
@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.utils.collections;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 
 /** This class, closely resembling a deque (except that it is not dynamically grown), 
diff --git a/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java b/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java
index e2b57b94b..c40b1108e 100644
--- a/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java
+++ b/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java
@@ -29,7 +29,6 @@ import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODItera
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java b/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java
index dd340a61b..b6d919499 100644
--- a/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.utils.fasta;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
diff --git a/java/src/org/broadinstitute/sting/utils/fastq/FastqRecord.java b/java/src/org/broadinstitute/sting/utils/fastq/FastqRecord.java
index ebf3396e7..087e1a54e 100755
--- a/java/src/org/broadinstitute/sting/utils/fastq/FastqRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/fastq/FastqRecord.java
@@ -1,10 +1,5 @@
 package org.broadinstitute.sting.utils.fastq;
 
-import org.broadinstitute.sting.utils.StingException;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-
 public class FastqRecord {
     private String seqHeader;
     private String seqLine;
diff --git a/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java b/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java
index 851c2c714..5ca9f0971 100644
--- a/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java
+++ b/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java
@@ -2,7 +2,6 @@ package org.broadinstitute.sting.utils.file;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
 import java.io.IOException;
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java b/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java
index 7a5c51b61..6cc943fea 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java
@@ -4,7 +4,6 @@ import edu.mit.broad.picard.genotype.DiploidGenotype;
 import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods;
 import net.sf.samtools.SAMFileHeader;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.HashMap;
 
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java
index bc289536d..7e481061c 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java
@@ -2,7 +2,6 @@ package org.broadinstitute.sting.utils.genotype.glf;
 
 import net.sf.samtools.util.BinaryCodec;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 
 /*
diff --git a/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java b/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java
index bfce3f197..cd51e3698 100644
--- a/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java
+++ b/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java
@@ -27,7 +27,6 @@ package org.broadinstitute.sting.utils.help;
 
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 
 import java.util.List;
diff --git a/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
index 4874f6205..f7760d5e7 100644
--- a/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
+++ b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
@@ -32,7 +32,6 @@ import java.io.PrintStream;
 import java.io.IOException;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.gatk.walkers.Walker;
diff --git a/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java b/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java
index c1dbf1018..1b9a5009d 100644
--- a/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java
+++ b/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java
@@ -25,7 +25,6 @@
 package org.broadinstitute.sting.utils.instrumentation;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.lang.instrument.Instrumentation;
 import java.lang.reflect.Field;
diff --git a/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
index 9e4ec5413..4c5f9db18 100644
--- a/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
+++ b/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
@@ -24,10 +24,8 @@
 
 package org.broadinstitute.sting.utils.pileup;
 
-import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.gatk.iterators.IterableIterator;
 
diff --git a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
index 70a51dd8a..f873ca076 100644
--- a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
+++ b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
@@ -25,7 +25,6 @@ package org.broadinstitute.sting.utils.pileup;
 
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.collections.Pair;
 
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
index 2c18e92dc..d26f61596 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -33,7 +33,6 @@ import net.sf.samtools.util.StringUtil;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.pileup.*;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 
 import java.util.ArrayList;
diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java
index 7eec6ed6f..c535b0d6d 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java
@@ -11,7 +11,6 @@ import java.io.UnsupportedEncodingException;
 import java.util.*;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 /**
diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java
index 45927175b..ced8e4f4b 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java
@@ -7,7 +7,6 @@ import net.sf.samtools.SAMRecord;
 import java.util.List;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 
 /*
diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
index aeefafa6c..88696d465 100755
--- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
@@ -3,7 +3,6 @@ package org.broadinstitute.sting.utils.sam;
 import net.sf.samtools.*;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
 import java.util.ArrayList;
diff --git a/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java b/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java
index 899b6cd5c..9e71e7836 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java
@@ -30,7 +30,6 @@ import net.sf.samtools.SAMFileReader;
 import java.io.File;
 
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 /**
  * Allows the user to steadily accumulate information about what
diff --git a/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java b/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java
index 36cb89686..d36617958 100644
--- a/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java
@@ -27,7 +27,6 @@ package org.broadinstitute.sting.utils.text;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
 import java.util.regex.Pattern;
diff --git a/java/test/org/broadinstitute/sting/BaseTest.java b/java/test/org/broadinstitute/sting/BaseTest.java
index a613e0e24..c7e248569 100755
--- a/java/test/org/broadinstitute/sting/BaseTest.java
+++ b/java/test/org/broadinstitute/sting/BaseTest.java
@@ -3,7 +3,6 @@ package org.broadinstitute.sting;
 import org.apache.log4j.*;
 import org.apache.log4j.spi.LoggingEvent;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.junit.*;
 
 import java.io.*;
diff --git a/java/test/org/broadinstitute/sting/WalkerTest.java b/java/test/org/broadinstitute/sting/WalkerTest.java
index d0d0582b5..20787a14e 100755
--- a/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -30,7 +30,6 @@ import org.broadinstitute.sting.gatk.CommandLineExecutable;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.junit.Test;
 import org.apache.commons.io.FileUtils;
diff --git a/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java b/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
index c97761897..c71d93902 100755
--- a/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
+++ b/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
@@ -27,7 +27,6 @@ package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GATKException;
-import org.broadinstitute.sting.utils.StingException;
 import org.junit.Test;
 import org.junit.Before;
 import org.junit.Assert;
diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java
index c4aef7351..952ee4361 100755
--- a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java
@@ -5,7 +5,6 @@ import org.junit.Before;
 import org.junit.Assert;
 import org.junit.Test;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Collection;
 import java.util.Collections;
diff --git a/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java b/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java
index 3982e3542..c4aec6c32 100644
--- a/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java
@@ -4,7 +4,6 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.StingException;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.junit.Assert;
diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java
index 9b327f7a1..7ca4fb092 100644
--- a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java
@@ -29,7 +29,6 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.StingException;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
index f3477139e..3f6172b07 100644
--- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
@@ -9,7 +9,6 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.TribbleRMDTrackBuilder;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.junit.Assert;
 import org.junit.Test;