diff --git a/ivy.xml b/ivy.xml
index 5a8c3986a..a96567889 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -100,6 +100,9 @@
     <!-- MongoDB for the GXDB project -->
     <dependency org="org.mongodb" name="mongo-java-driver" rev="2.7.3"/>
 
+    <!-- GSON for talking to the REST API on Vanilla Forums -->
+    <dependency org="com.google.code.gson" name="gson" rev="2.2.2"/>
+
     <!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
     <exclude org="javax.servlet" />
     <exclude org="javax.jms" />
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAMWalker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java
similarity index 98%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAMWalker.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java
index 3e07295e7..f8c9c5396 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAMWalker.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java
@@ -40,7 +40,7 @@ import java.util.Map;
  */
 
 @ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class})
-public class CompareBAMWalker extends LocusWalker<Map<CompareBAMWalker.TestName, Boolean>, CompareBAMWalker.TestResults> {
+public class CompareBAM extends LocusWalker<Map<CompareBAM.TestName, Boolean>, CompareBAM.TestResults> {
     @Argument(required = true,  shortName = "rr",  fullName = "reduced_readgroup", doc = "The read group ID corresponding to the compressed BAM being tested") public String reducedReadGroupID;
     @Argument(required = false, shortName = "teq", fullName = "test_equal_bases",  doc = "Test if the bases marked as '=' are indeed ref bases.")              public boolean TEST_EQUAL_BASES = false;
     @Argument(required = false, shortName = "tbc", fullName = "test_base_counts",  doc = "Test if the base counts tag in consensus reads are accurate.")       public boolean TEST_BASE_COUNTS = false;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java
index 0ac9630c2..44971ca38 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java
@@ -53,7 +53,7 @@ public class MultiSampleCompressor implements Compressor {
                                  final double minAltProportionToTriggerVariant,
                                  final double minIndelProportionToTriggerVariant,
                                  final int minBaseQual,
-                                 final ReduceReadsWalker.DownsampleStrategy downsampleStrategy) {
+                                 final ReduceReads.DownsampleStrategy downsampleStrategy) {
         for ( String name : SampleUtils.getSAMFileSamples(header) ) {
             compressorsPerSample.put(name,
                     new SingleSampleCompressor(name, contextSize, downsampleCoverage,
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
similarity index 99%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
index 1b11cbd4e..d793ae159 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
@@ -83,7 +83,7 @@ import java.util.*;
 
 @PartitionBy(PartitionType.INTERVAL)
 @ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class, BadCigarFilter.class})
-public class ReduceReadsWalker extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceReadsStash> {
+public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceReadsStash> {
 
     @Output
     protected StingSAMFileWriter out;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java
index fd0dfa1ff..6d2c2d215 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java
@@ -26,7 +26,7 @@ public class SingleSampleCompressor implements Compressor {
     protected double minIndelProportionToTriggerVariant;
     protected int minBaseQual;
 
-    protected ReduceReadsWalker.DownsampleStrategy downsampleStrategy;
+    protected ReduceReads.DownsampleStrategy downsampleStrategy;
 
     public SingleSampleCompressor(final String sampleName,
                                   final int contextSize,
@@ -35,7 +35,7 @@ public class SingleSampleCompressor implements Compressor {
                                   final double minAltProportionToTriggerVariant,
                                   final double minIndelProportionToTriggerVariant,
                                   final int minBaseQual,
-                                  final ReduceReadsWalker.DownsampleStrategy downsampleStrategy) {
+                                  final ReduceReads.DownsampleStrategy downsampleStrategy) {
         this.sampleName = sampleName;
         this.contextSize = contextSize;
         this.downsampleCoverage = downsampleCoverage;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
index 68dfd041b..60d7096a3 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
@@ -53,7 +53,7 @@ public class SlidingWindow {
     protected int MIN_BASE_QUAL_TO_COUNT;                                                                               // qual has to be greater than or equal to this value
     protected int MIN_MAPPING_QUALITY;
 
-    protected ReduceReadsWalker.DownsampleStrategy downsampleStrategy;
+    protected ReduceReads.DownsampleStrategy downsampleStrategy;
     private boolean hasIndelQualities;
 
     /**
@@ -82,7 +82,7 @@ public class SlidingWindow {
     }
 
 
-    public SlidingWindow(String contig, int contigIndex, int contextSize, SAMFileHeader header, GATKSAMReadGroupRecord readGroupAttribute, int windowNumber, final double minAltProportionToTriggerVariant, final double minIndelProportionToTriggerVariant, int minBaseQual, int minMappingQuality, int downsampleCoverage, final ReduceReadsWalker.DownsampleStrategy downsampleStrategy, boolean hasIndelQualities) {
+    public SlidingWindow(String contig, int contigIndex, int contextSize, SAMFileHeader header, GATKSAMReadGroupRecord readGroupAttribute, int windowNumber, final double minAltProportionToTriggerVariant, final double minIndelProportionToTriggerVariant, int minBaseQual, int minMappingQuality, int downsampleCoverage, final ReduceReads.DownsampleStrategy downsampleStrategy, boolean hasIndelQualities) {
         this.stopLocation = -1;
         this.contextSize = contextSize;
         this.downsampleCoverage = downsampleCoverage;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index bda94cc8f..546f53002 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -33,20 +33,21 @@ import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 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.filters.*;
+import org.broadinstitute.sting.gatk.filters.BadMateFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.walkers.ActiveRegionExtension;
+import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
+import org.broadinstitute.sting.gatk.walkers.PartitionBy;
+import org.broadinstitute.sting.gatk.walkers.PartitionType;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
 import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
 import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
 import org.broadinstitute.sting.utils.clipping.ReadClipper;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
@@ -56,6 +57,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 
 import java.io.FileNotFoundException;
 import java.io.PrintStream;
@@ -90,7 +92,7 @@ import java.util.*;
 
 @PartitionBy(PartitionType.LOCUS)
 @ActiveRegionExtension(extension=65, maxRegion=275)
-public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implements AnnotatorCompatibleWalker {
+public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implements AnnotatorCompatible {
 
     /**
      * A raw, unfiltered, highly specific callset in VCF format.
@@ -361,7 +363,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
     //---------------------------------------------------------------------------------------------------------------
 
     @Override
-    public Integer map( final ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker ) {
+    public Integer map( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker ) {
 
         final ArrayList<VariantContext> activeAllelesToGenotype = new ArrayList<VariantContext>();
 
@@ -476,7 +478,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
     //
     //---------------------------------------------------------------------------------------------------------------
 
-    private void finalizeActiveRegion( final ActiveRegion activeRegion ) {
+    private void finalizeActiveRegion( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) {
         if( DEBUG ) { System.out.println("\nAssembling " + activeRegion.getExtendedLoc() + " with " + activeRegion.size() + " reads:"); }
         final ArrayList<GATKSAMRecord> finalizedReadList = new ArrayList<GATKSAMRecord>();
         final FragmentCollection<GATKSAMRecord> fragmentCollection = FragmentUtils.create( ReadUtils.sortReadsByCoordinate(activeRegion.getReads()) );
@@ -503,7 +505,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         }
     }
 
-    private List<GATKSAMRecord> filterNonPassingReads( final ActiveRegion activeRegion ) {
+    private List<GATKSAMRecord> filterNonPassingReads( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) {
         final ArrayList<GATKSAMRecord> readsToRemove = new ArrayList<GATKSAMRecord>();
         for( final GATKSAMRecord rec : activeRegion.getReads() ) {
             if( rec.getReadLength() < 24 || rec.getMappingQuality() <= 20 || BadMateFilter.hasBadMate(rec) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) {
@@ -514,7 +516,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         return readsToRemove;
     }
 
-    private GenomeLoc getPaddedLoc( final ActiveRegion activeRegion ) {
+    private GenomeLoc getPaddedLoc( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) {
         final int padLeft = Math.max(activeRegion.getReferenceLoc().getStart()-REFERENCE_PADDING, 1);
         final int padRight = Math.min(activeRegion.getReferenceLoc().getStop()+REFERENCE_PADDING, referenceReader.getSequenceDictionary().getSequence(activeRegion.getReferenceLoc().getContig()).getSequenceLength());
         return getToolkit().getGenomeLocParser().createGenomeLoc(activeRegion.getReferenceLoc().getContig(), padLeft, padRight);
diff --git a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
rename to public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java
index a342cf932..7af83d14b 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java
@@ -46,7 +46,7 @@ import java.util.Iterator;
  * @author mhanna
  * @version 0.1
  */
-public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
+public class AlignmentValidation extends ReadWalker<Integer,Integer> {
     /**
      * The supporting BWT index generated using BWT. 
      */
diff --git a/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java b/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignments.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
rename to public/java/src/org/broadinstitute/sting/alignment/CountBestAlignments.java
index d91b83e7a..b0580fe50 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignments.java
@@ -48,7 +48,7 @@ import java.util.TreeMap;
  * @author mhanna
  * @version 0.1
  */
-public class CountBestAlignmentsWalker extends ReadWalker<Integer,Integer> {
+public class CountBestAlignments extends ReadWalker<Integer,Integer> {
     /**
      * The supporting BWT index generated using BWT.
      */
diff --git a/public/java/src/org/broadinstitute/sting/gatk/Categorize.java b/public/java/src/org/broadinstitute/sting/gatk/Categorize.java
new file mode 100644
index 000000000..b8a222983
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/Categorize.java
@@ -0,0 +1,38 @@
+/*
+ * Copyright (c) 2012, 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;
+
+import java.lang.annotation.*;
+
+/**
+ * Allows the walker to be tagged, they can have an unlimited number of categories.
+ */
+@Documented
+@Inherited
+@Retention(RetentionPolicy.RUNTIME)
+@Target(ElementType.TYPE)
+public @interface Categorize {
+    public Category[] value() default {Category.UNCATEGORIZED};
+}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/Category.java b/public/java/src/org/broadinstitute/sting/gatk/Category.java
new file mode 100644
index 000000000..d1f890f95
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/Category.java
@@ -0,0 +1,68 @@
+/*
+ * Copyright (c) 2012, 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;
+
+public enum Category {
+
+    BAM_PROCESSING("Walker", "BAM Processing and Analysis Tools"),
+
+    COMPANION("Walker", "Companion Utilities"),
+
+    CANCER_SPECIFIC("Walker", "Cancer-specific Variant Discovery Tools"),
+
+    QUALITY_CONTROL("Walker", "Quality Control and Simple Analysis Tools"),
+
+    VALIDATION("Walker", "Validation Utilities"),
+
+    VARIANT_DETECTION("ex", "Variant Detection"),
+
+    VARIANT_DISCOVERY("Walker", "Variant Discovery Tools"),
+
+    VARIANT_EVALUATION("Walker", "Variant Evaluation and Manipulation Tools"),
+
+    EXPERIMENTAL("Walker", "Miscellaneous Experimental (and Potentially Unstable) Tools"),
+
+    UNCATEGORIZED("all", "No category");
+
+    private final String description;
+
+    /**
+     * Accepted strings are from the GATKDocWorkUnit.group
+     */
+    private final String type;
+
+    private Category(String type, String description) {
+        this.description = description;
+        this.type = type;
+    }
+
+    public String type() {
+        return type;
+    }
+
+    public String getDescription() {
+        return description;
+    }
+}
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 16487054b..b35abb775 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
@@ -11,7 +11,6 @@ import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.io.DirectOutputTracker;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 import org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.SampleUtils;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
index 6d0ec0e7c..1b9c12fb0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
@@ -6,10 +6,12 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.providers.*;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.walkers.ActiveRegionExtension;
+import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
 import org.broadinstitute.sting.utils.activeregion.ActivityProfile;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@@ -28,7 +30,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
      */
     protected static Logger logger = Logger.getLogger(TraversalEngine.class);
 
-    private final LinkedList<ActiveRegion> workQueue = new LinkedList<ActiveRegion>();
+    private final LinkedList<org.broadinstitute.sting.utils.activeregion.ActiveRegion> workQueue = new LinkedList<org.broadinstitute.sting.utils.activeregion.ActiveRegion>();
     private final LinkedHashSet<GATKSAMRecord> myReads = new LinkedHashSet<GATKSAMRecord>();
 
     @Override
@@ -109,18 +111,18 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
             // add these blocks of work to the work queue
             // band-pass filter the list of isActive probabilities and turn into active regions
             final ActivityProfile bandPassFiltered = profile.bandPassFilter();
-            final List<ActiveRegion> activeRegions = bandPassFiltered.createActiveRegions( activeRegionExtension, maxRegionSize );
+            final List<org.broadinstitute.sting.utils.activeregion.ActiveRegion> activeRegions = bandPassFiltered.createActiveRegions( activeRegionExtension, maxRegionSize );
 
             // add active regions to queue of regions to process
             // first check if can merge active regions over shard boundaries
             if( !activeRegions.isEmpty() ) {
                 if( !workQueue.isEmpty() ) {
-                    final ActiveRegion last = workQueue.getLast();
-                    final ActiveRegion first = activeRegions.get(0);
+                    final org.broadinstitute.sting.utils.activeregion.ActiveRegion last = workQueue.getLast();
+                    final org.broadinstitute.sting.utils.activeregion.ActiveRegion first = activeRegions.get(0);
                     if( last.isActive == first.isActive && last.getLocation().contiguousP(first.getLocation()) && last.getLocation().size() + first.getLocation().size() <= maxRegionSize ) {
                         workQueue.removeLast();
                         activeRegions.remove(first);
-                        workQueue.add( new ActiveRegion(last.getLocation().union(first.getLocation()), first.isActive, this.engine.getGenomeLocParser(), activeRegionExtension) );
+                        workQueue.add( new org.broadinstitute.sting.utils.activeregion.ActiveRegion(last.getLocation().union(first.getLocation()), first.isActive, this.engine.getGenomeLocParser(), activeRegionExtension) );
                     }
                 }
                 workQueue.addAll( activeRegions );
@@ -183,7 +185,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
      */
     private void writeActiveRegionsToStream( final ActiveRegionWalker<M,T> walker ) {
         // Just want to output the active regions to a file, not actually process them
-        for( final ActiveRegion activeRegion : workQueue ) {
+        for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion : workQueue ) {
             if( activeRegion.isActive ) {
                 walker.activeRegionOutStream.println( activeRegion.getLocation() );
             }
@@ -196,7 +198,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
         while( workQueue.peek() != null ) {
             final GenomeLoc extendedLoc = workQueue.peek().getExtendedLoc();
             if ( extendedLoc.getStop() < minStart || (currentContig != null && !workQueue.peek().getExtendedLoc().getContig().equals(currentContig))) {
-                final ActiveRegion activeRegion = workQueue.remove();
+                final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion = workQueue.remove();
                 sum = processActiveRegion( activeRegion, myReads, workQueue, sum, walker );
             } else {
                 break;
@@ -206,15 +208,15 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
         return sum;
     }
 
-    private T processActiveRegion( final ActiveRegion activeRegion, final LinkedHashSet<GATKSAMRecord> reads, final Queue<ActiveRegion> workQueue, final T sum, final ActiveRegionWalker<M,T> walker ) {
+    private T processActiveRegion( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final LinkedHashSet<GATKSAMRecord> reads, final Queue<org.broadinstitute.sting.utils.activeregion.ActiveRegion> workQueue, final T sum, final ActiveRegionWalker<M,T> walker ) {
         final ArrayList<GATKSAMRecord> placedReads = new ArrayList<GATKSAMRecord>();
         for( final GATKSAMRecord read : reads ) {
             final GenomeLoc readLoc = this.engine.getGenomeLocParser().createGenomeLoc( read );
             if( activeRegion.getLocation().overlapsP( readLoc ) ) {
                 // The region which the highest amount of overlap is chosen as the primary region for the read (tie breaking is done as right most region)
                 long maxOverlap = activeRegion.getLocation().sizeOfOverlap( readLoc );
-                ActiveRegion bestRegion = activeRegion;
-                for( final ActiveRegion otherRegionToTest : workQueue ) {
+                org.broadinstitute.sting.utils.activeregion.ActiveRegion bestRegion = activeRegion;
+                for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion otherRegionToTest : workQueue ) {
                     if( otherRegionToTest.getLocation().sizeOfOverlap(readLoc) >= maxOverlap ) {
                         maxOverlap = otherRegionToTest.getLocation().sizeOfOverlap( readLoc );
                         bestRegion = otherRegionToTest;
@@ -227,7 +229,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
                     if( !bestRegion.equals(activeRegion) ) {
                         activeRegion.add( read );
                     }
-                    for( final ActiveRegion otherRegionToTest : workQueue ) {
+                    for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion otherRegionToTest : workQueue ) {
                         if( !bestRegion.equals(otherRegionToTest) && otherRegionToTest.getExtendedLoc().overlapsP( readLoc ) ) {
                             otherRegionToTest.add( read );
                         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
index f217268d2..e38e166ea 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java
@@ -12,7 +12,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalSetRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
@@ -76,7 +75,7 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
     public abstract double isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context);
 
     // Map over the ActiveRegion
-    public abstract MapType map(final ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker);
+    public abstract MapType map(final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker);
 
     public final GenomeLocSortedSet extendIntervals( final GenomeLocSortedSet intervals, final GenomeLocParser genomeLocParser, IndexedFastaSequenceFile reference ) {
         final int activeRegionExtension = this.getClass().getAnnotation(ActiveRegionExtension.class).extension();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
index 74d8a8180..fb265d4e0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
@@ -149,7 +149,7 @@ import java.util.regex.Pattern;
  * @since 2010
  */
 @Requires({DataSource.READS})
-public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithData, ClipReadsWalker.ClippingData> {
+public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipReads.ClippingData> {
     /**
      * If provided, ClipReads will write summary statistics about the clipping operations applied
      * to the reads to this file.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNames.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNames.java
index 7f9269725..f6f091cfc 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNames.java
@@ -49,7 +49,7 @@ import java.util.Set;
  */
 @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT)
 @Requires({DataSource.READS, DataSource.REFERENCE})
-public class FindReadsWithNamesWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
+public class FindReadsWithNames extends ReadWalker<SAMRecord, SAMFileWriter> {
     /** an optional argument to dump the reads out to a BAM file */
     @Output(doc="Write output to this BAM filename instead of STDOUT")
     SAMFileWriter out;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java
index 0777037bf..e5f77018c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java
@@ -42,12 +42,12 @@ import java.text.NumberFormat;
  * @author aaron
  */
 @Requires({DataSource.READS})
-public class FlagStatWalker extends ReadWalker<Integer, Integer> {
+public class FlagStat extends ReadWalker<Integer, Integer> {
     @Output
     PrintStream out;
 
     // what comes out of the flagstat
-    static class FlagStat {
+    static class FlagStatus {
         long readCount = 0L;
         long QC_failure = 0L;
         long duplicates = 0L;
@@ -117,7 +117,7 @@ public class FlagStatWalker extends ReadWalker<Integer, Integer> {
     }
 
 
-    private FlagStat myStat = new FlagStat();
+    private FlagStatus myStat = new FlagStatus();
 
     public Integer map( ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker ) {
         myStat.readCount++;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java
index b3062c546..12b575760 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java
@@ -60,7 +60,7 @@ import java.util.List;
  * Associated command:
  * samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate] <in.alignment>
  */
-public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeReducible<Integer> {
+public class Pileup extends LocusWalker<Integer, Integer> implements TreeReducible<Integer> {
     @Output
     PrintStream out;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java
index 7960f5c35..cfc096ea2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java
@@ -39,7 +39,7 @@ import java.io.PrintStream;
  * Prints out all of the RODs in the input data set. Data is rendered using the toString() method
  * of the given ROD.
  */
-public class PrintRODsWalker extends RodWalker<Integer, Integer> {
+public class PrintRODs extends RodWalker<Integer, Integer> {
     @Input(fullName="input", shortName = "input", doc="The input ROD which should be printed out.", required=true)
     public RodBinding<Feature> input;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
index 4159a67b7..6e9960f3a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java
@@ -90,7 +90,7 @@ import java.util.TreeSet;
  */
 @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT)
 @Requires({DataSource.READS, DataSource.REFERENCE})
-public class PrintReadsWalker extends ReadWalker<GATKSAMRecord, SAMFileWriter> {
+public class PrintReads extends ReadWalker<GATKSAMRecord, SAMFileWriter> {
 
     @Output(doc="Write output to this BAM filename instead of STDOUT", required = true)
     SAMFileWriter out;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java
index baaaf9e28..e0ee072fe 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java
@@ -47,14 +47,14 @@ import java.util.Map;
  */
 @WalkerName("SplitSamFile")
 @Requires({DataSource.READS})
-public class SplitSamFileWalker extends ReadWalker<SAMRecord, Map<String, SAMFileWriter>> {
+public class SplitSamFile extends ReadWalker<SAMRecord, Map<String, SAMFileWriter>> {
     @Argument(fullName="outputRoot", doc="output BAM file", required=false)
     public String outputRoot = null;
 
     @Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files", required = false)
     public Integer BAMcompression = 5;    
 
-    private static Logger logger = Logger.getLogger(SplitSamFileWalker.class);
+    private static Logger logger = Logger.getLogger(SplitSamFile.class);
     private static String VERSION = "0.0.1";
 
     public void initialize() {
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 dc589699a..30f81b20c 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
@@ -28,7 +28,7 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@@ -51,7 +51,7 @@ public class AlleleBalance extends InfoFieldAnnotation {
 
 
     char[] BASES = {'A','C','G','T'};
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 
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 fd23fb8f6..11c9c3a99 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
@@ -3,7 +3,7 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.utils.MathUtils;
@@ -14,7 +14,9 @@ import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.List;
 
 
 /**
@@ -22,7 +24,7 @@ import java.util.*;
  */
 public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation {
 
-    public void annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, final GenotypeBuilder gb) {
+    public void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, final GenotypeBuilder gb) {
         Double ratio = annotateSNP(stratifiedContext, vc, g);
         if (ratio == null)
             return;
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 46aa6d0f3..c3b6de65a 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
@@ -34,7 +34,7 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@@ -52,7 +52,7 @@ import java.util.Map;
  */
 public class BaseCounts extends InfoFieldAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 
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 3d07e3a7a..54837baad 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
@@ -29,18 +29,17 @@ 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.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 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.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 
@@ -62,14 +61,14 @@ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnn
 
     private Set<String> founderIds = new HashSet<String>();
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( ! vc.hasGenotypes() )
             return null;
 
         return VariantContextUtils.calculateChromosomeCounts(vc, new HashMap<String, Object>(), true,founderIds);
     }
 
-    public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ){
+    public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ){
         //If families were given, get the founders ids
         founderIds = ((Walker)walker).getSampleDB().getFounderIds();
     }
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 b36de0dac..28ca77f18 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
@@ -4,7 +4,7 @@ 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.ActiveRegionBasedAnnotation;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 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;
@@ -38,7 +38,7 @@ import java.util.Map;
  */
 public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 
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 d56daadea..523aa81b1 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
@@ -3,10 +3,12 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
@@ -14,7 +16,9 @@ import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
 
 
 /**
@@ -42,7 +46,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
 
     private static final String DEL = "DEL"; // constant, for speed: no need to create a key string for deletion allele every time
 
-    public void annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, GenotypeBuilder gb) {
+    public void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, GenotypeBuilder gb) {
         if ( g == null || !g.isCalled() )
             return;
 
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 6dc0ba3e1..4669cfef8 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
@@ -29,7 +29,7 @@ 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.ActiveRegionBasedAnnotation;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 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;
@@ -55,7 +55,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
     private static final String FS = "FS";
     private static final double MIN_PVALUE = 1E-320;
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( !vc.isVariant() )
             return null;
 
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 11a64b49f..263320d1b 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
@@ -3,7 +3,7 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.BaseUtils;
@@ -22,7 +22,7 @@ import java.util.Map;
  */
 public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         double content = computeGCContent(ref);
         Map<String, Object> map = new HashMap<String, Object>();
         map.put(getKeyNames().get(0), String.format("%.2f", content));
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 606de1b88..45444e05d 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
@@ -28,7 +28,7 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 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;
@@ -60,7 +60,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
     private final static int MAX_CONSENSUS_HAPLOTYPES_TO_CONSIDER = 50;
     private final static char REGEXP_WILDCARD = '.';
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if (stratifiedContexts.size() == 0) // size 0 means that call was made by someone else and we have no data here
             return null;
 
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 795cdbeb5..6ba85de07 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
@@ -4,7 +4,7 @@ import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation;
 import org.broadinstitute.sting.utils.QualityUtils;
@@ -29,7 +29,7 @@ public class HardyWeinberg extends InfoFieldAnnotation implements WorkInProgress
     private static final int MIN_GENOTYPE_QUALITY = 10;
     private static final int MIN_LOG10_PERROR = MIN_GENOTYPE_QUALITY / 10;
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
 
         final GenotypesContext genotypes = vc.getGenotypes();
         if ( genotypes == null || genotypes.size() < MIN_SAMPLES )
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 7c4b0b42e..9f20bf375 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
@@ -3,9 +3,8 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 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;
@@ -23,7 +22,7 @@ public class HomopolymerRun extends InfoFieldAnnotation {
 
     private boolean ANNOTATE_INDELS = true;
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
 
         if ( !vc.isBiallelic() )
             return null;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
index 0d2b3478d..fa3a7459b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
@@ -3,9 +3,9 @@ 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.ActiveRegionBasedAnnotation;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.MathUtils;
@@ -33,7 +33,7 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno
     private static final int MIN_SAMPLES = 10;
     private Set<String> founderIds;
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         //If available, get the founder IDs and cache them. the IC will only be computed on founders then.
         if(founderIds == null)
             founderIds =  ((Walker)walker).getSampleDB().getFounderIds();
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 e0abfcf3c..babaf7ee6 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
@@ -3,7 +3,7 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.IndelUtils;
@@ -18,7 +18,7 @@ import java.util.*;
  */
 public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
 
          int run;
         if (vc.isMixed()) {
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 4651782ef..7f5033adf 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
@@ -3,12 +3,11 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 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;
@@ -22,7 +21,7 @@ import java.util.Map;
  */
 public class LowMQ extends InfoFieldAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
index 07fbfc3d2..b6f24433e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
@@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.samples.Sample;
 import org.broadinstitute.sting.gatk.samples.SampleDB;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
@@ -32,7 +32,7 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment
     private String fatherId;
     private String childId;
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( mendelianViolation == null ) {
             if (checkAndSetSamples(((Walker) walker).getSampleDB())) {
                 mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).minGenotypeQualityP );
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 780206f30..372d5bc9e 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
@@ -3,7 +3,7 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 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;
@@ -24,7 +24,7 @@ import java.util.Map;
  */
 public class MappingQualityZero extends InfoFieldAnnotation implements StandardAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 
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 c12923be5..b5252f15b 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
@@ -28,7 +28,7 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
@@ -47,7 +47,7 @@ import java.util.List;
  */
 public class MappingQualityZeroBySample extends GenotypeAnnotation {
     public void annotate(RefMetaDataTracker tracker,
-                         AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext context,
+                         AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext context,
                          VariantContext vc, Genotype g, GenotypeBuilder gb) {
         if ( g == null || !g.isCalled() )
             return;
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 e8490959c..9f542e3bd 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
@@ -3,7 +3,7 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 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;
@@ -22,7 +22,7 @@ import java.util.Map;
  */
 public class MappingQualityZeroFraction extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 
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 8f0bc876a..ba4303b4a 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
@@ -3,7 +3,7 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@@ -20,7 +20,7 @@ import java.util.Map;
  * The number of N bases, counting only SOLiD data
  */
 public class NBaseCount extends InfoFieldAnnotation {
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if( stratifiedContexts.size() == 0 )
             return null;
 
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 5da6492a6..b62cd374b 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
@@ -4,7 +4,7 @@ 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.ActiveRegionBasedAnnotation;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 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;
@@ -28,7 +28,7 @@ import java.util.Map;
  */
 public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( !vc.hasLog10PError() || stratifiedContexts.size() == 0 )
             return null;
 
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 fb5767b34..842fde8ad 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
@@ -4,7 +4,7 @@ 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.ActiveRegionBasedAnnotation;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.MathUtils;
@@ -29,7 +29,7 @@ import java.util.Map;
  */
 public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 
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 1955c87b8..bf6adcfac 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
@@ -4,9 +4,8 @@ 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.ActiveRegionBasedAnnotation;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 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.MannWhitneyU;
 import org.broadinstitute.sting.utils.QualityUtils;
@@ -32,7 +31,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveR
     static final double INDEL_LIKELIHOOD_THRESH = 0.1;
     static final boolean DEBUG = false;
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if (stratifiedContexts.size() == 0)
             return null;
 
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 cbf536e4f..7e4d44cf2 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
@@ -28,7 +28,7 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 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;
@@ -46,7 +46,7 @@ import java.util.Map;
  */
 public class SampleList extends InfoFieldAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( vc.isMonomorphicInSamples() || !vc.hasGenotypes() )
             return null;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
index 6c860fce6..4d990e738 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
@@ -30,7 +30,7 @@ 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.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
 import org.broadinstitute.sting.utils.Utils;
@@ -203,7 +203,7 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio
         }
     }
 
-    public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) {
+    public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) {
         // Make sure that we actually have a valid SnpEff rod binding (just in case the user specified -A SnpEff
         // without providing a SnpEff rod via --snpEffFile):
         validateRodBinding(walker.getSnpEffRodBinding());
@@ -225,7 +225,7 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio
         headerLines.add(new VCFHeaderLine(OUTPUT_VCF_HEADER_COMMAND_LINE_KEY, snpEffCommandLine.getValue()));
     }
 
-    public Map<String, Object> annotate ( RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc ) {
+    public Map<String, Object> annotate ( RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc ) {
         RodBinding<VariantContext> snpEffRodBinding = walker.getSnpEffRodBinding();
 
         // Get only SnpEff records that start at this locus, not merely span it:
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 d7529c8ef..af2df8e6a 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
@@ -3,7 +3,7 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 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;
@@ -22,7 +22,7 @@ import java.util.Map;
  */
 public class SpanningDeletions extends InfoFieldAnnotation implements StandardAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
index c4d6ea474..eced387b3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
@@ -27,10 +27,9 @@ 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.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 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;
@@ -48,7 +47,7 @@ public class TandemRepeatAnnotator extends InfoFieldAnnotation implements Standa
     private static final String STR_PRESENT = "STR";
     private static final String REPEAT_UNIT_KEY = "RU";
     private static final String REPEATS_PER_ALLELE_KEY = "RPA";
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( !vc.isIndel())
             return null;
 
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 f4feb9aa8..63694d809 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
@@ -4,7 +4,7 @@ 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.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 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;
@@ -28,7 +28,7 @@ public class TechnologyComposition extends InfoFieldAnnotation implements Experi
     private String n454 ="Num454";
     private String nSolid = "NumSOLiD";
     private String nOther = "NumOther";
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
index 1f8ccf652..2e3578dcb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
@@ -4,7 +4,7 @@ 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.samples.Sample;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
@@ -28,7 +28,7 @@ public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implemen
     private Set<Sample> trios = null;
     private final static int MIN_NUM_VALID_TRIOS = 5; // don't calculate this population-level statistic if there are less than X trios with full genotype likelihood information
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( trios == null ) {
             if ( walker instanceof VariantAnnotator ) {
                 trios =  ((VariantAnnotator) walker).getSampleDB().getChildrenWithParents();
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 8f7f46c20..d6d2beb91 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
@@ -38,8 +38,8 @@ import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 
 import java.util.*;
 
@@ -79,7 +79,7 @@ import java.util.*;
 @Allows(value={DataSource.READS, DataSource.REFERENCE})
 @Reference(window=@Window(start=-50,stop=50))
 @By(DataSource.REFERENCE)
-public class VariantAnnotator extends RodWalker<Integer, Integer> implements AnnotatorCompatibleWalker {
+public class VariantAnnotator extends RodWalker<Integer, Integer> implements AnnotatorCompatible {
 
     @ArgumentCollection
     protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
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 46212c19c..073faf54e 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
@@ -46,7 +46,7 @@ public class VariantAnnotatorEngine {
     private List<VAExpression> requestedExpressions = new ArrayList<VAExpression>();
 
     private final HashMap<RodBinding<VariantContext>, String> dbAnnotations = new HashMap<RodBinding<VariantContext>, String>();
-    private final AnnotatorCompatibleWalker walker;
+    private final AnnotatorCompatible walker;
     private final GenomeAnalysisEngine toolkit;
 
     private boolean requireStrictAlleleMatch = false;
@@ -75,7 +75,7 @@ public class VariantAnnotatorEngine {
     }
 
     // use this constructor if you want all possible annotations
-    public VariantAnnotatorEngine(List<String> annotationsToExclude, AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) {
+    public VariantAnnotatorEngine(List<String> annotationsToExclude, AnnotatorCompatible walker, GenomeAnalysisEngine toolkit) {
         this.walker = walker;
         this.toolkit = toolkit;
         requestedInfoAnnotations = AnnotationInterfaceManager.createAllInfoFieldAnnotations();
@@ -85,7 +85,7 @@ public class VariantAnnotatorEngine {
     }
 
     // use this constructor if you want to select specific annotations (and/or interfaces)
-    public VariantAnnotatorEngine(List<String> annotationGroupsToUse, List<String> annotationsToUse, List<String> annotationsToExclude, AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) {
+    public VariantAnnotatorEngine(List<String> annotationGroupsToUse, List<String> annotationsToUse, List<String> annotationsToExclude, AnnotatorCompatible walker, GenomeAnalysisEngine toolkit) {
         this.walker = walker;
         this.toolkit = toolkit;
         initializeAnnotations(annotationGroupsToUse, annotationsToUse, annotationsToExclude);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java
similarity index 93%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java
index 1331ad5df..f610a2ba8 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java
@@ -5,7 +5,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.List;
 
-public interface AnnotatorCompatibleWalker {
+public interface AnnotatorCompatible {
 
     // getter methods for various used bindings
     public abstract RodBinding<VariantContext> getSnpEffRodBinding();
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 c44c834de..bc20f6c97 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
@@ -9,12 +9,11 @@ import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.List;
-import java.util.Map;
 
 public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation {
 
     // return annotations for the given contexts/genotype split by sample
-    public abstract void annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker,
+    public abstract void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker,
                                   ReferenceContext ref, AlignmentContext stratifiedContext,
                                   VariantContext vc, Genotype g, GenotypeBuilder gb );
 
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 b94bee31b..1569a605f 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
@@ -11,7 +11,7 @@ import java.util.Map;
 
 public abstract class InfoFieldAnnotation extends VariantAnnotatorAnnotation {
     // return annotations for the given contexts split by sample
-    public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker,
+    public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker,
                                                  ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc);
 
     // return the descriptions used for the VCF INFO meta field
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
index 521f89016..996d85a67 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
@@ -37,5 +37,5 @@ public abstract class VariantAnnotatorAnnotation {
     public abstract List<String> getKeyNames();
 
     // initialization method (optional for subclasses, and therefore non-abstract)
-    public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) { }
+    public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) { }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
index 31006f4d8..627d561f6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
@@ -31,13 +31,13 @@ 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.utils.codecs.beagle.BeagleFeature;
 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.beagle.BeagleFeature;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 
 import java.util.*;
 
@@ -72,7 +72,7 @@ import static java.lang.Math.log10;
  <p> Note that Beagle produces some of these files compressed as .gz, so gunzip must be run on them before walker is run in order to decompress them </p>
 
  */
-public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
+public class BeagleOutputToVCF extends RodWalker<Integer, Integer> {
 
     @ArgumentCollection
     protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
index a8e280f43..14e92a066 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
@@ -37,10 +37,13 @@ import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibratio
 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.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFFilterHeaderLine;
+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.exceptions.StingException;
 import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 
 import java.io.File;
 import java.io.PrintStream;
@@ -72,7 +75,7 @@ import java.util.*;
  *
  */
 
-public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
+public class ProduceBeagleInput extends RodWalker<Integer, Integer> {
 
     @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java
index d6b19b377..6d83a1d2a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java
@@ -38,12 +38,12 @@ 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.variantcontext.writer.VariantContextWriter;
 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 org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 
 import java.io.PrintStream;
 import java.util.Arrays;
@@ -54,7 +54,7 @@ import java.util.Set;
  * in input variant file.  Will additional hold back a fraction of the sites for evaluation, marking the
  * genotypes at that sites as missing, and writing the truth of these sites to a second VCF file
  */
-public class VariantsToBeagleUnphasedWalker extends RodWalker<Integer, Integer> {
+public class VariantsToBeagleUnphased extends RodWalker<Integer, Integer> {
     @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
     public RodBinding<VariantContext> variants;
 
@@ -104,7 +104,7 @@ public class VariantsToBeagleUnphasedWalker extends RodWalker<Integer, Integer>
             GenomeLoc loc = context.getLocation();
             VariantContext vc = tracker.getFirstValue(variants, loc);
 
-            if ( ProduceBeagleInputWalker.canBeOutputToBeagle(vc) ) {
+            if ( ProduceBeagleInput.canBeOutputToBeagle(vc) ) {
                 // do we want to hold back this site?
                 boolean makeMissing = dropSite(vc);
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java
index 8210a11b7..1a03ce1ce 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java
@@ -47,7 +47,7 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.PrintStream;
 import java.lang.reflect.Constructor;
-import java.util.*;
+import java.util.ArrayList;
 
 /**
  * First pass of the base quality score recalibration -- Generates recalibration table based on various user-specified covariates (such as reported quality score, cycle, and dinucleotide).
@@ -106,7 +106,7 @@ import java.util.*;
 @Requires({DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES})                                         // filter out all reads with zero or unavailable mapping quality
 @PartitionBy(PartitionType.LOCUS)                                                                                       // this walker requires both -I input.bam and -R reference.fasta
 
-public class BaseQualityScoreRecalibrator extends LocusWalker<Long, Long> implements TreeReducible<Long> {
+public class BQSR extends LocusWalker<Long, Long> implements TreeReducible<Long> {
     @ArgumentCollection
     private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();                          // all the command line arguments for BQSR and it's covariates
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
index 34d99c018..55c04f1b7 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
@@ -105,6 +105,6 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP
      * @return the covariate keysets for this read
      */
     protected ReadCovariates covariateKeySetFrom(GATKSAMRecord read) {
-        return (ReadCovariates) read.getTemporaryAttribute(BaseQualityScoreRecalibrator.COVARS_ATTRIBUTE);
+        return (ReadCovariates) read.getTemporaryAttribute(BQSR.COVARS_ATTRIBUTE);
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
index 2a8940de0..bc791a5a4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
@@ -120,7 +120,7 @@ import java.io.PrintStream;
  * @since May 7, 2010
  */
 @By(DataSource.REFERENCE)
-public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableBaseState, CallableLociWalker.Integrator> {
+public class CallableLoci extends LocusWalker<CallableLoci.CallableBaseState, CallableLoci.Integrator> {
     @Output
     PrintStream out;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java
similarity index 74%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java
index cd5fdc505..64a51f1b3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java
@@ -41,7 +41,7 @@ import java.util.List;
 /**
  * Test routine for new VariantContext object
  */
-public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker.CallableBaseState>, long[][]> {
+public class CompareCallableLoci extends RodWalker<List<CallableLoci.CallableBaseState>, long[][]> {
     @Output
     protected PrintStream out;
 
@@ -54,8 +54,8 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
     @Argument(shortName="printState", doc="If provided, prints sites satisfying this state pair", required=false)
     protected String printState = null;
 
-    CallableLociWalker.CalledState printState1 = CallableLociWalker.CalledState.REF_N;
-    CallableLociWalker.CalledState printState2 = CallableLociWalker.CalledState.REF_N;
+    CallableLoci.CalledState printState1 = CallableLoci.CalledState.REF_N;
+    CallableLoci.CalledState printState2 = CallableLoci.CalledState.REF_N;
 
     // --------------------------------------------------------------------------------------------------------------
     //
@@ -66,8 +66,8 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
     public void initialize() {
         if ( printState != null ) {
             String[] states = printState.split(",");
-            printState1 = CallableLociWalker.CalledState.valueOf(states[0]);
-            printState2 = CallableLociWalker.CalledState.valueOf(states[1]);
+            printState1 = CallableLoci.CalledState.valueOf(states[0]);
+            printState2 = CallableLoci.CalledState.valueOf(states[1]);
         }
     }
 
@@ -77,10 +77,10 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
     // map
     //
     // --------------------------------------------------------------------------------------------------------------
-    public List<CallableLociWalker.CallableBaseState> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+    public List<CallableLoci.CallableBaseState> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         if ( tracker != null ) {
-            CallableLociWalker.CallableBaseState comp1 = getCallableBaseState(tracker, compTrack1);
-            CallableLociWalker.CallableBaseState comp2 = getCallableBaseState(tracker, compTrack2);
+            CallableLoci.CallableBaseState comp1 = getCallableBaseState(tracker, compTrack1);
+            CallableLoci.CallableBaseState comp2 = getCallableBaseState(tracker, compTrack2);
 
             if ( printState != null && comp1.getState() == printState1 && comp2.getState() == printState2 ) {
                 out.printf("%s %s %s %s%n", comp1.getLocation(), comp1.getState(), comp2.getLocation(), comp2.getState());
@@ -92,7 +92,7 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
         }
     }
 
-    private CallableLociWalker.CallableBaseState getCallableBaseState(RefMetaDataTracker tracker, RodBinding<BEDFeature> rodBinding) {
+    private CallableLoci.CallableBaseState getCallableBaseState(RefMetaDataTracker tracker, RodBinding<BEDFeature> rodBinding) {
         //System.out.printf("tracker %s%n", tracker);
         List<BEDFeature> bindings = tracker.getValues(rodBinding);
         if ( bindings.size() != 1 ) {
@@ -101,8 +101,8 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
 
         BEDFeature bed = bindings.get(0);
         GenomeLoc loc = getToolkit().getGenomeLocParser().createGenomeLoc(bed.getChr(), bed.getStart(), bed.getEnd());
-        CallableLociWalker.CalledState state = CallableLociWalker.CalledState.valueOf(bed.getName());
-        return new CallableLociWalker.CallableBaseState(getToolkit().getGenomeLocParser(),loc, state);
+        CallableLoci.CalledState state = CallableLoci.CalledState.valueOf(bed.getName());
+        return new CallableLoci.CallableBaseState(getToolkit().getGenomeLocParser(),loc, state);
     }
 
     // --------------------------------------------------------------------------------------------------------------
@@ -111,14 +111,14 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
     //
     // --------------------------------------------------------------------------------------------------------------
     public long[][] reduceInit() {
-        int n = CallableLociWalker.CalledState.values().length;
+        int n = CallableLoci.CalledState.values().length;
         return new long[n][n];
     }
 
-    public long[][] reduce(List<CallableLociWalker.CallableBaseState> comps, long[][] sum) {
+    public long[][] reduce(List<CallableLoci.CallableBaseState> comps, long[][] sum) {
         if ( comps != null ) {
-            CallableLociWalker.CallableBaseState comp1 = comps.get(0);
-            CallableLociWalker.CallableBaseState comp2 = comps.get(1);
+            CallableLoci.CallableBaseState comp1 = comps.get(0);
+            CallableLoci.CallableBaseState comp2 = comps.get(1);
 
             sum[comp1.getState().ordinal()][comp2.getState().ordinal()]++;
         }
@@ -127,8 +127,8 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
     }
 
     public void onTraversalDone(long[][] result) {
-        for ( CallableLociWalker.CalledState state1 : CallableLociWalker.CalledState.values() ) {
-            for ( CallableLociWalker.CalledState state2 : CallableLociWalker.CalledState.values() ) {
+        for ( CallableLoci.CalledState state1 : CallableLoci.CalledState.values() ) {
+            for ( CallableLoci.CalledState state2 : CallableLoci.CalledState.values() ) {
                 out.printf("%s %s %s %s %d%n", compTrack1.getName(), compTrack2.getName(), state1, state2, result[state1.ordinal()][state2.ordinal()]);
             }
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
index 70f444061..9fc1ec2f3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
@@ -34,9 +34,6 @@ 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.SeekableRODIterator;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
-import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
@@ -45,6 +42,9 @@ import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
+import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -117,7 +117,7 @@ import java.util.*;
 @By(DataSource.REFERENCE)
 @PartitionBy(PartitionType.NONE)
 @Downsample(by= DownsampleType.NONE, toCoverage=Integer.MAX_VALUE)
-public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partition,Map<String,int[]>>, CoveragePartitioner> implements TreeReducible<CoveragePartitioner> {
+public class DepthOfCoverage extends LocusWalker<Map<DoCOutputType.Partition,Map<String,int[]>>, CoveragePartitioner> implements TreeReducible<CoveragePartitioner> {
     @Output
     @Multiplex(value=DoCOutputMultiplexer.class,arguments={"partitionTypes","refSeqGeneList","omitDepthOutput","omitIntervals","omitSampleSummary","omitLocusTable"})
     Map<DoCOutputType,PrintStream> out;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByIntervalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByIntervalWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
index 124be2eb4..77d3aa897 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByIntervalWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
@@ -63,7 +63,7 @@ import java.util.List;
 @Allows(value = {DataSource.REFERENCE})
 @Requires(value = {DataSource.REFERENCE})
 @By(DataSource.REFERENCE)
-public class GCContentByIntervalWalker extends LocusWalker<Long, Long> {
+public class GCContentByInterval extends LocusWalker<Long, Long> {
     @Output
     protected PrintStream out;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
index ac60f5f28..8c4cab877 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
@@ -33,7 +33,6 @@ import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
 import org.broadinstitute.sting.gatk.walkers.PartitionBy;
 import org.broadinstitute.sting.gatk.walkers.PartitionType;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
 
 import java.io.PrintStream;
 
@@ -56,7 +55,7 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
     }
 
     @Override
-    public GenomeLoc map(final ActiveRegion activeRegion, final RefMetaDataTracker tracker) {
+    public GenomeLoc map(final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker tracker) {
         if (activeRegion.isActive)
             return activeRegion.getLocation();
         else
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
index 2b7a5612b..a04c4f01b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
@@ -131,7 +131,7 @@ import java.util.List;
  * @author Mark DePristo
  * @since 7/4/11
  */
-public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
+public class DiffObjects extends RodWalker<Integer, Integer> {
     /**
      * Writes out a file of the DiffEngine format:
      *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java
index 4e2c17bf6..0d390308e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java
@@ -73,7 +73,7 @@ import java.util.List;
 @WalkerName("FastaAlternateReferenceMaker")
 @Reference(window=@Window(start=-1,stop=50))
 @Requires(value={DataSource.REFERENCE})
-public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
+public class FastaAlternateReference extends FastaReference {
 
     /**
      * Variants from these input files are used by this tool to construct an alternate reference.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java
index 7ae5c5c75..f1eb6d028 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java
@@ -67,7 +67,7 @@ import java.io.PrintStream;
  *
  */
 @WalkerName("FastaReferenceMaker")
-public class FastaReferenceWalker extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
+public class FastaReference extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
 
     @Output PrintStream out;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStatsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
similarity index 87%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStatsWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
index f5c5f909f..8a1af623e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStatsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
@@ -37,10 +37,10 @@ import java.io.PrintStream;
 /**
  * Calculates basic statistics about the reference sequence itself
  */
-public class FastaStatsWalker extends RefWalker<Byte, FastaStatsWalker.FastaStats> {
+public class FastaStats extends RefWalker<Byte, FastaStats.FastaStatistics> {
     @Output PrintStream out;
 
-    protected class FastaStats {
+    protected class FastaStatistics {
         long nBases = 0, nRegBases = 0;
     }
 
@@ -50,19 +50,19 @@ public class FastaStatsWalker extends RefWalker<Byte, FastaStatsWalker.FastaStat
 	}
 
     @Override
-    public FastaStats reduceInit() {
-        return new FastaStats();
+    public FastaStatistics reduceInit() {
+        return new FastaStatistics();
     }
 
     @Override
-	public FastaStats reduce(Byte base, FastaStats stats) {
+	public FastaStatistics reduce(Byte base, FastaStatistics stats) {
         stats.nBases++;
         if (BaseUtils.isRegularBase(base)) stats.nRegBases++;
         return stats;
 	}
 
     @Override
-    public void onTraversalDone(FastaStats sum) {
+    public void onTraversalDone(FastaStatistics sum) {
         out.printf("Total bases   %d%n", sum.nBases);
         out.printf("Regular bases %d%n", sum.nRegBases);
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
index 1d85abbcd..4ce291ca3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
@@ -31,13 +31,15 @@ import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgume
 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.walkers.Reference;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 
 import java.util.*;
 
@@ -74,7 +76,7 @@ import java.util.*;
  *
  */
 @Reference(window=@Window(start=-50,stop=50))
-public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
+public class VariantFiltration extends RodWalker<Integer, Integer> {
 
     @ArgumentCollection
     protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
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 d504badab..10c8c0d69 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
@@ -35,16 +35,16 @@ import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
-import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 
 import java.io.PrintStream;
 import java.util.*;
@@ -121,7 +121,7 @@ import java.util.*;
 // TODO -- When LocusIteratorByState gets cleaned up, we should enable multiple @By sources:
 // TODO -- @By( {DataSource.READS, DataSource.REFERENCE_ORDERED_DATA} )
 @Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
-public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, UnifiedGenotyper.UGStatistics> implements TreeReducible<UnifiedGenotyper.UGStatistics>, AnnotatorCompatibleWalker {
+public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, UnifiedGenotyper.UGStatistics> implements TreeReducible<UnifiedGenotyper.UGStatistics>, AnnotatorCompatible {
 
     @ArgumentCollection
     private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
index 504359f3f..ef0909c2f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import net.sf.samtools.*;
 import org.apache.commons.jexl2.Expression;
 import org.apache.commons.jexl2.JexlContext;
 import org.apache.commons.jexl2.JexlEngine;
@@ -53,7 +52,6 @@ import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
 import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
 import org.broadinstitute.sting.utils.codecs.refseq.Transcript;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.collections.CircularArray;
 import org.broadinstitute.sting.utils.collections.PrimitivePair;
 import org.broadinstitute.sting.utils.exceptions.StingException;
@@ -64,6 +62,7 @@ import org.broadinstitute.sting.utils.interval.OverlappingIntervalIterator;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 
 import java.io.*;
 import java.util.*;
@@ -127,7 +126,7 @@ import java.util.*;
  */
 
 @ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class})
-public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
+public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
 //    @Output
 //    PrintStream out;
     @Output(doc="File to write variants (indels) in VCF format",required=true)
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
index 4bf24cf86..630d99ce9 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
@@ -113,7 +113,7 @@ class PhasingUtils {
             Map<String, Object> mergedGtAttribs = new HashMap<String, Object>();
             PhaseAndQuality phaseQual = calcPhaseForMergedGenotypes(gt1, gt2);
             if (phaseQual.PQ != null)
-                mergedGtAttribs.put(ReadBackedPhasingWalker.PQ_KEY, phaseQual.PQ);
+                mergedGtAttribs.put(ReadBackedPhasing.PQ_KEY, phaseQual.PQ);
 
             Genotype mergedGt = new GenotypeBuilder(gt1.getSampleName(), mergedAllelesForSample).log10PError(mergedGQ).attributes(mergedGtAttribs).phased(phaseQual.isPhased).make();
             mergedGenotypes.add(mergedGt);
@@ -373,7 +373,7 @@ class PhasingUtils {
         public PhaseAndQuality(Genotype gt) {
             this.isPhased = gt.isPhased();
             if (this.isPhased) {
-                this.PQ = gt.getAttributeAsDouble(ReadBackedPhasingWalker.PQ_KEY, -1);
+                this.PQ = gt.getAttributeAsDouble(ReadBackedPhasing.PQ_KEY, -1);
                 if ( this.PQ == -1 ) this.PQ = 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/ReadBackedPhasing.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
index 261c51bcc..154c8c789 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
@@ -91,7 +91,7 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
 // Filter out all reads with zero mapping quality
 @ReadFilters({MappingQualityZeroFilter.class})
 
-public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
+public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
     private static final boolean DEBUG = false;
     /**
      * The VCF file we are phasing variants from.
@@ -255,7 +255,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         for (VariantContext vc : tracker.getValues(variantCollection.variants, context.getLocation())) {
             if (samplesToPhase != null) vc = reduceVCToSamples(vc, samplesToPhase);
 
-            if (ReadBackedPhasingWalker.processVariantInPhasing(vc)) {
+            if (ReadBackedPhasing.processVariantInPhasing(vc)) {
                 VariantAndReads vr = new VariantAndReads(vc, context);
                 unphasedSiteQueue.add(vr);
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBasesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBasesWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java
index b846ce6b0..1ec22b03e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBasesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java
@@ -37,7 +37,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
  *
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
-public class CountBasesWalker extends ReadWalker<Integer, Long> {
+public class CountBases extends ReadWalker<Integer, Long> {
     public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
 
         return read.getReadLength();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java
similarity index 94%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java
index 09113704a..11cf0fe39 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java
@@ -37,7 +37,7 @@ import java.io.PrintStream;
  * </pre>
  *
  */
-public class CountLociWalker extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
+public class CountLoci extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
     @Output(doc="Write count to this file instead of STDOUT")
     PrintStream out;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java
index dbbd8e761..0856fcda0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java
@@ -39,7 +39,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
  * --read-filter command line argument).  Simplest example of a read-backed analysis.
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
-public class CountMalesWalker extends ReadWalker<Integer, Integer> {
+public class CountMales extends ReadWalker<Integer, Integer> {
     public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
         Sample sample = getSampleDB().getSample(read);
         return sample.getGender() == Gender.MALE ? 1 : 0;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java
index edbd5ff75..67ecea1f0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java
@@ -70,7 +70,7 @@ import java.util.*;
  * </pre>
  *
  */
-public class CountRODsWalker extends RodWalker<CountRODsWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> implements TreeReducible<Pair<ExpandingArrayList<Long>, Long>> {
+public class CountRODs extends RodWalker<CountRODs.Datum, Pair<ExpandingArrayList<Long>, Long>> implements TreeReducible<Pair<ExpandingArrayList<Long>, Long>> {
     @Output
     public PrintStream out;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRefWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java
similarity index 90%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRefWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java
index 7c7d6417a..f71362c40 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRefWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java
@@ -63,7 +63,7 @@ import java.util.List;
  * </pre>
  *
  */
-public class CountRODsByRefWalker extends RefWalker<CountRODsWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> {
+public class CountRODsByRef extends RefWalker<CountRODs.Datum, Pair<ExpandingArrayList<Long>, Long>> {
 
     /**
      * One or more input rod files
@@ -77,14 +77,14 @@ public class CountRODsByRefWalker extends RefWalker<CountRODsWalker.Datum, Pair<
     @Argument(fullName = "showSkipped", shortName = "s", doc="If true, this tool will print out the skipped locations", required = false)
     public boolean showSkipped = false;
 
-    CountRODsWalker crw = new CountRODsWalker();
+    CountRODs crw = new CountRODs();
 
     public void initialize() {
         crw.verbose = verbose;
         crw.showSkipped = showSkipped;
     }
 
-    public CountRODsWalker.Datum map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+    public CountRODs.Datum map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         return crw.map(tracker, ref, context);
     }
 
@@ -92,7 +92,7 @@ public class CountRODsByRefWalker extends RefWalker<CountRODsWalker.Datum, Pair<
         return crw.reduceInit();
     }
 
-    public Pair<ExpandingArrayList<Long>, Long> reduce(CountRODsWalker.Datum point, Pair<ExpandingArrayList<Long>, Long> sum) {
+    public Pair<ExpandingArrayList<Long>, Long> reduce(CountRODs.Datum point, Pair<ExpandingArrayList<Long>, Long> sum) {
         return crw.reduce(point, sum);
     }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEventsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEventsWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java
index c5ab0426d..d0c917650 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEventsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java
@@ -42,7 +42,7 @@ import java.util.Map;
 
 
 @Requires({DataSource.READS, DataSource.REFERENCE})
-public class CountReadEventsWalker extends ReadWalker<Map<CigarOperator, ArrayList<Integer>> , Map<Integer, Map<CigarOperator, Long>>> {
+public class CountReadEvents extends ReadWalker<Map<CigarOperator, ArrayList<Integer>> , Map<Integer, Map<CigarOperator, Long>>> {
     @Output (doc = "GATKReport table output")
     PrintStream out;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
index b5a2d183f..c9108054e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
@@ -37,7 +37,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
  *
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
-public class CountReadsWalker extends ReadWalker<Integer, Integer> {
+public class CountReads extends ReadWalker<Integer, Integer> {
     public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
 
         return 1;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEventWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java
similarity index 96%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEventWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java
index 9208cbae8..1fff50800 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEventWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java
@@ -37,7 +37,7 @@ import java.util.List;
  * </pre>
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
-public class CountTerminusEventWalker extends ReadWalker<Pair<Long, Long>, Pair<Long, Long>> {
+public class CountTerminusEvent extends ReadWalker<Pair<Long, Long>, Pair<Long, Long>> {
     public Pair<Long, Long> map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
         List<CigarElement> cigarElements = read.getCigar().getCigarElements();
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQuality.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQuality.java
index 1cb1579d0..86d8458de 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQuality.java
@@ -56,7 +56,7 @@ import java.util.*;
  * --read-filter command line argument).  Simplest example of a read-backed analysis.
  */
 @Requires({DataSource.READS})
-public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
+public class CycleQuality extends ReadWalker<Integer,Integer> {
     @Output
     protected PrintStream out;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java
similarity index 96%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowingWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java
index 6f0490fd3..500f27980 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java
@@ -36,7 +36,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 /**
  * a walker that simply throws errors.  Allows us to test that the engine is behaving as expected with error handling
  */
-public class ErrorThrowingWalker extends RodWalker<Integer,Integer> implements TreeReducible<Integer> {
+public class ErrorThrowing extends RodWalker<Integer,Integer> implements TreeReducible<Integer> {
     @Input(fullName="exception", shortName = "E", doc="Java class of exception to throw", required=true)
     public String exceptionToThrow;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRefWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java
similarity index 90%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRefWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java
index ab5324e39..814f1c8c2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRefWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java
@@ -26,24 +26,15 @@ package org.broadinstitute.sting.gatk.walkers.qc;
 
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.picard.reference.ReferenceSequence;
-import net.sf.samtools.SAMSequenceRecord;
-import org.broad.tribble.Feature;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
 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.BaseUtils;
-import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
-import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 
 import java.io.PrintStream;
-import java.util.Collections;
-import java.util.List;
 
 /**
  * Prints out counts of the number of reference ordered data objects encountered.
@@ -67,7 +58,7 @@ import java.util.List;
  * </pre>
  *
  */
-public class QCRefWalker extends RefWalker<Integer, Integer> {
+public class QCRef extends RefWalker<Integer, Integer> {
     @Output
     public PrintStream out;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java
index 27f9d7b6d..92030a7d9 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java
@@ -52,7 +52,7 @@ import java.util.Arrays;
  * of the clipping to the output stream.
  */
 @Requires({DataSource.READS})
-public class ReadClippingStatsWalker extends ReadWalker<ReadClippingStatsWalker.ReadClippingInfo,Integer> {
+public class ReadClippingStats extends ReadWalker<ReadClippingStats.ReadClippingInfo,Integer> {
     @Output
     protected PrintStream out;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidation.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidation.java
index 4425f92c4..5f062c861 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidation.java
@@ -44,7 +44,7 @@ import java.util.List;
  * the same read is not passed to the walker multiple consecutive times.
  * @author aaron
  */
-public class ReadValidationWalker extends ReadWalker<SAMRecord, SAMRecord> {
+public class ReadValidation extends ReadWalker<SAMRecord, SAMRecord> {
 
     // our MD5 sum
     private MessageDigest m;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java
index c9602cd6f..3a9add950 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java
@@ -32,7 +32,6 @@ 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.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
@@ -51,7 +50,7 @@ import java.util.List;
  * a walker for validating (in the style of validating pile-up) the ROD system.
  */
 @Reference(window=@Window(start=-40,stop=40))
-public class RodSystemValidationWalker extends RodWalker<Integer,Integer> {
+public class RodSystemValidation extends RodWalker<Integer,Integer> {
 
     // the divider to use in some of the text output
     private static final String DIVIDER = ",";
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java
similarity index 94%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java
index cd17e4592..f249df475 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java
@@ -32,9 +32,12 @@ import org.broadinstitute.sting.commandline.RodBinding;
 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.sampileup.SAMPileupFeature;
-import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -48,7 +51,7 @@ import java.util.Arrays;
  * should be specified using the command-line argument '-B pileup,SAMPileup,<your sam pileup file>'.
  */
 @Requires(value={DataSource.READS,DataSource.REFERENCE})
-public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats>  implements TreeReducible<ValidationStats> {
+public class ValidatingPileup extends LocusWalker<Integer, ValidationStats> implements TreeReducible<ValidationStats> {
     @Input(fullName = "pileup", doc="The SAMPileup containing the expected output", required = true)
     RodBinding<SAMPileupFeature> pileup;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
index 2e3fc26f6..3d008de43 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
@@ -38,10 +38,10 @@ 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.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 
 import java.util.Map;
 import java.util.Set;
@@ -195,7 +195,7 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
 @Reference(window=@Window(start=-200,stop=200))
 
 
-public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalker.CountedData, GenotypeAndValidateWalker.CountedData> implements TreeReducible<GenotypeAndValidateWalker.CountedData> {
+public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedData, GenotypeAndValidate.CountedData> implements TreeReducible<GenotypeAndValidate.CountedData> {
 
     /**
      * The optional output file that will have all the variants used in the Genotype and Validation essay.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelectorWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
index 78fe37fa3..cdcac2300 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelectorWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
@@ -30,10 +30,12 @@ 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.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+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.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 
 import java.io.File;
 import java.util.*;
@@ -94,7 +96,7 @@ import java.util.*;
  * </pre>
  *
  */
-public class ValidationSiteSelectorWalker extends RodWalker<Integer, Integer> {
+public class ValidationSiteSelector extends RodWalker<Integer, Integer> {
 
     public enum AF_COMPUTATION_MODE {
         KEEP_AF_SPECTRUM,
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
index b9e768274..cdf7b19c6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval;
 
-import com.google.java.contract.Requires;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.picard.util.IntervalTree;
 import net.sf.samtools.SAMSequenceRecord;
@@ -88,7 +87,7 @@ import java.util.*;
  */
 @Reference(window=@Window(start=-50, stop=50))
 @PartitionBy(PartitionType.NONE)
-public class VariantEvalWalker extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
+public class VariantEval extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
     public static final String IS_SINGLETON_KEY = "ISSINGLETON";
 
     @Output
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 ff3bf66f7..97a8b4dda 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
@@ -4,7 +4,7 @@ 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.samples.Sample;
-import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
+import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.MendelianViolation;
@@ -104,7 +104,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
     MendelianViolation mv;
     Map<String,Set<Sample>> families;
 
-    public void initialize(VariantEvalWalker walker) {
+    public void initialize(VariantEval walker) {
         super.initialize(walker);
         mv = new MendelianViolation(walker.getMendelianViolationQualThreshold(),false);
         families = walker.getSampleDB().getFamilies();
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 df4c3e860..c08ff379b 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
@@ -3,23 +3,23 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
 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.VariantEval;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 public abstract class VariantEvaluator implements Comparable<VariantEvaluator> {
-    private VariantEvalWalker walker;
+    private VariantEval walker;
     private final String simpleName;
 
     protected VariantEvaluator() {
         this.simpleName = getClass().getSimpleName();
     }
 
-    public void initialize(VariantEvalWalker walker) {
+    public void initialize(VariantEval walker) {
         this.walker = walker;
     }
 
-    public VariantEvalWalker getWalker() {
+    public VariantEval getWalker() {
         return walker;
     }
 
@@ -57,7 +57,7 @@ public abstract class VariantEvaluator implements Comparable<VariantEvaluator> {
      * @return true if eval was originally a singleton site
      */
     protected static boolean variantWasSingleton(final VariantContext eval) {
-        return eval.getAttributeAsBoolean(VariantEvalWalker.IS_SINGLETON_KEY, false);
+        return eval.getAttributeAsBoolean(VariantEval.IS_SINGLETON_KEY, false);
     }
 
     public final String getSimpleName() {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
index 014381bea..71ea6af98 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
@@ -29,7 +29,7 @@ import org.apache.log4j.Logger;
 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.VariantEval;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.GenomeLoc;
@@ -150,7 +150,7 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
     }
 
 
-    public void initialize(VariantEvalWalker walker) {
+    public void initialize(VariantEval walker) {
         super.initialize(walker);
 
         nSamples = walker.getSampleNamesForEvaluation().size();
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 07ba424a2..90b6230ca 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
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
 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.VariantEval;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.Stratifier;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -13,7 +13,7 @@ import java.util.List;
 import java.util.Set;
 
 public abstract class VariantStratifier implements Comparable<VariantStratifier>, Stratifier {
-    private VariantEvalWalker variantEvalWalker;
+    private VariantEval variantEvalWalker;
     final private String name;
     final protected ArrayList<Object> states = new ArrayList<Object>();
 
@@ -40,7 +40,7 @@ public abstract class VariantStratifier implements Comparable<VariantStratifier>
     /**
      * @return a reference to the parent VariantEvalWalker running this stratification
      */
-    public final VariantEvalWalker getVariantEvalWalker() {
+    public final VariantEval getVariantEvalWalker() {
         return variantEvalWalker;
     }
 
@@ -48,7 +48,7 @@ public abstract class VariantStratifier implements Comparable<VariantStratifier>
      * Should only be called by VariantEvalWalker itself
      * @param variantEvalWalker
      */
-    public final void setVariantEvalWalker(VariantEvalWalker variantEvalWalker) {
+    public final void setVariantEvalWalker(VariantEval variantEvalWalker) {
         this.variantEvalWalker = variantEvalWalker;
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java
index 390682837..c98c05a9a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java
@@ -3,27 +3,27 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 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.VariantEval;
 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.stratifications.manager.StratificationManager;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Set;
+import java.util.TreeSet;
 
 public final class EvaluationContext {
     // NOTE: must be hashset to avoid O(log n) cost of iteration in the very frequently called apply function
-    final VariantEvalWalker walker;
+    final VariantEval walker;
     private final ArrayList<VariantEvaluator> evaluationInstances;
     private final Set<Class<? extends VariantEvaluator>> evaluationClasses;
 
-    public EvaluationContext(final VariantEvalWalker walker, final Set<Class<? extends VariantEvaluator>> evaluationClasses) {
+    public EvaluationContext(final VariantEval walker, final Set<Class<? extends VariantEvaluator>> evaluationClasses) {
         this(walker, evaluationClasses, true);
     }
 
-    private EvaluationContext(final VariantEvalWalker walker, final Set<Class<? extends VariantEvaluator>> evaluationClasses, final boolean doInitialize) {
+    private EvaluationContext(final VariantEval walker, final Set<Class<? extends VariantEvaluator>> evaluationClasses, final boolean doInitialize) {
         this.walker = walker;
         this.evaluationClasses = evaluationClasses;
         this.evaluationInstances = new ArrayList<VariantEvaluator>(evaluationClasses.size());
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 3b28747fb..3dcc1f85f 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
@@ -28,7 +28,7 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.sting.commandline.RodBinding;
 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.VariantEval;
 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;
@@ -45,10 +45,10 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import java.util.*;
 
 public class VariantEvalUtils {
-    private final VariantEvalWalker variantEvalWalker;
+    private final VariantEval variantEvalWalker;
     Logger logger;
 
-    public VariantEvalUtils(VariantEvalWalker variantEvalWalker) {
+    public VariantEvalUtils(VariantEval variantEvalWalker) {
         this.variantEvalWalker = variantEvalWalker;
         this.logger = variantEvalWalker.getLogger();
     }
@@ -216,7 +216,7 @@ public class VariantEvalUtils {
             VariantContextBuilder builder = new VariantContextBuilder(vcsub);
 
             if ( isSingleton )
-                builder.attribute(VariantEvalWalker.IS_SINGLETON_KEY, true);
+                builder.attribute(VariantEval.IS_SINGLETON_KEY, true);
 
             if ( ! hasChrCountAnnotations )
                 VariantContextUtils.calculateChromosomeCounts(builder, true);
@@ -270,7 +270,7 @@ public class VariantEvalUtils {
                 }
 
                 if ((byFilter || !vcsub.isFiltered())) {
-                    addMapping(mapping, VariantEvalWalker.getAllSampleName(), vcsub);
+                    addMapping(mapping, VariantEval.getAllSampleName(), vcsub);
                 }
 
                 // Now, if stratifying, split the subsetted vc per sample and add each as a new context
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java
index cd645943b..b4e07716c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+ * Copyright (c) 2012, The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
@@ -25,11 +25,17 @@
 package org.broadinstitute.sting.utils.help;
 
 public class GATKDocUtils {
-    /** The URL root for RELEASED GATKDOC units */
+    /**
+     * The URL root for RELEASED GATKDOC units
+     */
     public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/";
-    /** The URL root for STABLE GATKDOC units */
+    /**
+     * The URL root for STABLE GATKDOC units
+     */
     public final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/";
-    /** The URL root for UNSTABLE GATKDOC units */
+    /**
+     * The URL root for UNSTABLE GATKDOC units
+     */
     public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
 
     /**
@@ -49,6 +55,7 @@ public class GATKDocUtils {
     /**
      * Returns a full URL http://etc/ linking to the documentation for class (assuming it
      * exists).  Currently points to the RELEASE doc path only.
+     *
      * @param c
      * @return
      */
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java
index 41c855329..0ff5ddc6a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+ * Copyright (c) 2012, The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
@@ -25,41 +25,63 @@
 package org.broadinstitute.sting.utils.help;
 
 import com.sun.javadoc.ClassDoc;
+import org.broadinstitute.sting.gatk.Category;
 
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 
 /**
  * Simple collection of all relevant information about something the GATKDoclet can document
- *
+ * <p/>
  * Created by IntelliJ IDEA.
  * User: depristo
  * Date: 7/24/11
  * Time: 7:59 PM
  */
 class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
-    /** The class that's being documented */
+    /**
+     * The class that's being documented
+     */
     final Class clazz;
-    /** The name of the thing we are documenting */
+    /**
+     * The name of the thing we are documenting
+     */
     final String name;
-    /** the filename where we will be writing the docs for this class */
+    /**
+     * the filename where we will be writing the docs for this class
+     */
     final String filename;
-    /** The name of the documentation group (e.g., walkers, read filters) class belongs to */
+    /**
+     * The name of the documentation group (e.g., walkers, read filters) class belongs to
+     */
     final String group;
-    /** The documentation handler for this class */
+    /**
+     * The categories that this class belongs to
+     */
+    final List<Category> categories;
+    /**
+     * The documentation handler for this class
+     */
     final DocumentedGATKFeatureHandler handler;
-    /** The javadoc documentation for clazz */
+    /**
+     * The javadoc documentation for clazz
+     */
     final ClassDoc classDoc;
-    /** The annotation that lead to this Class being in GATKDoc */
+    /**
+     * The annotation that lead to this Class being in GATKDoc
+     */
     final DocumentedGATKFeatureObject annotation;
-    /** When was this walker built, and what's the absolute version number */
+    /**
+     * When was this walker built, and what's the absolute version number
+     */
     final String buildTimestamp, absoluteVersion;
 
     // set by the handler
     String summary;
     Map<String, Object> forTemplate;
 
-    public GATKDocWorkUnit(String name, String filename, String group,
+    public GATKDocWorkUnit(String name, String filename, String group, List<Category> categories,
                            DocumentedGATKFeatureObject annotation, DocumentedGATKFeatureHandler handler,
                            ClassDoc classDoc, Class clazz,
                            String buildTimestamp, String absoluteVersion) {
@@ -67,6 +89,7 @@ class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
         this.name = name;
         this.filename = filename;
         this.group = group;
+        this.categories = categories;
         this.handler = handler;
         this.classDoc = classDoc;
         this.clazz = clazz;
@@ -76,6 +99,7 @@ class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
 
     /**
      * Called by the GATKDoclet to set handler provided context for this work unit
+     *
      * @param summary
      * @param forTemplate
      */
@@ -86,6 +110,7 @@ class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
 
     /**
      * Return a String -> String map suitable for FreeMarker to create an index to this WorkUnit
+     *
      * @return
      */
     public Map<String, String> indexDataMap() {
@@ -99,6 +124,7 @@ class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
 
     /**
      * Sort in order of the name of this WorkUnit
+     *
      * @param other
      * @return
      */
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
index 7f26f22f5..f40675a43 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+ * Copyright (c) 2012, The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
@@ -24,6 +24,7 @@
 
 package org.broadinstitute.sting.utils.help;
 
+import com.google.gson.Gson;
 import com.sun.javadoc.ClassDoc;
 import com.sun.javadoc.RootDoc;
 import freemarker.template.Configuration;
@@ -34,41 +35,51 @@ import org.apache.commons.io.FileUtils;
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import org.broad.tribble.FeatureCodec;
+import org.broadinstitute.sting.gatk.Categorize;
+import org.broadinstitute.sting.gatk.Category;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.walkers.qc.DocumentationTest;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.*;
+import java.lang.annotation.Annotation;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.util.*;
 
 /**
  * Javadoc Doclet that combines javadoc, GATK ParsingEngine annotations, and FreeMarker
  * templates to produce html formatted GATKDocs for walkers
  * and other classes.
- *
+ * <p/>
  * This document has the following workflow:
- *
+ * <p/>
  * 1 -- walk the javadoc heirarchy, looking for class that have the
- *   DocumentedGATKFeature annotation or are in the type heirarchy in the
- *   static list of things to document, and are to be documented
+ * DocumentedGATKFeature annotation or are in the type heirarchy in the
+ * static list of things to document, and are to be documented
  * 2 -- construct for each a GATKDocWorkUnit, resulting in the complete
- *   set of things to document
+ * set of things to document
  * 3 -- for each unit, actually generate an html page documenting it
- *   as well as links to related features via their units.  Writing
- *   of a specific class HTML is accomplished by a generate DocumentationHandler
+ * as well as links to related features via their units.  Writing
+ * of a specific class HTML is accomplished by a generate DocumentationHandler
  * 4 -- write out an index of all units, organized by group
- *
+ * <p/>
  * The documented classes are restricted to only those with @DocumentedGATKFeature
  * annotation or are in the STATIC_DOCS class.
  */
 public class GATKDoclet {
     final protected static Logger logger = Logger.getLogger(GATKDoclet.class);
 
-    /** Where we find the help FreeMarker templates */
+    /**
+     * Where we find the help FreeMarker templates
+     */
     final protected static File SETTINGS_DIR = new File("settings/helpTemplates");
 
-    /** Where we write the GATKDoc html directory */
+    /**
+     * Where we write the GATKDoc html directory
+     */
     final protected static File DESTINATION_DIR = new File("gatkdocs");
 
     // ----------------------------------------------------------------------
@@ -88,10 +99,14 @@ public class GATKDoclet {
     private static final List<Class<?>> testOnlyKeepers = Arrays.asList(
             DocumentationTest.class, CommandLineGATK.class, UserException.class);
 
-    /** The javadoc root doc */
+    /**
+     * The javadoc root doc
+     */
     RootDoc rootDoc;
 
-    /** The set of all things we are going to document */
+    /**
+     * The set of all things we are going to document
+     */
     Set<GATKDocWorkUnit> myWorkUnits;
 
     /**
@@ -103,6 +118,7 @@ public class GATKDoclet {
      * codecs).
      */
     final static Collection<DocumentedGATKFeatureObject> STATIC_DOCS = new ArrayList<DocumentedGATKFeatureObject>();
+
     static {
         STATIC_DOCS.add(new DocumentedGATKFeatureObject(FeatureCodec.class,
                 "Reference ordered data (ROD) codecs",
@@ -112,6 +128,7 @@ public class GATKDoclet {
 
     /**
      * Extracts the contents of certain types of javadoc and adds them to an XML file.
+     *
      * @param rootDoc The documentation root.
      * @return Whether the JavaDoc run succeeded.
      * @throws java.io.IOException if output can't be written.
@@ -120,8 +137,8 @@ public class GATKDoclet {
         logger.setLevel(Level.INFO);
 
         // load arguments
-        for(String[] options: rootDoc.options()) {
-            if(options[0].equals("-build-timestamp"))
+        for (String[] options : rootDoc.options()) {
+            if (options[0].equals("-build-timestamp"))
                 buildTimestamp = options[1];
             if (options[0].equals("-absolute-version"))
                 absoluteVersion = options[1];
@@ -139,15 +156,16 @@ public class GATKDoclet {
 
     /**
      * Validate the given options against options supported by this doclet.
+     *
      * @param option Option to validate.
      * @return Number of potential parameters; 0 if not supported.
      */
     public static int optionLength(String option) {
-        if(option.equals("-build-timestamp") ||
+        if (option.equals("-build-timestamp") ||
                 option.equals("-absolute-version") ||
                 option.equals("-include-hidden")) {
             return 2;
-        } else if ( option.equals("-test") )
+        } else if (option.equals("-test"))
             return 1;
         else
             return 0;
@@ -155,6 +173,7 @@ public class GATKDoclet {
 
     /**
      * Are we supposed to include @Hidden annotations in our documented output?
+     *
      * @return
      */
     public boolean showHiddenFeatures() {
@@ -162,7 +181,6 @@ public class GATKDoclet {
     }
 
     /**
-     *
      * @param rootDoc
      */
     private void processDocs(RootDoc rootDoc) {
@@ -172,7 +190,11 @@ public class GATKDoclet {
         try {
             // basic setup
             DESTINATION_DIR.mkdirs();
-            FileUtils.copyFile(new File(SETTINGS_DIR + "/style.css"), new File(DESTINATION_DIR + "/style.css"));
+            FileUtils.copyFile(new File(SETTINGS_DIR + "/bootstrap.min.css"), new File(DESTINATION_DIR + "/bootstrap.min.css"));
+            FileUtils.copyFile(new File(SETTINGS_DIR + "/bootstrap.min.js"), new File(DESTINATION_DIR + "/bootstrap.min.js"));
+            FileUtils.copyFile(new File(SETTINGS_DIR + "/jquery.min.js"), new File(DESTINATION_DIR + "/jquery.min.js"));
+            // print the Version number
+            FileUtils.writeByteArrayToFile(new File(DESTINATION_DIR + "/current.version.txt"), getSimpleVersion(absoluteVersion).getBytes());
 
             /* ------------------------------------------------------------------- */
             /* You should do this ONLY ONCE in the whole application life-cycle:   */
@@ -184,31 +206,109 @@ public class GATKDoclet {
             cfg.setObjectWrapper(new DefaultObjectWrapper());
 
             myWorkUnits = computeWorkUnits();
-            for ( GATKDocWorkUnit workUnit : myWorkUnits ) {
-                processDocWorkUnit(cfg, workUnit);
+
+            Map<Category, List<Map<String, String>>> catNav = getCategories(new ArrayList<GATKDocWorkUnit>(myWorkUnits));
+
+            processCategories(catNav, myWorkUnits);
+
+            for (GATKDocWorkUnit workUnit : myWorkUnits) {
+                processDocWorkUnit(cfg, workUnit, catNav);
             }
 
             processIndex(cfg, new ArrayList<GATKDocWorkUnit>(myWorkUnits));
-        } catch ( FileNotFoundException e ) {
+        } catch (FileNotFoundException e) {
             throw new RuntimeException(e);
-        } catch ( IOException e ) {
+        } catch (IOException e) {
             throw new RuntimeException(e);
         }
     }
 
+    private void processCategories(Map<Category, List<Map<String, String>>> getCategories, Set<GATKDocWorkUnit> classes) throws IOException {
+        List<Object> categories = new LinkedList<Object>();
+        for (Category cat : getCategories.keySet()) {
+            Map<String, Object> properties = new HashMap<String, Object>();
+            properties.put("Name", cat.getDescription());
+            properties.put("UrlSlug", cat.name().toLowerCase().replace('_', '-'));
+            categories.add(properties);
+        }
+        writeJson(DESTINATION_DIR + "/categories.json", categories);
+
+        List<Object> posts = new LinkedList<Object>();
+        for (GATKDocWorkUnit unit : classes) {
+            Map<String, Object> properties = new HashMap<String, Object>();
+            properties.put("Post Title", unit.name + " Documentation");
+            properties.put("Categories", unit.categories);
+            List<String> tags = new ArrayList<String>();
+            tags.add(unit.name);
+            tags.add(unit.group);
+            properties.put("Tags", tags);
+            String body = String.format("<a href='%s'>%s</a><hr /><p>%s</p>",
+                    GATKDocUtils.URL_ROOT_FOR_RELEASE_GATKDOCS + unit.filename, unit.name + " Documentation", unit.summary);
+            properties.put("Body", body);
+            posts.add(properties);
+        }
+
+        writeJson(DESTINATION_DIR + "/posts.json", posts);
+    }
+
+    private void writeJson(String filename, Object source) throws IOException {
+        Gson gson = new Gson();
+        BufferedWriter out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(new File(filename))), 1024 * 1024);
+
+        out.write(gson.toJson(source));
+
+        out.close();
+
+    }
+
+    public static void postRestJson(String URL, String json) {
+        try {
+            URL url = new URL(URL);
+            HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+            conn.setDoOutput(true);
+            conn.setRequestMethod("POST");
+            conn.setRequestProperty("Content-Type", "application/json");
+
+            OutputStream os = conn.getOutputStream();
+            os.write(json.getBytes());
+            os.flush();
+
+            if (conn.getResponseCode() != HttpURLConnection.HTTP_CREATED) {
+                throw new RuntimeException("Failed : HTTP error code : "
+                        + conn.getResponseCode());
+            }
+
+            BufferedReader br = new BufferedReader(new InputStreamReader(
+                    (conn.getInputStream())));
+
+            String output;
+            System.out.println("Output from Server .... \n");
+            while ((output = br.readLine()) != null) {
+                System.out.println(output);
+            }
+
+            conn.disconnect();
+        } catch (MalformedURLException e) {
+            e.printStackTrace();
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+
     /**
      * Returns the set of all GATKDocWorkUnits that we are going to generate docs for.
+     *
      * @return
      */
     private Set<GATKDocWorkUnit> computeWorkUnits() {
         TreeSet<GATKDocWorkUnit> m = new TreeSet<GATKDocWorkUnit>();
 
-        for ( ClassDoc doc : rootDoc.classes() ) {
+        for (ClassDoc doc : rootDoc.classes()) {
             //logger.debug("Considering " + doc);
             Class clazz = getClassForClassDoc(doc);
 
             // don't add anything that's not DocumentationTest if we are in test mode
-            if ( clazz != null && testOnly && ! testOnlyKeepers.contains(clazz) )
+            if (clazz != null && testOnly && !testOnlyKeepers.contains(clazz))
                 continue;
 
             //if ( clazz != null && clazz.getName().equals("org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance"))
@@ -216,11 +316,12 @@ public class GATKDoclet {
 
             DocumentedGATKFeatureObject feature = getFeatureForClassDoc(doc);
             DocumentedGATKFeatureHandler handler = createHandler(doc, feature);
-            if ( handler != null && handler.includeInDocs(doc) ) {
+            if (handler != null && handler.includeInDocs(doc)) {
                 logger.info("Generating documentation for class " + doc);
                 String filename = handler.getDestinationFilename(doc, clazz);
+                Category[] categories = getClassAnnotationValue(clazz, Categorize.class, "value");
                 GATKDocWorkUnit unit = new GATKDocWorkUnit(doc.name(),
-                        filename, feature.groupName(),
+                        filename, feature.groupName(), (categories == null) ? new ArrayList<Category>() : Arrays.asList(categories),
                         feature, handler, doc, clazz,
                         buildTimestamp, absoluteVersion);
                 m.add(unit);
@@ -233,13 +334,14 @@ public class GATKDoclet {
     /**
      * Create a handler capable of documenting the class doc according to feature.  Returns
      * null if no appropriate handler is found or doc shouldn't be documented at all.
+     *
      * @param doc
      * @param feature
      * @return
      */
     private DocumentedGATKFeatureHandler createHandler(ClassDoc doc, DocumentedGATKFeatureObject feature) {
-        if ( feature != null ) {
-            if ( feature.enable() ) {
+        if (feature != null) {
+            if (feature.enable()) {
                 DocumentedGATKFeatureHandler handler = new GenericDocumentationHandler();
                 handler.setDoclet(this);
                 return handler;
@@ -261,15 +363,15 @@ public class GATKDoclet {
     private DocumentedGATKFeatureObject getFeatureForClassDoc(ClassDoc doc) {
         Class<? extends Object> docClass = getClassForClassDoc(doc);
 
-        if ( docClass == null )
+        if (docClass == null)
             return null; // not annotated so it shouldn't be documented
 
-        if ( docClass.isAnnotationPresent(DocumentedGATKFeature.class) ) {
+        if (docClass.isAnnotationPresent(DocumentedGATKFeature.class)) {
             DocumentedGATKFeature f = docClass.getAnnotation(DocumentedGATKFeature.class);
             return new DocumentedGATKFeatureObject(docClass, f.enable(), f.groupName(), f.summary(), f.extraDocs());
         } else {
-            for ( DocumentedGATKFeatureObject staticDocs : STATIC_DOCS ) {
-                if ( staticDocs.getClassToDoc().isAssignableFrom(docClass) ) {
+            for (DocumentedGATKFeatureObject staticDocs : STATIC_DOCS) {
+                if (staticDocs.getClassToDoc().isAssignableFrom(docClass)) {
                     return new DocumentedGATKFeatureObject(docClass, staticDocs.enable(), staticDocs.groupName(), staticDocs.summary(), staticDocs.extraDocs());
                 }
             }
@@ -279,26 +381,28 @@ public class GATKDoclet {
 
     /**
      * Return the Java class described by the ClassDoc doc
+     *
      * @param doc
      * @return
      */
     private Class<? extends Object> getClassForClassDoc(ClassDoc doc) {
         try {
             // todo -- what do I need the ? extends Object to pass the compiler?
-            return (Class<? extends Object>)HelpUtils.getClassForDoc(doc);
-        } catch ( ClassNotFoundException e) {
+            return (Class<? extends Object>) HelpUtils.getClassForDoc(doc);
+        } catch (ClassNotFoundException e) {
             //logger.warn("Couldn't find class for ClassDoc " + doc);
             // we got a classdoc for a class we can't find.  Maybe in a library or something
             return null;
-        } catch ( NoClassDefFoundError e ) {
+        } catch (NoClassDefFoundError e) {
             return null;
-        } catch ( UnsatisfiedLinkError e) {
+        } catch (UnsatisfiedLinkError e) {
             return null; // naughty BWA bindings
         }
     }
 
     /**
      * Create the html index listing all of the GATKDocs features
+     *
      * @param cfg
      * @param indexData
      * @throws IOException
@@ -312,7 +416,7 @@ public class GATKDoclet {
         try {
             temp.process(groupIndexData(indexData), out);
             out.flush();
-        } catch ( TemplateException e ) {
+        } catch (TemplateException e) {
             throw new ReviewedStingException("Failed to create GATK documentation", e);
         }
     }
@@ -320,6 +424,7 @@ public class GATKDoclet {
     /**
      * Helpful function to create the html index.  Given all of the already run GATKDocWorkUnits,
      * create the high-level grouping data listing individual features by group.
+     *
      * @param indexData
      * @return
      */
@@ -334,9 +439,9 @@ public class GATKDoclet {
         List<Map<String, String>> groups = new ArrayList<Map<String, String>>();
         Set<String> seenDocumentationFeatures = new HashSet<String>();
         List<Map<String, String>> data = new ArrayList<Map<String, String>>();
-        for ( GATKDocWorkUnit workUnit : indexData ) {
+        for (GATKDocWorkUnit workUnit : indexData) {
             data.add(workUnit.indexDataMap());
-            if ( ! seenDocumentationFeatures.contains(workUnit.annotation.groupName()) ) {
+            if (!seenDocumentationFeatures.contains(workUnit.annotation.groupName())) {
                 groups.add(toMap(workUnit.annotation));
                 seenDocumentationFeatures.add(workUnit.annotation.groupName());
             }
@@ -347,16 +452,20 @@ public class GATKDoclet {
         root.put("timestamp", buildTimestamp);
         root.put("version", absoluteVersion);
 
+        root.put("categories", getCategories(indexData));
+
         return root;
     }
 
     /**
      * Trivial helper routine that returns the map of name and summary given the annotation
+     *
      * @param annotation
      * @return
      */
     private static final Map<String, String> toMap(DocumentedGATKFeatureObject annotation) {
         Map<String, String> root = new HashMap<String, String>();
+        root.put("id", annotation.groupName().replaceAll("\\W", ""));
         root.put("name", annotation.groupName());
         root.put("summary", annotation.summary());
         return root;
@@ -364,18 +473,20 @@ public class GATKDoclet {
 
     /**
      * Helper function that finding the GATKDocWorkUnit associated with class from among all of the work units
+     *
      * @param c the class we are looking for
      * @return the GATKDocWorkUnit whose .clazz.equals(c), or null if none could be found
      */
     public final GATKDocWorkUnit findWorkUnitForClass(Class c) {
-        for ( final GATKDocWorkUnit unit : this.myWorkUnits )
-            if ( unit.clazz.equals(c) )
+        for (final GATKDocWorkUnit unit : this.myWorkUnits)
+            if (unit.clazz.equals(c))
                 return unit;
         return null;
     }
 
     /**
      * Return the ClassDoc associated with clazz
+     *
      * @param clazz
      * @return
      */
@@ -390,12 +501,12 @@ public class GATKDoclet {
      * @param unit
      * @throws IOException
      */
-    private void processDocWorkUnit(Configuration cfg, GATKDocWorkUnit unit)
+    private void processDocWorkUnit(Configuration cfg, GATKDocWorkUnit unit, Map<Category, List<Map<String, String>>> categories)
             throws IOException {
         //System.out.printf("Processing documentation for class %s%n", unit.classDoc);
 
         unit.handler.processOne(unit);
-
+        unit.forTemplate.put("catNav", categories);
         // Get or create a template
         Template temp = cfg.getTemplate(unit.handler.getTemplateName(unit.classDoc));
 
@@ -405,8 +516,59 @@ public class GATKDoclet {
             Writer out = new OutputStreamWriter(new FileOutputStream(outputPath));
             temp.process(unit.forTemplate, out);
             out.flush();
-        } catch ( TemplateException e ) {
+        } catch (TemplateException e) {
             throw new ReviewedStingException("Failed to create GATK documentation", e);
         }
     }
-}
+
+    // hack - todo - is there a better way to process annotations?
+    private Category[] getClassAnnotationValue(Class classType, Class annotationType, String attributeName) {
+        Category[] value = null;
+
+        Annotation annotation = classType.getAnnotation(annotationType);
+        if (annotation != null) {
+            try {
+                value = (Category[]) annotation.annotationType().getMethod(attributeName).invoke(annotation);
+            } catch (Exception ex) {
+            }
+        }
+
+        return value;
+    }
+
+    private Map<Category, List<Map<String, String>>> getCategories(List<GATKDocWorkUnit> classes) {
+        Map<Category, List<Map<String, String>>> output = new TreeMap<Category, List<Map<String, String>>>();
+
+        for (Category cat : Category.values()) {
+            output.put(cat, new ArrayList<Map<String, String>>());
+        }
+
+        for (GATKDocWorkUnit unit : classes) {
+            Category[] categories = getClassAnnotationValue(unit.clazz, Categorize.class, "value");
+
+            if (categories != null) {
+                for (Category cat : categories) {
+                    unit.handler.processOne(unit);
+
+                    Map<String, String> datum = unit.indexDataMap();
+
+                    output.get(cat).add(datum);
+                }
+            }
+        }
+
+        return output;
+    }
+
+    private static String getSimpleVersion(String absoluteVersion) {
+        String[] parts = absoluteVersion.split("-");
+
+        // by skipping i=0, there is no trailing separator
+        for (int i = 1; i < 2; i++) {
+            parts[0] = parts[0].concat("-");
+            parts[0] = parts[0].concat(parts[i]);
+        }
+
+        return parts[0];
+    }
+}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
index 20f9eccd3..71c82053f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2011, The Broad Institute
+ * Copyright (c) 2012, The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person
  * obtaining a copy of this software and associated documentation
@@ -28,14 +28,11 @@ import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import com.sun.javadoc.ClassDoc;
 import com.sun.javadoc.FieldDoc;
-import com.sun.javadoc.RootDoc;
 import com.sun.javadoc.Tag;
 import org.apache.log4j.Logger;
 import org.broad.tribble.Feature;
-import org.broad.tribble.bed.FullBEDFeature;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
@@ -43,7 +40,7 @@ import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 
-import java.io.*;
+import java.io.IOException;
 import java.lang.reflect.*;
 import java.util.*;
 
@@ -59,16 +56,18 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
      */
     private static final int MAX_DISPLAY_NAME = 30;
 
-    /** The Class we are documenting */
+    /**
+     * The Class we are documenting
+     */
     private GATKDocWorkUnit toProcess;
 
     @Override
     public boolean includeInDocs(ClassDoc doc) {
         try {
             Class type = HelpUtils.getClassForDoc(doc);
-            boolean hidden = ! getDoclet().showHiddenFeatures() && type.isAnnotationPresent(Hidden.class);
-            return ! hidden && JVMUtils.isConcrete(type);
-        } catch ( ClassNotFoundException e ) {
+            boolean hidden = !getDoclet().showHiddenFeatures() && type.isAnnotationPresent(Hidden.class);
+            return !hidden && JVMUtils.isConcrete(type);
+        } catch (ClassNotFoundException e) {
             return false;
         }
     }
@@ -90,7 +89,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         addArgumentBindings(root);
         addRelatedBindings(root);
 
-        toProcess.setHandlerContent((String)root.get("summary"), root);
+        toProcess.setHandlerContent((String) root.get("summary"), root);
     }
 
     /**
@@ -104,34 +103,37 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
 
         // Extract overrides from the doc tags.
         StringBuilder summaryBuilder = new StringBuilder();
-        for(Tag tag: toProcess.classDoc.firstSentenceTags())
+        for (Tag tag : toProcess.classDoc.firstSentenceTags())
             summaryBuilder.append(tag.text());
         root.put("summary", summaryBuilder.toString());
         root.put("description", toProcess.classDoc.commentText().substring(summaryBuilder.toString().length()));
         root.put("timestamp", toProcess.buildTimestamp);
         root.put("version", toProcess.absoluteVersion);
+        root.put("categories", toProcess.categories);
 
-        for(Tag tag: toProcess.classDoc.tags()) {
+        for (Tag tag : toProcess.classDoc.tags()) {
             root.put(tag.name(), tag.text());
         }
     }
 
     /**
      * Add bindings describing related GATK capabilites to toProcess
+     *
      * @param root
      */
     protected void addRelatedBindings(Map<String, Object> root) {
         List<Map<String, Object>> extraDocsData = new ArrayList<Map<String, Object>>();
 
         // add in all of the explicitly related items
-        for ( final Class extraDocClass : toProcess.annotation.extraDocs() ) {
+        for (final Class extraDocClass : toProcess.annotation.extraDocs()) {
             final GATKDocWorkUnit otherUnit = getDoclet().findWorkUnitForClass(extraDocClass);
-            if ( otherUnit == null )
+            if (otherUnit == null)
                 throw new ReviewedStingException("Requested extraDocs for class without any documentation: " + extraDocClass);
             extraDocsData.add(
-                    new HashMap<String, Object>(){{
+                    new HashMap<String, Object>() {{
                         put("filename", otherUnit.filename);
-                        put("name", otherUnit.name);}});
+                        put("name", otherUnit.name);
+                    }});
 
         }
         root.put("extradocs", extraDocsData);
@@ -149,16 +151,16 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         root.put("arguments", args);
         try {
             // loop over all of the arguments according to the parsing engine
-            for ( final ArgumentSource argumentSource : parsingEngine.extractArgumentSources(HelpUtils.getClassForDoc(toProcess.classDoc)) ) {
+            for (final ArgumentSource argumentSource : parsingEngine.extractArgumentSources(HelpUtils.getClassForDoc(toProcess.classDoc))) {
                 // todo -- why can you have multiple ones?
                 ArgumentDefinition argDef = argumentSource.createArgumentDefinitions().get(0);
                 FieldDoc fieldDoc = getFieldDoc(toProcess.classDoc, argumentSource.field.getName());
                 Map<String, Object> argBindings = docForArgument(fieldDoc, argumentSource, argDef);
-                if ( ! argumentSource.isHidden() || getDoclet().showHiddenFeatures() ) {
+                if (!argumentSource.isHidden() || getDoclet().showHiddenFeatures()) {
                     final String kind = docKindOfArg(argumentSource);
 
                     final Object value = argumentValue(toProcess.clazz, argumentSource);
-                    if ( value != null )
+                    if (value != null)
                         argBindings.put("defaultValue", prettyPrintValueString(value));
 
                     args.get(kind).add(argBindings);
@@ -167,31 +169,33 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
             }
 
             // sort the arguments
-            for (Map.Entry<String,List<Map<String, Object>>> entry : args.entrySet()) {
+            for (Map.Entry<String, List<Map<String, Object>>> entry : args.entrySet()) {
                 entry.setValue(sortArguments(entry.getValue()));
             }
-        } catch ( ClassNotFoundException e ) {
+        } catch (ClassNotFoundException e) {
             throw new RuntimeException(e);
         }
     }
 
     /**
      * Return the argument kind (required, advanced, hidden, etc) of this argumentSource
+     *
      * @param argumentSource
      * @return
      */
     @Requires("argumentSource != null")
     @Ensures("result != null")
     private String docKindOfArg(ArgumentSource argumentSource) {
-        if ( argumentSource.isRequired() ) return "required";
-        else if ( argumentSource.isAdvanced() ) return "advanced";
-        else if ( argumentSource.isHidden() ) return "hidden";
-        else if ( argumentSource.isDeprecated() ) return "depreciated";
+        if (argumentSource.isRequired()) return "required";
+        else if (argumentSource.isAdvanced()) return "advanced";
+        else if (argumentSource.isHidden()) return "hidden";
+        else if (argumentSource.isDeprecated()) return "depreciated";
         else return "optional";
     }
 
     /**
      * Attempts to determine the value of argumentSource in an instantiated version of c
+     *
      * @param c
      * @param argumentSource
      * @return value of argumentSource, or null if this isn't possible
@@ -201,12 +205,12 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         // get the value of the field
         // attempt to instantiate the class
         final Object instance = makeInstanceIfPossible(toProcess.clazz);
-        if ( instance != null ) {
+        if (instance != null) {
             final Object value = getFieldValue(instance, argumentSource.field.getName());
-            if ( value != null )
+            if (value != null)
                 return value;
 
-            if ( argumentSource.createsTypeDefault() ) {
+            if (argumentSource.createsTypeDefault()) {
                 try { // handle the case where there's an implicit default
                     return argumentSource.typeDefaultDocString();
                 } catch (ReviewedStingException e) {
@@ -220,6 +224,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
 
     /**
      * Create the argument map for holding class arguments
+     *
      * @return
      */
     private Map<String, List<Map<String, Object>>> createArgumentMap() {
@@ -236,6 +241,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
 
     /**
      * Sorts the individual argument list in unsorted according to CompareArgumentsByName
+     *
      * @param unsorted
      * @return
      */
@@ -254,9 +260,9 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
 
         private String elt(Map<String, Object> m) {
             String v = m.get("name").toString().toLowerCase();
-            if ( v.startsWith("--") )
+            if (v.startsWith("--"))
                 return v.substring(2);
-            else if ( v.startsWith("-") )
+            else if (v.startsWith("-"))
                 return v.substring(1);
             else
                 throw new RuntimeException("Expect to see arguments beginning with at least one -, but found " + v);
@@ -267,7 +273,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
      * Utility function that finds the value of fieldName in any fields of ArgumentCollection fields in
      * instance of class c.
      *
-     * @param instance the object to query for the field value
+     * @param instance  the object to query for the field value
      * @param fieldName the name of the field we are looking for in instance
      * @return The value assigned to field in the ArgumentCollection, otherwise null
      */
@@ -280,14 +286,14 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         // @ArgumentCollection
         // protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
         //
-        for ( Field field : JVMUtils.getAllFields(instance.getClass()) ) {
-            if ( field.isAnnotationPresent(ArgumentCollection.class) ) {
+        for (Field field : JVMUtils.getAllFields(instance.getClass())) {
+            if (field.isAnnotationPresent(ArgumentCollection.class)) {
                 //System.out.printf("Searching for %s in argument collection field %s%n", fieldName, field);
                 Object fieldValue = JVMUtils.getFieldValue(field, instance);
                 Object value = getFieldValue(fieldValue, fieldName);
-                if ( value != null )
+                if (value != null)
                     return value;
-            } else if ( field.getName().equals(fieldName) ) {
+            } else if (field.getName().equals(fieldName)) {
                 return JVMUtils.getFieldValue(field, instance);
             }
         }
@@ -297,38 +303,39 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
 
     /**
      * Pretty prints value
-     *
+     * <p/>
      * Assumes value != null
+     *
      * @param value
      * @return
      */
     private Object prettyPrintValueString(Object value) {
-        if ( value.getClass().isArray() ) {
+        if (value.getClass().isArray()) {
             Class type = value.getClass().getComponentType();
-            if ( boolean.class.isAssignableFrom(type) )
-                return Arrays.toString((boolean[])value);
-            if ( byte.class.isAssignableFrom(type) )
-                return Arrays.toString((byte[])value);
-            if ( char.class.isAssignableFrom(type) )
-                return Arrays.toString((char[])value);
-            if ( double.class.isAssignableFrom(type) )
-                return Arrays.toString((double[])value);
-            if ( float.class.isAssignableFrom(type) )
-                return Arrays.toString((float[])value);
-            if ( int.class.isAssignableFrom(type) )
-                return Arrays.toString((int[])value);
-            if ( long.class.isAssignableFrom(type) )
-                return Arrays.toString((long[])value);
-            if ( short.class.isAssignableFrom(type) )
-                return Arrays.toString((short[])value);
-            if ( Object.class.isAssignableFrom(type) )
-                return Arrays.toString((Object[])value);
+            if (boolean.class.isAssignableFrom(type))
+                return Arrays.toString((boolean[]) value);
+            if (byte.class.isAssignableFrom(type))
+                return Arrays.toString((byte[]) value);
+            if (char.class.isAssignableFrom(type))
+                return Arrays.toString((char[]) value);
+            if (double.class.isAssignableFrom(type))
+                return Arrays.toString((double[]) value);
+            if (float.class.isAssignableFrom(type))
+                return Arrays.toString((float[]) value);
+            if (int.class.isAssignableFrom(type))
+                return Arrays.toString((int[]) value);
+            if (long.class.isAssignableFrom(type))
+                return Arrays.toString((long[]) value);
+            if (short.class.isAssignableFrom(type))
+                return Arrays.toString((short[]) value);
+            if (Object.class.isAssignableFrom(type))
+                return Arrays.toString((Object[]) value);
             else
                 throw new RuntimeException("Unexpected array type in prettyPrintValue.  Value was " + value + " type is " + type);
-        } else if ( RodBinding.class.isAssignableFrom(value.getClass() ) ) {
+        } else if (RodBinding.class.isAssignableFrom(value.getClass())) {
             // annoying special case to handle the UnBound() constructor
             return "none";
-        } else if ( value instanceof String ) {
+        } else if (value instanceof String) {
             return value.equals("") ? "\"\"" : value;
         } else {
             return value.toString();
@@ -337,6 +344,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
 
     /**
      * Attempt to instantiate class c, if possible.  Returns null if this proves impossible.
+     *
      * @param c
      * @return
      */
@@ -344,21 +352,22 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         Object instance = null;
         try {
             // don't try to make something where we will obviously fail
-            if (! c.isEnum() && ! c.isAnnotation() && ! c.isAnonymousClass() &&
-                    ! c.isArray() && ! c.isPrimitive() & JVMUtils.isConcrete(c) ) {
+            if (!c.isEnum() && !c.isAnnotation() && !c.isAnonymousClass() &&
+                    !c.isArray() && !c.isPrimitive() & JVMUtils.isConcrete(c)) {
                 instance = c.newInstance();
                 //System.out.printf("Created object of class %s => %s%n", c, instance);
                 return instance;
             } else
                 return null;
+        } catch (IllegalAccessException e) {
+        } catch (InstantiationException e) {
+        } catch (ExceptionInInitializerError e) {
+        } catch (SecurityException e) {
         }
-        catch (IllegalAccessException e ) { }
-        catch (InstantiationException e ) { }
-        catch (ExceptionInInitializerError e ) { }
-        catch (SecurityException e ) { }
         // this last one is super dangerous, but some of these methods catch ClassNotFoundExceptions
         // and rethrow then as RuntimeExceptions
-        catch (RuntimeException e) {}
+        catch (RuntimeException e) {
+        }
 
         return instance;
     }
@@ -366,6 +375,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
 
     /**
      * Create an instance of the GATK parsing engine, for argument processing with GATKDoclet
+     *
      * @return
      */
     private ParsingEngine createStandardGATKParsingEngine() {
@@ -392,6 +402,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
 
     /**
      * Recursive helper routine to getFieldDoc()
+     *
      * @param classDoc
      * @param name
      * @param primary
@@ -399,21 +410,21 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
      */
     private FieldDoc getFieldDoc(ClassDoc classDoc, String name, boolean primary) {
         //System.out.printf("Looking for %s in %s%n", name, classDoc.name());
-        for ( FieldDoc fieldDoc : classDoc.fields(false) ) {
+        for (FieldDoc fieldDoc : classDoc.fields(false)) {
             //System.out.printf("fieldDoc " + fieldDoc + " name " + fieldDoc.name());
-            if ( fieldDoc.name().equals(name) )
+            if (fieldDoc.name().equals(name))
                 return fieldDoc;
 
             Field field = HelpUtils.getFieldForFieldDoc(fieldDoc);
-            if ( field == null )
+            if (field == null)
                 throw new RuntimeException("Could not find the field corresponding to " + fieldDoc + ", presumably because the field is inaccessible");
-            if ( field.isAnnotationPresent(ArgumentCollection.class) ) {
+            if (field.isAnnotationPresent(ArgumentCollection.class)) {
                 ClassDoc typeDoc = getRootDoc().classNamed(fieldDoc.type().qualifiedTypeName());
-                if ( typeDoc == null )
+                if (typeDoc == null)
                     throw new ReviewedStingException("Tried to get javadocs for ArgumentCollection field " + fieldDoc + " but could't find the class in the RootDoc");
                 else {
                     FieldDoc result = getFieldDoc(typeDoc, name, false);
-                    if ( result != null )
+                    if (result != null)
                         return result;
                     // else keep searching
                 }
@@ -421,11 +432,11 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         }
 
         // if we didn't find it here, wander up to the superclass to find the field
-        if ( classDoc.superclass() != null ) {
+        if (classDoc.superclass() != null) {
             return getFieldDoc(classDoc.superclass(), name, false);
         }
 
-        if ( primary )
+        if (primary)
             throw new RuntimeException("No field found for expected field " + name);
         else
             return null;
@@ -439,20 +450,20 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
      * @param s1 the short argument name without -, or null if not provided
      * @param s2 the long argument name without --, or null if not provided
      * @return A pair of fully qualified names (with - or --) for the argument.  The first
-     *  element is the primary display name while the second (potentially null) is a
-     *  synonymous name.
+     *         element is the primary display name while the second (potentially null) is a
+     *         synonymous name.
      */
     Pair<String, String> displayNames(String s1, String s2) {
         s1 = s1 == null ? null : "-" + s1;
         s2 = s2 == null ? null : "--" + s2;
 
-        if ( s1 == null ) return new Pair<String, String>(s2, null);
-        if ( s2 == null ) return new Pair<String, String>(s1, null);
+        if (s1 == null) return new Pair<String, String>(s2, null);
+        if (s2 == null) return new Pair<String, String>(s1, null);
 
         String l = s1.length() > s2.length() ? s1 : s2;
         String s = s1.length() > s2.length() ? s2 : s1;
 
-        if ( l.length() > MAX_DISPLAY_NAME )
+        if (l.length() > MAX_DISPLAY_NAME)
             return new Pair<String, String>(s, l);
         else
             return new Pair<String, String>(l, s);
@@ -460,7 +471,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
 
     /**
      * Returns a human readable string that describes the Type type of a GATK argument.
-     *
+     * <p/>
      * This will include parameterized types, so that Set{T} shows up as Set(T) and not
      * just Set in the docs.
      *
@@ -469,13 +480,13 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
      */
     protected String argumentTypeString(Type type) {
         if (type instanceof ParameterizedType) {
-            ParameterizedType parameterizedType = (ParameterizedType)type;
+            ParameterizedType parameterizedType = (ParameterizedType) type;
             List<String> subs = new ArrayList<String>();
-            for (Type actualType: parameterizedType.getActualTypeArguments())
+            for (Type actualType : parameterizedType.getActualTypeArguments())
                 subs.add(argumentTypeString(actualType));
-            return argumentTypeString(((ParameterizedType)type).getRawType()) + "[" + Utils.join(",", subs) + "]";
+            return argumentTypeString(((ParameterizedType) type).getRawType()) + "[" + Utils.join(",", subs) + "]";
         } else if (type instanceof GenericArrayType) {
-            return  argumentTypeString(((GenericArrayType)type).getGenericComponentType()) + "[]";
+            return argumentTypeString(((GenericArrayType) type).getGenericComponentType()) + "[]";
         } else if (type instanceof WildcardType) {
             throw new RuntimeException("We don't support wildcards in arguments: " + type);
         } else if (type instanceof Class<?>) {
@@ -489,18 +500,19 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
      * Helper routine that returns the Feature.class required by a RodBinding,
      * either T for RodBinding{T} or List{RodBinding{T}}.  Returns null if
      * the Type doesn't fit either model.
+     *
      * @param type
      * @return
      */
     protected Class<? extends Feature> getFeatureTypeIfPossible(Type type) {
-        if ( type instanceof ParameterizedType) {
-            ParameterizedType paramType = (ParameterizedType)type;
-            if ( RodBinding.class.isAssignableFrom((Class<?>)paramType.getRawType()) ) {
-                return (Class<? extends Feature>)JVMUtils.getParameterizedTypeClass(type);
+        if (type instanceof ParameterizedType) {
+            ParameterizedType paramType = (ParameterizedType) type;
+            if (RodBinding.class.isAssignableFrom((Class<?>) paramType.getRawType())) {
+                return (Class<? extends Feature>) JVMUtils.getParameterizedTypeClass(type);
             } else {
-                for ( Type paramtype : paramType.getActualTypeArguments() ) {
+                for (Type paramtype : paramType.getActualTypeArguments()) {
                     Class<? extends Feature> x = getFeatureTypeIfPossible(paramtype);
-                    if ( x != null )
+                    if (x != null)
                         return x;
                 }
             }
@@ -512,6 +524,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
     /**
      * High-level entry point for creating a FreeMarker map describing the GATK argument
      * source with definition def, with associated javadoc fieldDoc.
+     *
      * @param fieldDoc
      * @param source
      * @param def
@@ -521,9 +534,9 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         Map<String, Object> root = new HashMap<String, Object>();
         Pair<String, String> names = displayNames(def.shortName, def.fullName);
 
-        root.put("name", names.getFirst() );
+        root.put("name", names.getFirst());
 
-        if ( names.getSecond() != null )
+        if (names.getSecond() != null)
             root.put("synonyms", names.getSecond());
 
         root.put("required", def.required ? "yes" : "no");
@@ -532,11 +545,11 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         root.put("type", argumentTypeString(source.field.getGenericType()));
 
         Class<? extends Feature> featureClass = getFeatureTypeIfPossible(source.field.getGenericType());
-        if ( featureClass != null ) {
+        if (featureClass != null) {
             // deal with the allowable types
             FeatureManager manager = new FeatureManager();
             List<String> rodTypes = new ArrayList<String>();
-            for (FeatureManager.FeatureDescriptor descriptor : manager.getByFeature(featureClass) ) {
+            for (FeatureManager.FeatureDescriptor descriptor : manager.getByFeature(featureClass)) {
                 rodTypes.add(String.format("<a href=%s>%s</a>",
                         GATKDocUtils.htmlFilenameForClass(descriptor.getCodecClass()),
                         descriptor.getName()));
@@ -550,14 +563,14 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         root.put("fulltext", fieldDoc.commentText());
 
         // What are our enum options?
-        if ( def.validOptions != null )
+        if (def.validOptions != null)
             root.put("options", docForEnumArgument(source.field.getType()));
 
         // general attributes
         List<String> attributes = new ArrayList<String>();
-        if ( def.required ) attributes.add("required");
-        if ( source.isDeprecated() ) attributes.add("depreciated");
-        if ( attributes.size() > 0 )
+        if (def.required) attributes.add("required");
+        if (source.isDeprecated()) attributes.add("depreciated");
+        if (attributes.size() > 0)
             root.put("attributes", Utils.join(", ", attributes));
 
         return root;
@@ -566,21 +579,23 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
     /**
      * Helper routine that provides a FreeMarker map for an enumClass, grabbing the
      * values of the enum and their associated javadoc documentation.
+     *
      * @param enumClass
      * @return
      */
     @Requires("enumClass.isEnum()")
     private List<Map<String, Object>> docForEnumArgument(Class enumClass) {
         ClassDoc doc = this.getDoclet().getClassDocForClass(enumClass);
-        if ( doc == null ) //  || ! doc.isEnum() )
+        if (doc == null) //  || ! doc.isEnum() )
             throw new RuntimeException("Tried to get docs for enum " + enumClass + " but got instead: " + doc);
 
         List<Map<String, Object>> bindings = new ArrayList<Map<String, Object>>();
-        for (final FieldDoc field : doc.fields(false) ) {
+        for (final FieldDoc field : doc.fields(false)) {
             bindings.add(
-                    new HashMap<String, Object>(){{
+                    new HashMap<String, Object>() {{
                         put("name", field.name());
-                        put("summary", field.commentText());}});
+                        put("summary", field.commentText());
+                    }});
         }
 
         return bindings;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
index 2f8b1e9b5..d8905ad35 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
@@ -28,7 +28,7 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.commandline.ArgumentException;
 import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
-import org.broadinstitute.sting.gatk.walkers.PrintReadsWalker;
+import org.broadinstitute.sting.gatk.walkers.PrintReads;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.testng.annotations.Test;
 
@@ -71,7 +71,7 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
     public void testEmptyIntervalSetHandling() throws Exception {
         GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
 
-        testEngine.setWalker(new PrintReadsWalker());
+        testEngine.setWalker(new PrintReads());
         testEngine.setIntervals(new GenomeLocSortedSet(null));
 
         testEngine.validateSuppliedIntervals();
diff --git a/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java
index 6149a1e51..38be6d2a8 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java
@@ -24,13 +24,12 @@
 
 package org.broadinstitute.sting.gatk;
 
-import org.testng.Assert;
 import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker;
+import org.broadinstitute.sting.gatk.walkers.qc.CountLoci;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-
+import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -48,7 +47,7 @@ public class WalkerManagerUnitTest {
     @Test
     public void testPresentWalker() {
         Walker countLociWalker = walkerManager.createByName("CountLoci");
-        Assert.assertEquals(CountLociWalker.class,countLociWalker.getClass());
+        Assert.assertEquals(CountLoci.class,countLociWalker.getClass());
     }
 
     @Test(expectedExceptions=UserException.class)
diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java
index 564d1e2a3..66585c872 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java
@@ -35,8 +35,8 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker;
-import org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker;
+import org.broadinstitute.sting.gatk.walkers.qc.CountLoci;
+import org.broadinstitute.sting.gatk.walkers.qc.CountReads;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
@@ -99,7 +99,7 @@ public class GATKWalkerBenchmark extends ReadProcessingBenchmark {
     private enum WalkerType {
         COUNT_READS {
             @Override
-            Walker create() { return new CountReadsWalker(); }
+            Walker create() { return new CountReads(); }
         },
         COUNT_BASES_IN_READ {
             @Override
@@ -108,8 +108,8 @@ public class GATKWalkerBenchmark extends ReadProcessingBenchmark {
         COUNT_LOCI {
             @Override
             Walker create() {
-                CountLociWalker walker = new CountLociWalker();
-                JVMUtils.setFieldValue(JVMUtils.findField(CountLociWalker.class,"out"),walker,System.out);
+                CountLoci walker = new CountLoci();
+                JVMUtils.setFieldValue(JVMUtils.findField(CountLoci.class,"out"),walker,System.out);
                 return walker;
             }
         };
diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java
index 9226f97e2..7845515d8 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java
@@ -1,25 +1,22 @@
 package org.broadinstitute.sting.gatk.traversals;
 
-import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.picard.reference.ReferenceSequenceFile;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
+import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.reads.ReadShardBalancer;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
-import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
+import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
-import org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.gatk.walkers.qc.CountReads;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-
-import static org.testng.Assert.fail;
-
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
@@ -31,6 +28,8 @@ import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.List;
 
+import static org.testng.Assert.fail;
+
 /**
  *
  * User: aaron
@@ -106,7 +105,7 @@ public class TraverseReadsUnitTest extends BaseTest {
 
         bamList = new ArrayList<SAMReaderID>();
         bamList.add(bam);
-        countReadWalker = new CountReadsWalker();
+        countReadWalker = new CountReads();
         
         traversalEngine = new TraverseReads();
         traversalEngine.initialize(engine);
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java
index 0fcaad3bf..1aaa00aee 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java
@@ -59,7 +59,7 @@ public class PrintReadsUnitTest extends BaseTest {
     private ReferenceContext bases = null;
     //private ReferenceContext ref = new ReferenceContext()
 
-    PrintReadsWalker walker;
+    PrintReads walker;
     ArtificialSAMFileWriter writer;
 
     @BeforeMethod
@@ -67,7 +67,7 @@ public class PrintReadsUnitTest extends BaseTest {
         trav = new ArtificialReadsTraversal();
         readTotal = ( ( trav.endingChr - trav.startingChr ) + 1 ) * trav.readsPerChr + trav.unMappedReads;
 
-        walker = new PrintReadsWalker();
+        walker = new PrintReads();
         writer = new ArtificialSAMFileWriter();
         walker.out = writer;
         walker.initialize();
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java
index ca06ca699..f6c12f443 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java
@@ -49,13 +49,13 @@ import java.util.*;
 
 
 public class VariantEvalWalkerUnitTest extends BaseTest {
-    VariantEvalWalker VEwalker;
+    VariantEval VEwalker;
     VariantContext eval;
 
 
     @BeforeMethod
     public void init() {
-        VEwalker = new VariantEvalWalker();
+        VEwalker = new VariantEval();
         eval = new VariantContextBuilder("x", "chr1", 1, 1, Collections.singleton(Allele.create("A", true))).make();
     }
 
diff --git a/public/packages/GATK-Picard.xml b/public/packages/GATK-Picard.xml
index 29057d398..251f584f7 100644
--- a/public/packages/GATK-Picard.xml
+++ b/public/packages/GATK-Picard.xml
@@ -17,12 +17,12 @@
     <dependencies>
       <!-- Filters -->
       <package name="org.broadinstitute.sting.gatk.filters" />
-      <class name="org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.PileupWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.PrintReadsWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker" />
+      <class name="org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverage" />
+      <class name="org.broadinstitute.sting.gatk.walkers.Pileup" />
+      <class name="org.broadinstitute.sting.gatk.walkers.PrintReads" />
+      <class name="org.broadinstitute.sting.gatk.walkers.qc.CountLoci" />
+      <class name="org.broadinstitute.sting.gatk.walkers.qc.CountReads" />
+      <class name="org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileup" />
       <!-- Recalibration Covariates -->
       <class name="org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate" />
       <class name="org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate" />
diff --git a/settings/helpTemplates/bootstrap.min.css b/settings/helpTemplates/bootstrap.min.css
new file mode 100755
index 000000000..a4b669001
--- /dev/null
+++ b/settings/helpTemplates/bootstrap.min.css
@@ -0,0 +1,727 @@
+/*!
+ * Bootstrap v2.0.4
+ *
+ * Copyright 2012 Twitter, Inc
+ * Licensed under the Apache License v2.0
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Designed and built with all the love in the world @twitter by @mdo and @fat.
+ */
+.clearfix{*zoom:1;}.clearfix:before,.clearfix:after{display:table;content:"";}
+.clearfix:after{clear:both;}
+.hide-text{font:0/0 a;color:transparent;text-shadow:none;background-color:transparent;border:0;}
+.input-block-level{display:block;width:100%;min-height:28px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;}
+article,aside,details,figcaption,figure,footer,header,hgroup,nav,section{display:block;}
+audio,canvas,video{display:inline-block;*display:inline;*zoom:1;}
+audio:not([controls]){display:none;}
+html{font-size:100%;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%;}
+a:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;}
+a:hover,a:active{outline:0;}
+sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline;}
+sup{top:-0.5em;}
+sub{bottom:-0.25em;}
+img{max-width:100%;vertical-align:middle;border:0;-ms-interpolation-mode:bicubic;}
+#map_canvas img{max-width:none;}
+button,input,select,textarea{margin:0;font-size:100%;vertical-align:middle;}
+button,input{*overflow:visible;line-height:normal;}
+button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0;}
+button,input[type="button"],input[type="reset"],input[type="submit"]{cursor:pointer;-webkit-appearance:button;}
+input[type="search"]{-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;-webkit-appearance:textfield;}
+input[type="search"]::-webkit-search-decoration,input[type="search"]::-webkit-search-cancel-button{-webkit-appearance:none;}
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+a{color:#0088cc;text-decoration:none;}
+a:hover{color:#005580;text-decoration:underline;}
+.row{margin-left:-20px;*zoom:1;}.row:before,.row:after{display:table;content:"";}
+.row:after{clear:both;}
+[class*="span"]{float:left;margin-left:20px;}
+.container,.navbar-fixed-top .container,.navbar-fixed-bottom .container{width:940px;}
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diff --git a/settings/helpTemplates/bootstrap.min.js b/settings/helpTemplates/bootstrap.min.js
new file mode 100644
index 000000000..2c00b6f1d
--- /dev/null
+++ b/settings/helpTemplates/bootstrap.min.js
@@ -0,0 +1,7 @@
+/**
+* Bootstrap.js by @fat & @mdo
+* plugins: bootstrap-transition.js, bootstrap-modal.js, bootstrap-dropdown.js, bootstrap-scrollspy.js, bootstrap-tab.js, bootstrap-tooltip.js, bootstrap-popover.js, bootstrap-alert.js, bootstrap-button.js, bootstrap-collapse.js, bootstrap-carousel.js, bootstrap-typeahead.js
+* Copyright 2012 Twitter, Inc.
+* http://www.apache.org/licenses/LICENSE-2.0.txt
+*/
+!function(a){a(function(){a.support.transition=function(){var a=function(){var a=document.createElement("bootstrap"),b={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd",msTransition:"MSTransitionEnd",transition:"transitionend"},c;for(c in b)if(a.style[c]!==undefined)return b[c]}();return a&&{end:a}}()})}(window.jQuery),!function(a){function c(){var b=this,c=setTimeout(function(){b.$element.off(a.support.transition.end),d.call(b)},500);this.$element.one(a.support.transition.end,function(){clearTimeout(c),d.call(b)})}function d(a){this.$element.hide().trigger("hidden"),e.call(this)}function e(b){var c=this,d=this.$element.hasClass("fade")?"fade":"";if(this.isShown&&this.options.backdrop){var e=a.support.transition&&d;this.$backdrop=a('<div class="modal-backdrop '+d+'" 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e=this,f=function(){c.type=="show"&&e.reset(),e.transitioning=0,e.$element.trigger(d)};this.$element.trigger(c);if(c.isDefaultPrevented())return;this.transitioning=1,this.$element[b]("in"),a.support.transition&&this.$element.hasClass("collapse")?this.$element.one(a.support.transition.end,f):f()},toggle:function(){this[this.$element.hasClass("in")?"hide":"show"]()}},a.fn.collapse=function(c){return this.each(function(){var d=a(this),e=d.data("collapse"),f=typeof c=="object"&&c;e||d.data("collapse",e=new b(this,f)),typeof c=="string"&&e[c]()})},a.fn.collapse.defaults={toggle:!0},a.fn.collapse.Constructor=b,a(function(){a("body").on("click.collapse.data-api","[data-toggle=collapse]",function(b){var c=a(this),d,e=c.attr("data-target")||b.preventDefault()||(d=c.attr("href"))&&d.replace(/.*(?=#[^\s]+$)/,""),f=a(e).data("collapse")?"toggle":c.data();a(e).collapse(f)})})}(window.jQuery),!function(a){var b=function(b,c){this.$element=a(b),this.options=c,this.options.slide&&this.slide(this.options.slide),this.options.pause=="hover"&&this.$element.on("mouseenter",a.proxy(this.pause,this)).on("mouseleave",a.proxy(this.cycle,this))};b.prototype={cycle:function(b){return b||(this.paused=!1),this.options.interval&&!this.paused&&(this.interval=setInterval(a.proxy(this.next,this),this.options.interval)),this},to:function(b){var c=this.$element.find(".active"),d=c.parent().children(),e=d.index(c),f=this;if(b>d.length-1||b<0)return;return this.sliding?this.$element.one("slid",function(){f.to(b)}):e==b?this.pause().cycle():this.slide(b>e?"next":"prev",a(d[b]))},pause:function(a){return a||(this.paused=!0),clearInterval(this.interval),this.interval=null,this},next:function(){if(this.sliding)return;return this.slide("next")},prev:function(){if(this.sliding)return;return this.slide("prev")},slide:function(b,c){var d=this.$element.find(".active"),e=c||d[b](),f=this.interval,g=b=="next"?"left":"right",h=b=="next"?"first":"last",i=this,j=a.Event("slide");this.sliding=!0,f&&this.pause(),e=e.length?e:this.$element.find(".item")[h]();if(e.hasClass("active"))return;if(a.support.transition&&this.$element.hasClass("slide")){this.$element.trigger(j);if(j.isDefaultPrevented())return;e.addClass(b),e[0].offsetWidth,d.addClass(g),e.addClass(g),this.$element.one(a.support.transition.end,function(){e.removeClass([b,g].join(" ")).addClass("active"),d.removeClass(["active",g].join(" ")),i.sliding=!1,setTimeout(function(){i.$element.trigger("slid")},0)})}else{this.$element.trigger(j);if(j.isDefaultPrevented())return;d.removeClass("active"),e.addClass("active"),this.sliding=!1,this.$element.trigger("slid")}return f&&this.cycle(),this}},a.fn.carousel=function(c){return this.each(function(){var d=a(this),e=d.data("carousel"),f=a.extend({},a.fn.carousel.defaults,typeof c=="object"&&c);e||d.data("carousel",e=new b(this,f)),typeof c=="number"?e.to(c):typeof c=="string"||(c=f.slide)?e[c]():f.interval&&e.cycle()})},a.fn.carousel.defaults={interval:5e3,pause:"hover"},a.fn.carousel.Constructor=b,a(function(){a("body").on("click.carousel.data-api","[data-slide]",function(b){var c=a(this),d,e=a(c.attr("data-target")||(d=c.attr("href"))&&d.replace(/.*(?=#[^\s]+$)/,"")),f=!e.data("modal")&&a.extend({},e.data(),c.data());e.carousel(f),b.preventDefault()})})}(window.jQuery),!function(a){var b=function(b,c){this.$element=a(b),this.options=a.extend({},a.fn.typeahead.defaults,c),this.matcher=this.options.matcher||this.matcher,this.sorter=this.options.sorter||this.sorter,this.highlighter=this.options.highlighter||this.highlighter,this.updater=this.options.updater||this.updater,this.$menu=a(this.options.menu).appendTo("body"),this.source=this.options.source,this.shown=!1,this.listen()};b.prototype={constructor:b,select:function(){var a=this.$menu.find(".active").attr("data-value");return this.$element.val(this.updater(a)).change(),this.hide()},updater:function(a){return a},show:function(){var b=a.extend({},this.$element.offset(),{height:this.$element[0].offsetHeight});return this.$menu.css({top:b.top+b.height,left:b.left}),this.$menu.show(),this.shown=!0,this},hide:function(){return this.$menu.hide(),this.shown=!1,this},lookup:function(b){var c=this,d,e;return this.query=this.$element.val(),this.query?(d=a.grep(this.source,function(a){return c.matcher(a)}),d=this.sorter(d),d.length?this.render(d.slice(0,this.options.items)).show():this.shown?this.hide():this):this.shown?this.hide():this},matcher:function(a){return~a.toLowerCase().indexOf(this.query.toLowerCase())},sorter:function(a){var b=[],c=[],d=[],e;while(e=a.shift())e.toLowerCase().indexOf(this.query.toLowerCase())?~e.indexOf(this.query)?c.push(e):d.push(e):b.push(e);return b.concat(c,d)},highlighter:function(a){var b=this.query.replace(/[\-\[\]{}()*+?.,\\\^$|#\s]/g,"\\$&");return a.replace(new RegExp("("+b+")","ig"),function(a,b){return"<strong>"+b+"</strong>"})},render:function(b){var c=this;return b=a(b).map(function(b,d){return b=a(c.options.item).attr("data-value",d),b.find("a").html(c.highlighter(d)),b[0]}),b.first().addClass("active"),this.$menu.html(b),this},next:function(b){var c=this.$menu.find(".active").removeClass("active"),d=c.next();d.length||(d=a(this.$menu.find("li")[0])),d.addClass("active")},prev:function(a){var b=this.$menu.find(".active").removeClass("active"),c=b.prev();c.length||(c=this.$menu.find("li").last()),c.addClass("active")},listen:function(){this.$element.on("blur",a.proxy(this.blur,this)).on("keypress",a.proxy(this.keypress,this)).on("keyup",a.proxy(this.keyup,this)),(a.browser.webkit||a.browser.msie)&&this.$element.on("keydown",a.proxy(this.keypress,this)),this.$menu.on("click",a.proxy(this.click,this)).on("mouseenter","li",a.proxy(this.mouseenter,this))},keyup:function(a){switch(a.keyCode){case 40:case 38:break;case 9:case 13:if(!this.shown)return;this.select();break;case 27:if(!this.shown)return;this.hide();break;default:this.lookup()}a.stopPropagation(),a.preventDefault()},keypress:function(a){if(!this.shown)return;switch(a.keyCode){case 9:case 13:case 27:a.preventDefault();break;case 38:if(a.type!="keydown")break;a.preventDefault(),this.prev();break;case 40:if(a.type!="keydown")break;a.preventDefault(),this.next()}a.stopPropagation()},blur:function(a){var b=this;setTimeout(function(){b.hide()},150)},click:function(a){a.stopPropagation(),a.preventDefault(),this.select()},mouseenter:function(b){this.$menu.find(".active").removeClass("active"),a(b.currentTarget).addClass("active")}},a.fn.typeahead=function(c){return this.each(function(){var d=a(this),e=d.data("typeahead"),f=typeof c=="object"&&c;e||d.data("typeahead",e=new b(this,f)),typeof c=="string"&&e[c]()})},a.fn.typeahead.defaults={source:[],items:8,menu:'<ul class="typeahead dropdown-menu"></ul>',item:'<li><a href="#"></a></li>'},a.fn.typeahead.Constructor=b,a(function(){a("body").on("focus.typeahead.data-api",'[data-provide="typeahead"]',function(b){var c=a(this);if(c.data("typeahead"))return;b.preventDefault(),c.typeahead(c.data())})})}(window.jQuery)
\ No newline at end of file
diff --git a/settings/helpTemplates/common.html b/settings/helpTemplates/common.html
index 1554a1d40..a753b9ded 100644
--- a/settings/helpTemplates/common.html
+++ b/settings/helpTemplates/common.html
@@ -1,15 +1,147 @@
-<#macro makeHeader title>
-  <head>
-    <title>${title}</title>
-    <link href="style.css" type="text/css" rel="stylesheet"> 
-  </head>
-</#macro>
+<!--
+  ~ Copyright (c) 2012, 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.
+  -->
 
-<#macro headerInfo>
-</#macro>
+<#--
+        This file contains all the theming neccesary to present GATKDocs on the GATK website
+        Included are the paths to our bootstrap assets as well as helper functions to generate relevant links
 
-<#macro footerInfo>
-    <p class="see-also">See also <a href="index.html">Main index</a> | <a href="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit">GATK wiki</a> | <a href="http://getsatisfaction.com/gsa">GATK support forum</a></p>
-    <p class="version">GATK version ${version} built at ${timestamp}.</p>
-</#macro>
+        -->
 
+    <#global siteRoot = "http://gsa-stage:8080/" />
+    <#global forum = "http://gatk.vanillaforums.com/" />
+
+    <#macro makeHeader title isIndex>
+        <?php ob_start(); ?>
+        <!DOCTYPE html>
+        <html lang='en'>
+        <head>
+            <meta charset='utf-8'>
+            <title>${title} documentation</title>
+            <meta name='viewport' content='width=device-width, initial-scale=1.0'>
+            <meta name='description' content=''>
+
+            <link type="text/css" rel="stylesheet" href="bootstrap.min.css">
+            <script src="jquery.min.js"></script>
+            <script src="bootstrap.min.js"></script>
+            <style>
+                @media (min-width: 980px) {
+                    body {
+                        padding-top : 60px;
+                    }
+            </style>
+
+
+        </head>
+        <body>
+        <div class="navbar navbar-fixed-top">
+            <div class="navbar-inner">
+                <div class="container-fluid">
+                    <a class="brand" href="index.html">GATK Documentation</a>
+                </div>
+            </div>
+        </div>
+        <div class="container-fluid">
+            <?php
+
+    ob_clean();
+    include '../include/common.php';
+    printHeader("${title}", "Guides");
+    ?>
+
+            <div class="row-fluid">
+                <#if isIndex>
+                    <section class="span4">
+                        <aside class="well">
+                            <h2>About GATKdocs</h2>
+
+                            <p>He is some text describing the docs, what it is and stuf...nalysis ready SNP and indel
+                                calls
+                                with hand filtering when VQSR is not possib. nalysis ready SNP and indel calls with hand
+                                filtering when VQSR is not possib </p>
+                        </aside>
+                    </section>
+                    <div class="span8">
+                </#if>
+
+    </#macro>
+
+    <#macro footerInfo>
+        <hr>
+        <p class="see-also">See also <a href="index.html">Documentation index</a> | <a
+                href="${siteRoot}">GATK Site</a> | <a
+                href="${forum}">GATK support forum</a></p>
+
+        <p class="version">GATK version ${version} built at ${timestamp}.</p>
+    </#macro>
+
+    <#macro pageFooter>
+        </div><!--/.span-->
+        </div><!--/.row-->
+        </body>
+        <?php printFooter();
+        ob_end_flush();
+        ?>
+    </#macro>
+
+    <#macro getCategories map filter>
+        <style>
+            #sidenav .accordion-body a {
+                color : gray;
+            }
+
+            .accordion-body li {
+                list-style : none;
+            }
+        </style>
+
+        <ul class="nav nav-pills nav-stacked" id="sidenav">
+            <#list 0..(map?keys?size-1) as x>
+                <li><a data-toggle="collapse" data-parent="#sidenav"
+                       href="#${map?keys[x]}">${map?keys[x].getDescription()}</a>
+
+                    <div id="${map?keys[x]}"
+                    <?php echo (in_array('${map?keys[x]}', $categories)) ? 'class="accordion-body collapse in"'.chr(62) : 'class="accordion-body collapse"'.chr(62);?>
+                    <ul>
+                        <#assign items=map?values[x] />
+                        <#if filter !="all" >
+                            <#list items as datum>
+                                <#if datum.group == filter>
+                                    <li><a href="${datum.filename}" rel="tooltip"
+                                           title="${datum.summary}">${datum.name}</a>
+                                    </li>
+                                </#if>
+                            </#list>
+                            <#else>
+                                <#list items as datum>
+                                    <li><a href="${datum.filename}" rel="tooltip"
+                                           title="${datum.summary}">${datum.name}</a>
+                                    </li>
+                                </#list>
+                        </#if>
+                    </ul>
+                    </div>
+                </li>
+            </#list>
+        </ul>
+    </#macro>
\ No newline at end of file
diff --git a/settings/helpTemplates/generic.index.template.html b/settings/helpTemplates/generic.index.template.html
index 6c9e9f4e8..d092ec5a0 100644
--- a/settings/helpTemplates/generic.index.template.html
+++ b/settings/helpTemplates/generic.index.template.html
@@ -1,36 +1,50 @@
 <#include "common.html"/>
 
 <#macro emitGroup group>
-  <table id="hor-minimalist-b">
-  <h2>${group.name}</h2>
-  <p>
-  ${group.summary}  
-  <p>
-  <tr>
-     <th>Name</th>
-     <th>Summary</th>
-  </tr>
-    <#list data as datum>
-        <#if datum.group == group.name>
-            <tr>
-               <td><a href="${datum.filename}">${datum.name}</a></td>
-               <td>${datum.summary}</td>
-            </tr>
-        </#if>
-    </#list>
-  </table>
-</#macro>   
 
-<html>
-<@makeHeader title="GATK documentation index"/>
-<body>
-  <h1>GATK documentation index</h1>
-  <@headerInfo />
-  <#list groups?sort_by("name") as group>
+    <div class="accordion" id="index">
+        <div class="accordion-group">
+            <div class="accordion-heading">
+                <a class="accordion-toggle" data-toggle="collapse" data-parent="#index" href="#${group.id}"><h3>
+                    ${group.name}</h3></a>
+            </div>
+            <div class="accordion-body collapse" id="${group.id}">
+                <div class="accordion-inner">
+                    <p class="lead">${group.summary}
+
+                    <p>
+                        <#if group.id == "GATKwalkers">
+                            <h3>Categories</h3>
+                            <@getCategories map=categories filter="GATK walkers" />
+                            <#else>
+                                <table class="table table-striped table-bordered table-condensed">
+                                    <tr>
+                                        <th>Name</th>
+                                        <th>Summary</th>
+                                    </tr>
+                                    <#list data as datum>
+                                        <#if datum.group == group.name>
+                                            <tr>
+                                                <td><a href="${datum.filename}">${datum.name}</a></td>
+                                                <td>${datum.summary}</td>
+                                            </tr>
+                                        </#if>
+                                    </#list>
+                                </table>
+                        </#if>
+                </div>
+            </div>
+        </div>
+    </div>
+</#macro>
+
+<@makeHeader title="GATK documentation index" isIndex=true />
+<h1>GATK documentation index
+<small>${version}</small></h1>
+<hr>
+<#list groups?sort_by("name") as group>
     <@emitGroup group=group/>
-  </#list>
-  
-  <@footerInfo />
-</body>
-</html>
+</#list>
 
+<@footerInfo />
+<@pageFooter />
diff --git a/settings/helpTemplates/generic.template.html b/settings/helpTemplates/generic.template.html
index 7fc8cd7bd..7d02fa865 100644
--- a/settings/helpTemplates/generic.template.html
+++ b/settings/helpTemplates/generic.template.html
@@ -1,8 +1,10 @@
 <#include "common.html"/>
 
 <#macro argumentlist name myargs>
-    <#if myargs?size != 0> 
-        <tr><th colspan="4" id="row-divider">${name}</th></tr>
+    <#if myargs?size != 0>
+        <tr>
+            <th colspan="4" id="row-divider">${name}</th>
+        </tr>
         <#list myargs as arg>
             <tr>
                 <td><a href="#${arg.name}">${arg.name}</a></td>
@@ -11,116 +13,145 @@
                 <td>${arg.summary}</td>
             </tr>
             <#--
-                <td>${arg.required}</td>
+            <
+            td>${arg.required}</td>
             -->
         </#list>
     </#if>
-</#macro>    
-   
+</#macro>
+
 <#macro argumentDetails arg>
-    <h3><a name="${arg.name}">${arg.name}<#if arg.synonyms??> / ${arg.synonyms}</#if></a>
-    (<#if arg.attributes??>${arg.attributes} </#if>${arg.type}<#if arg.defaultValue??> with default value ${arg.defaultValue}</#if>)</h3>
+    <h3><a name="${arg.name}">${arg.name}
+        <#if arg.synonyms??> / ${arg.synonyms}</#if>
+    </a>
+        (
+        <#if arg.attributes??>${arg.attributes}</#if>
+        ${arg.type}
+        <#if arg.defaultValue??> with default value ${arg.defaultValue}</#if>
+        )
+    </h3>
     <p class="args">
-    ${arg.summary}. ${arg.fulltext}
-    <#if arg.rodTypes??>${arg.name} binds reference ordered data.  This argument supports ROD files of the
-    following types: ${arg.rodTypes}</#if>
-    <#if arg.options??>
-        <br>
-        The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values:
-        <dl class="enum">
-        <#list arg.options as option>
-            <dt class="enum">${option.name}</dt>
-            <dd class="enum">${option.summary}</dd>
-        </#list>
-        </dl>
-    </#if>
+        ${arg.summary}. ${arg.fulltext}
+        <#if arg.rodTypes??>${arg.name} binds reference ordered data. This argument supports ROD files of the
+            following types: ${arg.rodTypes}
+        </#if>
+        <#if arg.options??>
+            <br>
+            The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values:
+            <dl class="enum">
+                <#list arg.options as option>
+                    <dt class="enum">${option.name}</dt>
+                    <dd class="enum">${option.summary}</dd>
+                </#list>
+            </dl>
+        </#if>
     </p>
-</#macro>     
-   
+</#macro>
+
 <#macro relatedByType name type>
     <#list relatedDocs as relatedDoc>
         <#if relatedDoc.relation == type>
             <h3>${name}</h3>
             <ul>
-            <#list relatedDocs as relatedDoc>
-                <#if relatedDoc.relation == type>
-                    <li><a href="${relatedDoc.filename}">${relatedDoc.name}</a> is a ${relatedDoc.relation}</li>
-                </#if>
-            </#list>
+                <#list relatedDocs as relatedDoc>
+                    <#if relatedDoc.relation == type>
+                        <li><a href="${relatedDoc.filename}">${relatedDoc.name}</a> is a ${relatedDoc.relation}</li>
+                    </#if>
+                </#list>
             </ul>
-        <#break>        
+            <#break>
         </#if>
     </#list>
 </#macro>
 
-<html>
-<@makeHeader title="${name} documentation"/>
-<body>
-  <h1>${name}</h1>
-  <@headerInfo />
-  <p class="summary">${summary}</p>
-  <#if author??>
-      <h2>Author</h2>
-      ${author}
-  </#if>
-  <h2>Introduction</h2>
-  ${description}
-  
-  <#-- Create the argument summary -->
-  <#if arguments.all?size != 0> 
-      <hr>
-      <h2>${name} specific arguments</h2>
-      <table id="hor-minimalist-b">
-      <thead>
-      <tr>
-         <th>Name</th>
-         <th>Type</th>
-         <th>Default value</th>
-         <th>Summary</th>
-      </tr>
-      </thead>
-      <tbody>
-         <@argumentlist name="Required" myargs=arguments.required/>
-         <@argumentlist name="Optional" myargs=arguments.optional/>
-         <@argumentlist name="Advanced" myargs=arguments.advanced/>
-         <@argumentlist name="Hidden" myargs=arguments.hidden/>
-         <@argumentlist name="Depreciated" myargs=arguments.depreciated/>
-      </tbody>
-      </table>
-  </#if>
+<#list categories as cat>
+    <?php $categories[] = '${cat}'; ?>
+</#list>
+<@makeHeader title="${name} documentation" isIndex=false />
+<section class="span4">
+    <aside class="well">
+        <h2>Categories</h2>
+        <@getCategories map=catNav filter="all" />
+    </aside>
+    <?php getForumPosts( '${name}' ) ?>
 
-  <#-- Create references to additional capabilities if appropriate -->
-  <#if extradocs?size != 0> 
-      <hr>
-      <h2>Additional capabilities</h2>
-      The arguments described in the entries below can be supplied to this tool to modify
-      its behavior.  For example, the -L argument directs the GATK engine restricts processing 
-      to specific genomic intervals.  This capability is available to all GATK walkers.
-      <ul>
-      <#list extradocs as extradoc>
-          <li><a href="${extradoc.filename}">${extradoc.name}</a></li>
-      </#list>
-      </ul>
-  </#if>
-  
-  <#-- This class is related to other documented classes via sub/super relationships -->
-  <#if relatedDocs?? && relatedDocs?size != 0> 
-    <hr>
-    <h2>Related capabilities</h2>
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+
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+
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+    <p class="lead">${summary}</p>
+    <#if author??>
+        <h2>Author<br/>
+            <small>${author}</small>
+        </h2>
+    </#if>
+    <#if (categories?size > 0) >
+        <h3>Categories</h3>
+        <ul>
+            <#list categories as cat>
+                <li>${cat.getDescription()}</li>
+            </#list>
+        </ul>
+    </#if>
+    <h2>Introduction</h2>
+    ${description}
+
+    <#-- Create the argument summary -->
+        <#if arguments.all?size != 0>
+            <hr>
+            <h3>${name} specific arguments</h3>
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+                <@argumentlist name="Depreciated" myargs=arguments.depreciated/>
+                </tbody>
+            </table>
+        </#if>
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+        <#-- Create references to additional capabilities if appropriate -->
+            <#if extradocs?size != 0>
+                <hr>
+                <h2>Additional capabilities</h2>
+                The arguments described in the entries below can be supplied to this tool to modify
+                its behavior. For example, the -L argument directs the GATK engine restricts processing
+                to specific genomic intervals. This capability is available to all GATK walkers.
+                <ul>
+                    <#list extradocs as extradoc>
+                        <li><a href="${extradoc.filename}">${extradoc.name}</a></li>
+                    </#list>
+                </ul>
+            </#if>
+
+            <#-- This class is related to other documented classes via sub/super relationships -->
+                <#if relatedDocs?? && relatedDocs?size != 0>
+                    <hr>
+                    <h2>Related capabilities</h2>
+                    <@relatedByType name="Superclasses" type="superclass"/>
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+                <#-- List all of the -->
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+                            <#list arguments.all as arg>
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+                            </#list>
+                    </#if>
+
+                    <@footerInfo />
+                    <@pageFooter />
\ No newline at end of file
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