Removed the "Walker" suffix from all walkers that had it.

* Did not touch archived walkers... those can be named whatever.
   * Kept abstract classes that end in Walker untouched (e.g. LocusWalker, ReadWalker, ...)
   * Renamed a few inner classes due to conflict when stripping off Walker from their outer classes: ContigStats, FlagStats and FastaStats.

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" />

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;

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,

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;

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;

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;

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);

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. 
      */

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.
      */

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};
+}

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;
+    }
+}

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;
 

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 org.broadinstitute.sting.utils.activeregion.ActiveRegion last = workQueue.getLast();
-                    final ActiveRegion first = activeRegions.get(0);
+                    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;
+                org.broadinstitute.sting.utils.activeregion.ActiveRegion bestRegion = activeRegion;
-                for( final ActiveRegion otherRegionToTest : workQueue ) {
+                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 );
                         }

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();

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.

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;

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++;

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;
 

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;
 

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;

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() {

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;
 

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;

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;
 

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.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 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();
     }

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;
 

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;
 

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;
 

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));

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;
 

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 )

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;

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();

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()) {

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;
 

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 );

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;
 

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;

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;
 

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;
 

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;
 

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;
 

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;
 

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;
 

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:

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;
 

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;
 

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;
 

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();

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();

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);

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();

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 );
 

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

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 ) { }
 }

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();

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.codecs.vcf.VCFFilterHeaderLine;
-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.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();
 

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);
 

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
 

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);
     }
 }

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;
 

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;
+    CallableLoci.CalledState printState1 = CallableLoci.CalledState.REF_N;
-    CallableLociWalker.CalledState printState2 = CallableLociWalker.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]);
+            printState1 = CallableLoci.CalledState.valueOf(states[0]);
-            printState2 = CallableLociWalker.CalledState.valueOf(states[1]);
+            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);
+            CallableLoci.CallableBaseState comp1 = getCallableBaseState(tracker, compTrack1);
-            CallableLociWalker.CallableBaseState comp2 = getCallableBaseState(tracker, compTrack2);
+            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());
+        CallableLoci.CalledState state = CallableLoci.CalledState.valueOf(bed.getName());
-        return new CallableLociWalker.CallableBaseState(getToolkit().getGenomeLocParser(),loc, state);
+        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);
+            CallableLoci.CallableBaseState comp1 = comps.get(0);
-            CallableLociWalker.CallableBaseState comp2 = comps.get(1);
+            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 ( CallableLoci.CalledState state1 : CallableLoci.CalledState.values() ) {
-            for ( CallableLociWalker.CalledState state2 : CallableLociWalker.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()]);
             }
         }

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;

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;
 

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

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:
      *

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.

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;
 

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() {
+    public FastaStatistics reduceInit() {
-        return new FastaStats();
+        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);
     }

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();

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();

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)

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;
             }
         }

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);
 

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();

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;
 

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;

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;
 

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);
     }
 }

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;
 

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;

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();
 

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;
 

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;
 

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;
 

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;
 

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;

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 = ",";

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.DataSource;
-import org.broadinstitute.sting.gatk.walkers.*;
+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;
 

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.

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.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+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,

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

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();

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() {

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();

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;
     }
 

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());

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

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
      */

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
      */