Reorganized walker categories in GATKDocs (@DocumentedGATKFeature details)

-- Sorted out contents of BAM Processing vs. Diagnostics & QC Tools
-- Moved two validation-related walkers from Diagnostics & QC to Validation Utilities
-- Reworded some category names and descriptions to be more explicit and user-friendly

protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java

@@ -69,7 +69,7 @@ import java.util.Map;
 /**
  * The GC content (# GC bases / # all bases) of the reference within 50 bp +/- this site
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
     public Map<String, Object> annotate(final RefMetaDataTracker tracker,

protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java

@@ -127,7 +127,7 @@ import java.util.List;
  * </pre>
  */
 
-@DocumentedGATKFeature(groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class})
+@DocumentedGATKFeature(groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class})
 @BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN)
 @ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class, UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class})
 @PartitionBy(PartitionType.READ)

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java

@@ -87,7 +87,7 @@ import java.util.Map;
  * @since 10/30/11
  */
 
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 @ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class})
 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;

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java

@@ -102,7 +102,7 @@ import java.util.*;
  * </pre>
  */
 
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
 @PartitionBy(PartitionType.CONTIG)
 @ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class, BadCigarFilter.class})
 @Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=40)

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java

@@ -104,7 +104,7 @@ import java.util.*;
  * @author Mauricio Carneiro, Roger Zurawicki
  * @since 5/8/12
  */
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 @By(value = DataSource.READS)
 @PartitionBy(PartitionType.INTERVAL)
 public class DiagnoseTargets extends LocusWalker<Long, Long> {

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java

@@ -62,7 +62,7 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
 import java.io.PrintStream;
 
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 @PartitionBy(PartitionType.CONTIG)
 @ActiveRegionTraversalParameters(extension = 0, maxRegion = 50000)
 public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {

protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java

@@ -133,7 +133,7 @@ import java.util.*;
  *
  * @author ebanks
  */
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
 @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = ReadTransformer.ApplicationTime.ON_OUTPUT)
 public class IndelRealigner extends ReadWalker<Integer, Integer> {
 

protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java

@@ -87,7 +87,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
 public class LeftAlignIndels extends ReadWalker<Integer, Integer> {
 
     @Output(required=false, doc="Output bam")

protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java

@@ -117,7 +117,7 @@ import java.util.TreeSet;
  *
  * @author ebanks
  */
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
 @ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class, BadMateFilter.class, Platform454Filter.class, BadCigarFilter.class})
 @Reference(window=@Window(start=-1,stop=50))
 @Allows(value={DataSource.READS, DataSource.REFERENCE})

public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java

@@ -48,7 +48,7 @@ import java.util.Iterator;
  * @author mhanna
  * @version 0.1
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
 public class AlignmentValidation extends ReadWalker<Integer,Integer> {
     /**
      * The supporting BWT index generated using BWT. 

public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java

@@ -50,7 +50,7 @@ import java.util.*;
  * gatk all the parsed out information.  Pretty much anything dealing with the underlying system should go here,
  * the gatk engine should  deal with any data related information.
  */
-@DocumentedGATKFeature(groupName = "GATK Engine")
+@DocumentedGATKFeature(groupName = "GATK Engine (parameters available to all tools)")
 public class CommandLineGATK extends CommandLineExecutable {
     @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
     private String analysisName = null;

public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java

@@ -45,7 +45,7 @@ import java.util.Map;
 /**
  * Computes the coverage per sample for every position (use with -L argument!).
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 public class CoverageBySample extends LocusWalker<Integer, Integer> {
     @Output
     protected PrintStream out;    

public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java

@@ -34,7 +34,7 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
  * A SamRecordFilter that also depends on the header.
  */
 @DocumentedGATKFeature(
-        groupName = "Read filters",
+        groupName = "Read Filters",
         summary = "GATK Engine arguments that filter or transfer incoming SAM/BAM data files" )
 public abstract class ReadFilter implements SamRecordFilter {
     /**

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java

@@ -32,7 +32,7 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import java.util.List;
 import java.util.Set;
 
-@DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator annotations", summary = "VariantAnnotator annotations")
+@DocumentedGATKFeature(enable = true, groupName = "Variant Annotations", summary = "Annotations available to VariantAnnotator and the variant callers (some restrictions apply)")
 public abstract class VariantAnnotatorAnnotation {
     // return the INFO keys
     public abstract List<String> getKeyNames();

public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java

@@ -123,7 +123,7 @@ import java.io.PrintStream;
  * @author Mark DePristo
  * @since May 7, 2010
  */
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 @By(DataSource.REFERENCE)
 public class CallableLoci extends LocusWalker<CallableLoci.CallableBaseState, CallableLoci.Integrator> {
     @Output

public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java

@@ -46,7 +46,7 @@ import java.util.List;
 /**
  * Test routine for new VariantContext object
  */
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 public class CompareCallableLoci extends RodWalker<List<CallableLoci.CallableBaseState>, long[][]> {
     @Output
     protected PrintStream out;

public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java

@@ -63,7 +63,7 @@ import java.util.List;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 @Allows(value = {DataSource.REFERENCE})
 @Requires(value = {DataSource.REFERENCE})
 @By(DataSource.REFERENCE)

public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java

@@ -93,7 +93,7 @@ import java.io.PrintStream;
  *
  * @author Kiran Garimella, Mark DePristo
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 public class ErrorRatePerCycle extends LocusWalker<Integer, Integer> {
     @Output PrintStream out;
     @Argument(fullName="min_base_quality_score", shortName="mbq", doc="Minimum base quality required to consider a base for calling", required=false)

public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java

@@ -97,7 +97,7 @@ import java.util.Map;
  *
  * @author Mark DePristo
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 public class ReadGroupProperties extends ReadWalker<Integer, Integer> {
     @Output
     public PrintStream out;

public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java

@@ -71,7 +71,7 @@ import java.util.List;
  * @author Kiran Garimela
  */
 
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 public class ReadLengthDistribution extends ReadWalker<Integer, Integer> {
     @Output
     public PrintStream out;

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java

@@ -134,7 +134,7 @@ import java.util.List;
  * @author Mark DePristo
  * @since 7/4/11
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 public class DiffObjects extends RodWalker<Integer, Integer> {
     /**
      * Writes out a file of the DiffEngine format:

public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java

@@ -81,7 +81,7 @@ import java.util.List;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Reference Utilities", extraDocs = {CommandLineGATK.class} )
 @Reference(window=@Window(start=-1,stop=50))
 @Requires(value={DataSource.REFERENCE})
 public class FastaAlternateReferenceMaker extends FastaReferenceMaker {

public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java

@@ -67,7 +67,7 @@ import java.io.PrintStream;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Reference Utilities", extraDocs = {CommandLineGATK.class} )
 public class FastaReferenceMaker extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
 
     @Output PrintStream out;

public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java

@@ -39,7 +39,7 @@ import java.io.PrintStream;
 /**
  * Calculates basic statistics about the reference sequence itself
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 public class FastaStats extends RefWalker<Byte, FastaStats.FastaStatistics> {
     @Output PrintStream out;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java

@@ -58,7 +58,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class CountBases extends ReadWalker<Integer, Long> {
     public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java

@@ -48,7 +48,7 @@ import java.util.List;
  * very useful since overlapping intervals get merged, so you can count the number of intervals the GATK merges down to.
  * This was its very first use.
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 public class CountIntervals extends RefWalker<Long, Long> {
     @Output
     PrintStream out;

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java

@@ -65,7 +65,7 @@ import java.io.PrintStream;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 public class CountLoci extends LocusWalker<Integer, Long> implements TreeReducible<Long>, NanoSchedulable {
     @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;
 /**
  * Walks over the input data set, calculating the number of reads seen from male samples for diagnostic purposes.
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class CountMales extends ReadWalker<Integer, Integer> {
     public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java

@@ -73,7 +73,7 @@ import java.util.*;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 public class CountRODs extends RodWalker<CountRODs.Datum, Pair<ExpandingArrayList<Long>, Long>> implements TreeReducible<Pair<ExpandingArrayList<Long>, Long>>, NanoSchedulable {
     @Output
     public PrintStream out;

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java

@@ -65,7 +65,7 @@ import java.util.List;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 public class CountRODsByRef extends RefWalker<CountRODs.Datum, Pair<ExpandingArrayList<Long>, Long>> {
 
     /**

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java

@@ -66,7 +66,7 @@ import java.util.Map;
  * </pre>
  */
 
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class CountReadEvents extends ReadWalker<Map<CigarOperator, ArrayList<Integer>> , Map<Integer, Map<CigarOperator, Long>>> {
     @Output (doc = "GATKReport table output")

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java

@@ -63,7 +63,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class CountReads extends ReadWalker<Integer, Integer> implements NanoSchedulable {
     public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java

@@ -63,7 +63,7 @@ import java.util.List;
  *   [-L input.intervals]
  * </pre>
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class CountTerminusEvent extends ReadWalker<Pair<Long, Long>, Pair<Long, Long>> {
     public Pair<Long, Long> map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java

@@ -72,7 +72,7 @@ import java.text.NumberFormat;
  * reads with QC failure flag set, number of duplicates, percentage mapped, etc.
  * @author aaron
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 @Requires({DataSource.READS})
 public class FlagStat extends ReadWalker<FlagStat.FlagStatus, FlagStat.FlagStatus> implements NanoSchedulable {
     @Output

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java

@@ -54,7 +54,7 @@ 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>
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 public class Pileup extends LocusWalker<String, Integer> implements TreeReducible<Integer>, NanoSchedulable {
 
     private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java

@@ -42,7 +42,7 @@ 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.
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 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/qc/QCRef.java

@@ -61,7 +61,7 @@ import java.io.PrintStream;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 public class QCRef extends RefWalker<Integer, Integer> {
     @Output
     public PrintStream out;

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java

@@ -56,7 +56,7 @@ import java.util.Arrays;
  * Walks over the input reads, printing out statistics about the read length, number of clipping events, and length
  * of the clipping to the output stream.
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Diagnostics and Quality Control Tools", extraDocs = {CommandLineGATK.class} )
 @Requires({DataSource.READS})
 public class ReadClippingStats extends ReadWalker<ReadClippingStats.ReadClippingInfo,Integer> {
     @Output

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java

@@ -52,7 +52,7 @@ import java.util.Arrays;
  * each overlapping read, and quality score) to the reference pileup data generated by samtools.  Samtools' pileup data
  * should be specified using the command-line argument '-pileup:SAMPileup <your sam pileup file>'.
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} )
 @Requires(value={DataSource.READS,DataSource.REFERENCE})
 public class ValidatingPileup extends LocusWalker<Integer, ValidationStats> implements TreeReducible<ValidationStats> {
     @Input(fullName = "pileup", doc="The SAMPileup containing the expected output", required = true)

public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java

@@ -153,7 +153,7 @@ import java.util.regex.Pattern;
  * @author Mark DePristo
  * @since 2010
  */
-@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
 @Requires({DataSource.READS})
 public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipReads.ClippingData> {
     /**

public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java

@@ -90,7 +90,7 @@ import java.util.*;
  * </pre>
  *
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
 @ReadTransformersMode(ApplicationTime = ReadTransformer.ApplicationTime.HANDLED_IN_WALKER)
 @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = ReadTransformer.ApplicationTime.HANDLED_IN_WALKER)
 @Requires({DataSource.READS, DataSource.REFERENCE})

public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java

@@ -51,7 +51,7 @@ import java.util.Map;
  * Divides the input data set into separate BAM files, one for each sample in the input data set.  The split
  * files are named concatenating the sample name to the end of the provided outputRoot command-line argument.
  */
-@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
+@DocumentedGATKFeature( groupName = "BAM Processing Tools", extraDocs = {CommandLineGATK.class} )
 @WalkerName("SplitSamFile")
 @Requires({DataSource.READS})
 public class SplitSamFile extends ReadWalker<SAMRecord, Map<String, SAMFileWriter>> {

public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java

@@ -46,8 +46,8 @@ import java.io.File;
  * Time: 2:24:09 PM
  */
 @DocumentedGATKFeature(
-        groupName = "User exceptions",
+        groupName = "User Exceptions",
-        summary = "Exceptions caused by incorrect user behavior, such as bad files, bad arguments, etc." )
+        summary = "Errors caused by incorrect user behavior, such as bad files, bad arguments, etc." )
 public class UserException extends ReviewedStingException {
     /**
      * The URL where people can get help messages.  Printed when an error occurs

public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java

@@ -31,11 +31,11 @@ public class GATKDocUtils {
      */
     public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = HelpConstants.GATK_DOCS_URL;
     /**
-     * The URL root for STABLE GATKDOC units
+     * The URL root for STABLE GATKDOC units             //TODO: do sthing with this or remove -- URL goes nowhere
      */
     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           //TODO: do sthing with this or remove -- URL goes nowhere
      */
     public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
 
@@ -55,7 +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.
+     * exists).  Currently points to the RELEASE doc path only.     //TODO: do sthing with other paths or remove ?
      *
      * @param c
      * @return

public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java

@@ -117,8 +117,8 @@ public class GATKDoclet {
 
     static {
         STATIC_DOCS.add(new DocumentedGATKFeatureObject(FeatureCodec.class,
-                "Reference ordered data (ROD) codecs",
+                "ROD Codecs",
-                "Tribble codecs for reading reference ordered data such as VCF or BED files"));
+                "Tribble codecs for reading reference ordered data (ROD) files such as VCF or BED"));
     }