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
2013-02-12 12:48:20 -05:00 · 2013-02-12 12:48:20 -05:00 · dff5ef562b
parent 59484dfae4
commit dff5ef562b
45 changed files with 49 additions and 49 deletions
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
+++ b/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,
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
+++ b/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)
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java
+++ b/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;
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
+++ b/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)
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
+++ b/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> {
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
+++ b/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> {
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/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> {

--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
+++ b/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")
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/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})
--- a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java
+++ b/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. 
--- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/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;
--- a/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java
+++ b/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;    
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
+++ b/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 {
    /**
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
@ -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();
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
+++ b/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
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java
+++ b/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;
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
+++ b/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)
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
+++ b/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)
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
+++ b/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;
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java
+++ b/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;
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
+++ b/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:
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
+++ b/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 {
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java
+++ b/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;
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
+++ b/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;

--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java
+++ b/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) {
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java
+++ b/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;
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java
+++ b/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;
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java
+++ b/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) {
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java
+++ b/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;
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java
+++ b/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>> {

    /**
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java
+++ b/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")
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
+++ b/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) {
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java
+++ b/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) {
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java
+++ b/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
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java
+++ b/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
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java
+++ b/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;
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java
+++ b/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;
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java
+++ b/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
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java
+++ b/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)
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
+++ b/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> {
    /**
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java
+++ b/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})
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java
+++ b/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>> {
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/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",
-        summary = "Exceptions caused by incorrect user behavior, such as bad files, bad arguments, etc." )
+        groupName = "User Exceptions",
+        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
--- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java
+++ b/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
--- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
+++ b/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",
-                "Tribble codecs for reading reference ordered data such as VCF or BED files"));
+                "ROD Codecs",
+                "Tribble codecs for reading reference ordered data (ROD) files such as VCF or BED"));
    }