Add support for documentation generation for metrics classes.

src/main/java/picard/analysis/AlignmentSummaryMetrics.java

@@ -24,13 +24,19 @@
 
 package picard.analysis;
 
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.metrics.MultilevelMetrics;
+import picard.util.help.HelpConstants;
 
 /**
  * High level metrics about the alignment of reads within a SAM file, produced by
  * the CollectAlignmentSummaryMetrics program and usually stored in a file with
  * the extension ".alignment_summary_metrics".
  */
+@DocumentedFeature(
+        groupName = HelpConstants.DOC_CAT_METRICS,
+        groupSummary = HelpConstants.DOC_CAT_METRICS_SUMMARY,
+        summary = "Alignment metrics")
 public class AlignmentSummaryMetrics extends MultilevelMetrics {
     public enum Category {UNPAIRED, FIRST_OF_PAIR, SECOND_OF_PAIR, PAIR}
 

src/main/java/picard/analysis/BaseDistributionByCycleMetrics.java

@@ -25,7 +25,10 @@
 package picard.analysis;
 
 import htsjdk.samtools.metrics.MetricBase;
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import picard.util.help.HelpConstants;
 
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public class BaseDistributionByCycleMetrics extends MetricBase {
     public int READ_END;
     public int CYCLE;

src/main/java/picard/analysis/CollectOxoGMetrics.java

@@ -45,6 +45,7 @@
 import picard.cmdline.StandardOptionDefinitions;
 import picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup;
 import picard.util.DbSnpBitSetUtil;
+import picard.util.help.HelpConstants;
 
 import java.io.File;
 import java.util.*;
@@ -136,6 +137,7 @@ public class CollectOxoGMetrics extends CommandLineProgram {
     private static final String UNKNOWN_SAMPLE = "UnknownSample";
 
     /** Metrics class for outputs. */
+    @DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
     public static final class CpcgMetrics extends MetricBase {
         /** The name of the sample being assayed. */
         public String SAMPLE_ALIAS;

src/main/java/picard/analysis/CollectQualityYieldMetrics.java

@@ -35,6 +35,7 @@
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.cmdline.StandardOptionDefinitions;
 import picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup;
+import picard.util.help.HelpConstants;
 
 import java.io.File;
 
@@ -203,6 +204,7 @@ public void addMetricsToFile(final MetricsFile<QualityYieldMetrics, Integer> met
     /**
      * A set of metrics used to describe the general quality of a BAM file
      */
+    @DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
     public static class QualityYieldMetrics extends MergeableMetricBase {
 
         /**

src/main/java/picard/analysis/CollectRawWgsMetrics.java

@@ -29,6 +29,7 @@
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup;
+import picard.util.help.HelpConstants;
 
 /**
  * Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing
@@ -114,6 +115,7 @@ public CollectRawWgsMetrics() {
     }
 
     // rename the class so that in the metric file it is annotated differently.
+    @DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
     public static class RawWgsMetrics extends WgsMetrics {
         public RawWgsMetrics() {
             super();

src/main/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.java

@@ -42,6 +42,7 @@
 import picard.filter.CountingFilter;
 import picard.filter.CountingPairedFilter;
 import picard.util.RExecutor;
+import picard.util.help.HelpConstants;
 
 import java.io.File;
 import java.util.List;
@@ -87,6 +88,7 @@ public class CollectWgsMetricsWithNonZeroCoverage extends CollectWgsMetrics {
     /**
      * Metrics for evaluating the performance of whole genome sequencing experiments.
      */
+    @DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
     public static class WgsMetricsWithNonZeroCoverage extends WgsMetrics {
         public enum Category {WHOLE_GENOME, NON_ZERO_REGIONS}
 

src/main/java/picard/analysis/FingerprintingDetailMetrics.java

@@ -25,12 +25,15 @@
 package picard.analysis;
 
 import htsjdk.samtools.metrics.MetricBase;
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import picard.util.help.HelpConstants;
 
 /**
  * Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.
  *
  * @author Tim Fennell
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public class FingerprintingDetailMetrics extends MetricBase {
     /** The sequencing read group from which sequence data was fingerprinted. */
     public String READ_GROUP;

src/main/java/picard/analysis/FingerprintingSummaryMetrics.java

@@ -25,6 +25,8 @@
 package picard.analysis;
 
 import htsjdk.samtools.metrics.MetricBase;
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import picard.util.help.HelpConstants;
 
 /**
  * Summary fingerprinting metrics and statistics about the comparison of the sequence data
@@ -33,6 +35,7 @@
  *
  * @author Tim Fennell
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public class FingerprintingSummaryMetrics extends MetricBase {
     /** The read group from which sequence data was drawn for comparison. */
     public String READ_GROUP;

src/main/java/picard/analysis/GcBiasDetailMetrics.java

@@ -24,14 +24,17 @@
 
 package picard.analysis;
 
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.metrics.MultilevelMetrics;
+import picard.util.help.HelpConstants;
 
 /**
  * Class that holds detailed metrics about reads that fall within windows of a certain
  * GC bin on the reference genome.
  *
  * @author Tim Fennell
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public class GcBiasDetailMetrics extends MultilevelMetrics {
     public String ACCUMULATION_LEVEL;
     /** This option is used to mark including or excluding duplicates. */

src/main/java/picard/analysis/GcBiasSummaryMetrics.java

@@ -24,13 +24,16 @@
 
 package picard.analysis;
 
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.metrics.MultilevelMetrics;
+import picard.util.help.HelpConstants;
 
 /**
  * High level metrics that capture how biased the coverage in a certain lane is.
  *
  * @author Tim Fennell
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public class GcBiasSummaryMetrics extends MultilevelMetrics {
     public String ACCUMULATION_LEVEL;
 

src/main/java/picard/analysis/InsertSizeMetrics.java

@@ -25,7 +25,9 @@
 package picard.analysis;
 
 import htsjdk.samtools.SamPairUtil.PairOrientation;
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.metrics.MultilevelMetrics;
+import picard.util.help.HelpConstants;
 
 /**
  * Metrics about the insert size distribution of a paired-end library, created by the
@@ -35,6 +37,7 @@
  *
  * @author Doug Voet (dvoet at broadinstitute dot org)
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public class InsertSizeMetrics extends MultilevelMetrics {
 
     /** The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome. */

src/main/java/picard/analysis/JumpingLibraryMetrics.java

@@ -24,13 +24,16 @@
 package picard.analysis;
 
 import htsjdk.samtools.metrics.MetricBase;
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import picard.util.help.HelpConstants;
 
 /**
  * High level metrics about the presence of  outward- and inward-facing pairs
  * within a SAM file generated with a jumping library, produced by
  * the CollectJumpingLibraryMetrics program and usually stored in a file with
  * the extension ".jump_metrics".
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public class JumpingLibraryMetrics extends MetricBase {
 
     /**

src/main/java/picard/analysis/RnaSeqMetrics.java

@@ -23,12 +23,15 @@
  */
 package picard.analysis;
 
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.metrics.MultilevelMetrics;
+import picard.util.help.HelpConstants;
 
 /**
  * Metrics about the alignment of RNA-seq reads within a SAM file to genes, produced by the CollectRnaSeqMetrics
  * program and usually stored in a file with the extension ".rna_metrics".
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public class RnaSeqMetrics extends MultilevelMetrics {
     /** The total number of PF bases including non-aligned reads. */
     public long PF_BASES;

src/main/java/picard/analysis/RrbsCpgDetailMetrics.java

@@ -24,12 +24,15 @@
 
 package picard.analysis;
 
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.metrics.MultilevelMetrics;
+import picard.util.help.HelpConstants;
 
 /**
  * Holds information about CpG sites encountered for RRBS processing QC
  * @author jgentry
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public final class RrbsCpgDetailMetrics extends MultilevelMetrics {
 	/** Sequence the CpG is seen in */
 	public String SEQUENCE_NAME;

src/main/java/picard/analysis/RrbsMetrics.java

@@ -25,6 +25,8 @@
 package picard.analysis;
 
 import htsjdk.samtools.metrics.MetricBase;
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import picard.util.help.HelpConstants;
 
 import java.util.List;
 
@@ -37,6 +39,7 @@
  *
  * @author jgentry@broadinstitute.org
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 class RrbsMetrics extends MetricBase {
 	private final RrbsSummaryMetrics summaryMetrics;
 	private final List<RrbsCpgDetailMetrics> detailMetrics;

src/main/java/picard/analysis/RrbsSummaryMetrics.java

@@ -24,13 +24,16 @@
 
 package picard.analysis;
 
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.metrics.MultilevelMetrics;
+import picard.util.help.HelpConstants;
 
 /**
  * Holds summary statistics from RRBS processing QC
  *
  * @author jgentry
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public final class RrbsSummaryMetrics extends MultilevelMetrics {
 	/** Number of mapped reads processed */
 	public Integer READS_ALIGNED;

src/main/java/picard/analysis/TheoreticalSensitivityMetrics.java

@@ -25,6 +25,8 @@
 package picard.analysis;
 
 import htsjdk.samtools.metrics.MetricBase;
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import picard.util.help.HelpConstants;
 
 /**
  * TheoreticalSensitivityMetrics, are metrics calculated from TheoreticalSensitivity and parameters used in
@@ -35,6 +37,7 @@
  *
  * @author Mark Fleharty
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public class TheoreticalSensitivityMetrics extends MetricBase {
     /** The allele fraction which theoretical sensitivity is calculated for. */
     public double ALLELE_FRACTION;

src/main/java/picard/analysis/WgsMetrics.java

@@ -27,10 +27,13 @@
 import htsjdk.samtools.util.Histogram;
 import htsjdk.samtools.util.IntervalList;
 import htsjdk.samtools.util.QualityUtil;
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.PicardException;
 import picard.util.MathUtil;
+import picard.util.help.HelpConstants;
 
 /** Metrics for evaluating the performance of whole genome sequencing experiments. */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public class WgsMetrics extends MergeableMetricBase {
     private static final double LOG_ODDS_THRESHOLD = 3.0;
 

src/main/java/picard/analysis/artifacts/ErrorSummaryMetrics.java

@@ -1,6 +1,8 @@
 package picard.analysis.artifacts;
 
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.analysis.MergeableMetricBase;
+import picard.util.help.HelpConstants;
 
 /**
  * Summary metrics produced by {@link CollectSequencingArtifactMetrics} as a roll up of the
@@ -9,6 +11,7 @@
  * Errors are normalized to the lexically lower reference base and summarized together. E.g.
  * G>T is converted to C>A and merged with data from C>A for reporting.
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public class ErrorSummaryMetrics extends MergeableMetricBase {
     /** The reference base (or it's complement). */
     @MergeByAssertEquals public char REF_BASE;

src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java

@@ -2,6 +2,8 @@
 
 import htsjdk.samtools.metrics.MetricBase;
 import htsjdk.samtools.util.QualityUtil;
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import picard.util.help.HelpConstants;
 
 public class SequencingArtifactMetrics {
     public static final String PRE_ADAPTER_SUMMARY_EXT = ".pre_adapter_summary_metrics";
@@ -31,6 +33,7 @@ public class SequencingArtifactMetrics {
      * their contributions will cancel out in the calculation.
      *
      */
+    @DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
     public static class PreAdapterSummaryMetrics extends MetricBase {
         /** The name of the sample being assayed. */
         public String SAMPLE_ALIAS;
@@ -89,6 +92,7 @@ public void inferArtifactName() {
      * relative to sites with the flip (C positive / G negative). This is known as the "G-Ref" artifact.
      *
      */
+    @DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
     public static class BaitBiasSummaryMetrics extends MetricBase {
         /** The name of the sample being assayed. */
         public String SAMPLE_ALIAS;
@@ -138,6 +142,7 @@ public void inferArtifactName() {
     /**
      * Pre-adapter artifacts broken down by context.
      */
+    @DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
     public static class PreAdapterDetailMetrics extends MetricBase {
         /** The name of the sample being assayed. */
         public String SAMPLE_ALIAS;
@@ -200,6 +205,7 @@ public int compareTo(final PreAdapterDetailMetrics o) {
     /**
      * Bait bias artifacts broken down by context.
      */
+    @DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
     public static class BaitBiasDetailMetrics extends MetricBase {
         public String SAMPLE_ALIAS;
         /** The name of the library being assayed. */

src/main/java/picard/analysis/directed/HsMetrics.java

@@ -24,6 +24,9 @@
 
 package picard.analysis.directed;
 
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import picard.util.help.HelpConstants;
+
 /**
  * <p>Metrics generated by CollectHsMetrics for the analysis of target-capture sequencing experiments. The metrics
  * in this class fall broadly into three categories:</p>
@@ -46,6 +49,7 @@
  *
  * @author Tim Fennell
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public class HsMetrics extends PanelMetricsBase {
     /** The name of the bait set used in the hybrid selection. */
     public String BAIT_SET;

src/main/java/picard/analysis/directed/TargetMetrics.java

@@ -24,10 +24,14 @@
 
 package picard.analysis.directed;
 
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import picard.util.help.HelpConstants;
+
 /**
  * TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection
  * or Targeted PCR Techniques (TSCA).  TargetMetrics at the moment are the metrics that are shared by both HybridSelection and TargetedPcrMetrics.
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public class TargetMetrics extends TargetMetricsBase {
     /**  The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection run */
     public String PROBE_SET;

src/main/java/picard/analysis/directed/TargetedPcrMetrics.java

@@ -25,8 +25,12 @@
 package picard.analysis.directed;
 
 
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import picard.util.help.HelpConstants;
+
 /** Metrics class for the analysis of reads obtained from targeted pcr experiments e.g. the TruSeq Custom Amplicon
  * (TSCA) kit (Illumina).  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public class TargetedPcrMetrics extends TargetMetricsBase {
 
     /**  The name of the amplicon set used in this metrics collection run */