Add DocumentedFeature.

broadinstitute · Apr 4, 2022 · 7e32904 · 7e32904
1 parent 3a041ab
commit 7e32904
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Showing 6 changed files with 18 additions and 1 deletion.
diff --git a/src/main/java/org/broadinstitute/hellbender/metrics/InsertSizeMetrics.java b/src/main/java/org/broadinstitute/hellbender/metrics/InsertSizeMetrics.java
@@ -1,7 +1,8 @@
 package org.broadinstitute.hellbender.metrics;
 
 import htsjdk.samtools.SamPairUtil.PairOrientation;
-import org.broadinstitute.hellbender.metrics.MultiLevelMetrics;
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import picard.util.help.HelpConstants;
 
 import java.io.Serializable;
 
@@ -11,6 +12,7 @@
  * ".insertSizeMetrics".  In addition the insert size distribution is plotted to
  * a file with the extension ".insertSizeMetrics.pdf".
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public final class InsertSizeMetrics extends MultiLevelMetrics implements Serializable {
 
     private static final long serialVersionUID = 1L;

diff --git a/src/main/java/org/broadinstitute/hellbender/metrics/QualityYieldMetrics.java b/src/main/java/org/broadinstitute/hellbender/metrics/QualityYieldMetrics.java
@@ -1,13 +1,16 @@
 package org.broadinstitute.hellbender.metrics;
 
 import htsjdk.samtools.metrics.MetricBase;
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.read.GATKRead;
 import org.broadinstitute.hellbender.utils.read.ReadUtils;
+import picard.util.help.HelpConstants;
 
 import java.io.Serializable;
 
 /** 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 final class QualityYieldMetrics extends MetricBase implements Serializable {
     private static final long serialVersionUID = 1;
 

diff --git a/src/main/java/org/broadinstitute/hellbender/metrics/analysis/AlleleFrequencyQCMetric.java b/src/main/java/org/broadinstitute/hellbender/metrics/analysis/AlleleFrequencyQCMetric.java
@@ -1,7 +1,10 @@
 package org.broadinstitute.hellbender.metrics.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 AlleleFrequencyQCMetric extends MetricBase {
 
     public String SAMPLE;

diff --git a/...n/java/org/broadinstitute/hellbender/metrics/analysis/BaseDistributionByCycleMetrics.java b/...n/java/org/broadinstitute/hellbender/metrics/analysis/BaseDistributionByCycleMetrics.java
@@ -1,7 +1,10 @@
 package org.broadinstitute.hellbender.metrics.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 final class BaseDistributionByCycleMetrics extends MetricBase {
     public int READ_END;
     public int CYCLE;

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/loggers/PSFilterMetrics.java b/src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/loggers/PSFilterMetrics.java
@@ -1,10 +1,13 @@
 package org.broadinstitute.hellbender.tools.spark.pathseq.loggers;
 
 import htsjdk.samtools.metrics.MetricBase;
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import picard.util.help.HelpConstants;
 
 /**
  * Metrics that are calculated during the PathSeq filter
  */
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public final class PSFilterMetrics extends MetricBase {
 
     /**

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/loggers/PSScoreMetrics.java b/src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/loggers/PSScoreMetrics.java
@@ -1,11 +1,14 @@
 package org.broadinstitute.hellbender.tools.spark.pathseq.loggers;
 
 import htsjdk.samtools.metrics.MetricBase;
+import org.broadinstitute.barclay.help.DocumentedFeature;
+import picard.util.help.HelpConstants;
 
 /**
  * Metrics that are calculated during the PathSeq scoring
  */
 @SuppressWarnings("serial")
+@DocumentedFeature(groupName = HelpConstants.DOC_CAT_METRICS, summary = HelpConstants.DOC_CAT_METRICS_SUMMARY)
 public final class PSScoreMetrics extends MetricBase {
 
     /**