Merge pull request #978 from broadinstitute/shl_doc_tagtool

Tag 6 tools for documentation and add beta and experimental categorization to 3.

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

@@ -32,6 +32,8 @@
 import htsjdk.samtools.util.IntervalList;
 import htsjdk.samtools.util.Log;
 import htsjdk.samtools.util.StringUtil;
+import org.broadinstitute.barclay.argparser.BetaFeature;
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.PicardException;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
@@ -43,14 +45,16 @@
 import java.io.File;
 import java.util.List;
 
+@DocumentedFeature
+@BetaFeature
 @CommandLineProgramProperties(
         summary = CollectWgsMetricsWithNonZeroCoverage.USAGE_SUMMARY + CollectWgsMetricsWithNonZeroCoverage.USAGE_DETAILS,
         oneLineSummary = CollectWgsMetricsWithNonZeroCoverage.USAGE_SUMMARY,
         programGroup = Alpha.class
 )
 public class CollectWgsMetricsWithNonZeroCoverage extends CollectWgsMetrics {
 
-    static final String USAGE_SUMMARY = "Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.  ";
+    static final String USAGE_SUMMARY = "(Experimental) Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.  ";
     static final String USAGE_DETAILS = "This tool collects metrics about the percentages of reads that pass base- and mapping- quality " +
             "filters as well as coverage (read-depth) levels. Both minimum base- and mapping-quality values as well as the maximum " +
             "read depths (coverage cap) are user defined.  This extends CollectWgsMetrics by including metrics related only to sites" +

src/main/java/picard/analysis/replicates/CollectIndependentReplicateMetrics.java

@@ -58,6 +58,8 @@
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
 import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.BetaFeature;
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.cmdline.CommandLineProgram;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import picard.cmdline.StandardOptionDefinitions;
@@ -100,12 +102,13 @@
  * @author Yossi Farjoun
  *
  */
-
+@DocumentedFeature
+@BetaFeature
 @CommandLineProgramProperties(
         summary = "Estimates the rate of independent replication rate of reads within a bam. \n" +
                 "That is, it estimates the fraction of the reads which would be marked as duplicates but " +
                 "are actually biological replicates, independent observations of the data. ",
-        oneLineSummary = "Estimates the rate of independent replication of reads within a bam.",
+        oneLineSummary = "(Experimental) Estimates the rate of independent replication of reads within a bam.",
         programGroup = Alpha.class
 )
 public class CollectIndependentReplicateMetrics extends CommandLineProgram {

src/main/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java

@@ -27,6 +27,7 @@
 
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.cmdline.programgroups.Fingerprinting;
 
 import java.io.File;
@@ -41,6 +42,7 @@
  *
  * @deprecated 6/6/2017 Use {@link CrosscheckFingerprints} instead.
  */
+@DocumentedFeature
 @CommandLineProgramProperties(
         summary = "DEPRECATED: USE CrosscheckFingerprints. Checks if all read groups within a set of BAM files appear to come from the same individual",
         oneLineSummary = "DEPRECATED: USE CrosscheckFingerprints. Checks if all read groups appear to come from the same individual.",

src/main/java/picard/sam/SetNmAndUqTags.java

@@ -25,12 +25,14 @@
 package picard.sam;
 
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.cmdline.programgroups.SamOrBam;
 
 /**
  * @author Yossi Farjoun
  */
 @Deprecated
+@DocumentedFeature
 @CommandLineProgramProperties(
         summary = SetNmAndUqTags.USAGE_SUMMARY + SetNmMdAndUqTags.USAGE_DETAILS,
         oneLineSummary = SetNmAndUqTags.USAGE_SUMMARY,

src/main/java/picard/sam/markduplicates/SimpleMarkDuplicatesWithMateCigar.java

@@ -33,6 +33,8 @@
 import htsjdk.samtools.SAMRecordDuplicateComparator;
 import htsjdk.samtools.SAMTag;
 import htsjdk.samtools.util.*;
+import org.broadinstitute.barclay.argparser.BetaFeature;
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.PicardException;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import picard.cmdline.programgroups.Testing;
@@ -61,10 +63,12 @@
  *
  * @author nhomer
  */
+@DocumentedFeature
+@BetaFeature
 @CommandLineProgramProperties(
         summary = "Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules. " +
                 "All records are then written to the output file with the duplicate records flagged.",
-        oneLineSummary = "Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules.",
+        oneLineSummary = "(Experimental) Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules.",
         programGroup = Testing.class
 )
 public class SimpleMarkDuplicatesWithMateCigar extends MarkDuplicates {

src/main/java/picard/sam/markduplicates/UmiAwareMarkDuplicatesWithMateCigar.java

@@ -31,6 +31,7 @@
 import htsjdk.samtools.util.*;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
+import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.cmdline.programgroups.Alpha;
 
 import java.io.File;
@@ -48,6 +49,7 @@
  *
  * @author fleharty
  */
+@DocumentedFeature
 @CommandLineProgramProperties(
         summary = UmiAwareMarkDuplicatesWithMateCigar.USAGE_SUMMARY + UmiAwareMarkDuplicatesWithMateCigar.USAGE_DETAILS,
         oneLineSummary = UmiAwareMarkDuplicatesWithMateCigar.USAGE_SUMMARY,