From 3e5ff6095f88e51c089a86ab326731885d8748ab Mon Sep 17 00:00:00 2001 From: Valentin Ruano-Rubio Date: Fri, 21 Jun 2013 17:02:26 -0400 Subject: [PATCH] Added the pertinent DocumentedGATKFeature annotation ot AnalyzeCovariates --- .../sting/gatk/walkers/bqsr/AnalyzeCovariates.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariates.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariates.java index 7a7527dd1..c8c5eae0b 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariates.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariates.java @@ -49,12 +49,15 @@ import com.google.java.contract.Requires; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.recalibration.RecalUtils; import org.broadinstitute.sting.utils.recalibration.RecalibrationReport; import org.broadinstitute.sting.utils.recalibration.BaseRecalibration; @@ -199,6 +202,7 @@ import java.util.Map; * @version 6/16/2013 * @since 2.6 */ +@DocumentedGATKFeature(groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class}) public final class AnalyzeCovariates extends RodWalker {