diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index d8674c606..b1ad19e69 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -44,16 +44,15 @@ import org.broadinstitute.sting.utils.text.TextFormattingUtils; import java.util.*; /** + * All command line parameters accepted by all tools in the GATK. + * * The GATK engine itself. Manages map/reduce data access and runs walkers. * * We run command line GATK programs using this class. It gets the command line args, parses them, and hands the * 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", - summary = "Features and arguments for the GATK engine itself, available to all walkers.", - extraDocs = { UserException.class }) +@DocumentedGATKFeature(groupName = "GATK Engine") public class CommandLineGATK extends CommandLineExecutable { @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run") private String analysisName = null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java index 18c383ed9..6cd2e8aea 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java @@ -49,10 +49,7 @@ import java.util.List; @ReadFilters(MalformedReadFilter.class) @PartitionBy(PartitionType.NONE) @BAQMode(QualityMode = BAQ.QualityMode.OVERWRITE_QUALS, ApplicationTime = BAQ.ApplicationTime.ON_INPUT) -@DocumentedGATKFeature( - groupName = "GATK walkers", - summary = "General tools available for running on the command line as part of the GATK package", - extraDocs = {CommandLineGATK.class}) +@DocumentedGATKFeature(groupName = "Uncategorized", extraDocs = {CommandLineGATK.class}) public abstract class Walker { final protected static Logger logger = Logger.getLogger(Walker.class); private GenomeAnalysisEngine toolkit;