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Merged bug fix from Stable into Unstable

This commit is contained in:
Valentin Ruano-Rubio 2013-06-24 14:00:01 -04:00
parent 521d9c1df5 3e5ff6095f
commit b97f9a487d
1 changed files with 4 additions and 0 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariates.java
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@ -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<AnalyzeCovariates.None,AnalyzeCovariates.None> {