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SnpEff is now marked as a RodRequiringAnnotation instead of an ExperimentalAnnotation. 

Having SnpEff grouped with the Experimental annotations was proving problematic, since it
requires a rod. Placing it in its own group should improve the situation somewhat, making it
easier to request "all annotations except for SnpEff".
This commit is contained in:
David Roazen 2011-10-11 12:08:56 -04:00
parent 24b72334b3
commit 794f275871
2 changed files with 5 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
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@ -31,8 +31,8 @@ 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.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -50,7 +50,7 @@ import java.util.*;
*
* @author David Roazen
*/
public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotation {
public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotation {
private static Logger logger = Logger.getLogger(SnpEff.class);

3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java 100644
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@ -0,0 +1,3 @@
package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
public interface RodRequiringAnnotation extends AnnotationType {}