From 794f2758710eb1d26cb43c757c9aedc0aafcedbe Mon Sep 17 00:00:00 2001 From: David Roazen Date: Tue, 11 Oct 2011 12:08:56 -0400 Subject: [PATCH] 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". --- .../broadinstitute/sting/gatk/walkers/annotator/SnpEff.java | 4 ++-- .../walkers/annotator/interfaces/RodRequiringAnnotation.java | 3 +++ 2 files changed, 5 insertions(+), 2 deletions(-) create mode 100644 public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java index 973b3277d..85977bf8e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java @@ -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); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java new file mode 100644 index 000000000..9de3ca87c --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java @@ -0,0 +1,3 @@ +package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; + +public interface RodRequiringAnnotation extends AnnotationType {} \ No newline at end of file