Add classes from "annotation party" to BetaTesting group

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InsertSizeRankSum.java

@@ -52,6 +52,7 @@
 package org.broadinstitute.gatk.tools.walkers.annotator;
 
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AS_StandardAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.BetaTestingAnnotation;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
 import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
@@ -72,7 +73,7 @@ import java.util.List;
  *
  * */
 
-public class AS_InsertSizeRankSum extends AS_RankSumTest implements ExperimentalAnnotation {
+public class AS_InsertSizeRankSum extends AS_RankSumTest implements ExperimentalAnnotation, BetaTestingAnnotation {
     @Override
     public List<String> getKeyNames() { return Arrays.asList(GATKVCFConstants.AS_INSERT_SIZE_RANK_SUM_KEY);}
 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_MQMateRankSumTest.java

@@ -55,6 +55,7 @@ import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AS_StandardAnnotation;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.BetaTestingAnnotation;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.gatk.utils.pileup.PileupElement;
@@ -86,7 +87,7 @@ import java.util.Map;
  *     <li><b><a href="https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_annotator_AS_MappingQualityRankSumTest.php">AS_MappingQualityRankSumTest</a></b> outputs the same rank sum test on the mapping quality of the reads themselves rather than their mates.</li>
  * </ul>
  */
-public class AS_MQMateRankSumTest extends AS_RankSumTest {
+public class AS_MQMateRankSumTest extends AS_RankSumTest implements BetaTestingAnnotation {
     @Override
     public List<String> getKeyNames() { return Arrays.asList(GATKVCFConstants.AS_MATE_MAP_QUAL_RANK_SUM_KEY); }
 

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java

@@ -30,6 +30,7 @@ import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFConstants;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.BetaTestingAnnotation;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ReducibleAnnotation;
 import org.broadinstitute.gatk.utils.MathUtils;
@@ -61,7 +62,7 @@ import java.util.Map;
  * </ul>
  */
 
-public class FractionInformativeReads extends InfoFieldAnnotation implements ReducibleAnnotation {
+public class FractionInformativeReads extends InfoFieldAnnotation implements ReducibleAnnotation, BetaTestingAnnotation {
     @Override
     public String getRawKeyName() {
         return null;

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/BetaTestingAnnotation.java

@@ -0,0 +1,32 @@
+/*
+* Copyright 2012-2015 Broad Institute, Inc.
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
+
+/**
+ * Annotations implementing this interface are not guaranteed to persist between GATK versions
+ */
+public interface BetaTestingAnnotation {
+}