From d9f9bd1d56a984b8c01be5be1b7e5daf181ba658 Mon Sep 17 00:00:00 2001 From: Laura Gauthier Date: Wed, 9 Mar 2016 08:17:44 -0500 Subject: [PATCH] Add classes from "annotation party" to BetaTesting group --- .../annotator/AS_InsertSizeRankSum.java | 3 +- .../annotator/AS_MQMateRankSumTest.java | 3 +- .../annotator/FractionInformativeReads.java | 3 +- .../interfaces/BetaTestingAnnotation.java | 32 +++++++++++++++++++ 4 files changed, 38 insertions(+), 3 deletions(-) create mode 100644 public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/BetaTestingAnnotation.java diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InsertSizeRankSum.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InsertSizeRankSum.java index 4ee5ae7d0..85a0d5f5b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InsertSizeRankSum.java +++ b/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 getKeyNames() { return Arrays.asList(GATKVCFConstants.AS_INSERT_SIZE_RANK_SUM_KEY);} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_MQMateRankSumTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_MQMateRankSumTest.java index 5fa9d5d96..e4ec0363c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_MQMateRankSumTest.java +++ b/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; *
  • AS_MappingQualityRankSumTest outputs the same rank sum test on the mapping quality of the reads themselves rather than their mates.
    • * */ -public class AS_MQMateRankSumTest extends AS_RankSumTest { +public class AS_MQMateRankSumTest extends AS_RankSumTest implements BetaTestingAnnotation { @Override public List getKeyNames() { return Arrays.asList(GATKVCFConstants.AS_MATE_MAP_QUAL_RANK_SUM_KEY); } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java index 747e0fc23..708d6293c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java +++ b/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; * */ -public class FractionInformativeReads extends InfoFieldAnnotation implements ReducibleAnnotation { +public class FractionInformativeReads extends InfoFieldAnnotation implements ReducibleAnnotation, BetaTestingAnnotation { @Override public String getRawKeyName() { return null; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/BetaTestingAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/BetaTestingAnnotation.java new file mode 100644 index 000000000..5bc72d575 --- /dev/null +++ b/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 { +}