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Merge pull request #1311 from broadinstitute/ldg_BetaTestAnnotationsGroup 

Add classes from "annotation party" to BetaTesting group
This commit is contained in:
ldgauthier 2016-03-11 08:13:32 -05:00
parent 16ef36088e d9f9bd1d56
commit d0432713e0
4 changed files with 38 additions and 3 deletions
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3
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InsertSizeRankSum.java
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@ -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);}

3
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_MQMateRankSumTest.java
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@ -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); }

3
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java
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@ -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;

32
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/BetaTestingAnnotation.java 100644
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@ -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 {
}