From 641382eb8bbe1af0208021263829fe23ba626c62 Mon Sep 17 00:00:00 2001 From: Laura Gauthier Date: Wed, 1 Jun 2016 12:29:14 -0400 Subject: [PATCH] Fix BetaTestingAnnotation group Add test --- .../HaplotypeCallerGVCFIntegrationTest.java | 9 +++++++++ .../annotator/interfaces/BetaTestingAnnotation.java | 2 +- 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java index bb8373b20..bfd444274 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java @@ -340,6 +340,15 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { executeTest(" testASMQMateRankSumAnnotation", spec); } + @Test + public void testBetaTestingAnnotationGroup() { + final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -G BetaTesting --disableDithering", + HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("df746da577c1d8a340f93b9d5df4df80")); + spec.disableShadowBCF(); + executeTest(" testASMQMateRankSumAnnotation", spec); + } + @Test public void testASInsertSizeRankSum() { final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -G Standard -G AS_Standard --disableDithering -A AS_InsertSizeRankSum", 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 index 2a7887021..fa7bc5fde 100644 --- 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 @@ -28,5 +28,5 @@ package org.broadinstitute.gatk.tools.walkers.annotator.interfaces; /** * Annotations implementing this interface are not guaranteed to persist between GATK versions */ -public interface BetaTestingAnnotation { +public interface BetaTestingAnnotation extends AnnotationType { }