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Fix BetaTestingAnnotation group 

Add test
This commit is contained in:
Laura Gauthier 2016-06-01 12:29:14 -04:00
parent 5255435f0e
commit 641382eb8b
2 changed files with 10 additions and 1 deletions
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9
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
View File

@ -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",

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/BetaTestingAnnotation.java
View File

@ -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 {
}