Class org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest

all > org.broadinstitute.hellbender.cmdline.GATKPlugin > GATKAnnotationPluginDescriptorUnitTest

tests

failures

ignored

2.076s

duration

100%

successful

Tests
Standard error

Tests

Test	Duration	Result
testAnnotationArguments	0.024s	passed
testAnnotationGroupAdditive	0.005s	passed
testConfigFileControlsAnnotationPackages	1.886s	passed
testDanglingAnnotationArguments[0](InbreedingCoeff, --founder-id, s1)	0.005s	passed
testGetAllowedValuesForDescriptorHelpGroups	0.004s	passed
testGetAllowedValuesForDescriptorHelp[0]([])	0.005s	passed
testGetAllowedValuesForDescriptorHelp[1]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@7c0ff7a0])	0.005s	passed
testGetAllowedValuesForDescriptorHelp[2]([org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@4a47bc9c, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@5100c143])	0.004s	passed
testGetAllowedValuesForDescriptorHelp[3]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@17a77a7e, org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@7c840fe3])	0.003s	passed
testGetClassForPluginHelpFromReflection	0.003s	passed
testGetDefaultInstances	0.004s	passed
testGroupHierarchyBehavior[0]([Ljava.lang.String;@18ca9277, false, false)	0.004s	passed
testGroupHierarchyBehavior[1]([Ljava.lang.String;@56d5460f, true, true)	0.004s	passed
testGroupHierarchyBehavior[2]([Ljava.lang.String;@7cec3975, true, false)	0.004s	passed
testGroupHierarchyBehavior[3]([Ljava.lang.String;@460b77d6, true, true)	0.003s	passed
testGroupHierarchyBehavior[4]([Ljava.lang.String;@7d80e1b3, true, true)	0.003s	passed
testHierarchicalAnnotationDiscovery	0.002s	passed
testIncludeAllExcludeIndividual	0.013s	passed
testIncludeDefaultExcludeIndividual	0.003s	passed
testIncludeDefaultGroupExcludeIndividual	0.003s	passed
testIncludeUserGroupExcludeIndividual	0.003s	passed
testInvalidRequestedAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality])	0.004s	passed
testInvalidRequestedAnnotationGroups[1]([interface org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, interface org.broadinstitute.hellbender.tools.walkers.annotator.Annotation])	0.003s	passed
testInvalidRequestedAnnotationGroups[2]([class java.lang.Object])	0.003s	passed
testInvalidToolDefaultAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality])	0s	passed
testInvalidToolDefaultAnnotationGroups[1]([interface org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, interface org.broadinstitute.hellbender.tools.walkers.annotator.Annotation])	0s	passed
testInvalidToolDefaultAnnotationGroups[2]([class java.lang.Object])	0s	passed
testInvalidUserSpecifiedAnnotations[0]([-A, StandardAnnotation])	0.004s	passed
testInvalidUserSpecifiedAnnotations[1]([-A, RMSMappingQuality, -A, RMSMappingQuality])	0.003s	passed
testInvalidUserSpecifiedAnnotations[2]([-A, RMSMappingQuality, -AX, RMSMappingQuality])	0.003s	passed
testInvalidUserSpecifiedAnnotations[3]([G, StandardAnnotation, -AX, RMSMappingQuality, -AX, RMSMappingQuality])	0.002s	passed
testInvalidUserSpecifiedAnnotations[4]([-A, foo])	0.003s	passed
testInvalidUserSpecifiedAnnotations[5]([-A, VariantAnnotator])	0.003s	passed
testMultipleOptionalArguments[0]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@5d77be8e, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@55a055cc], [Ljava.lang.String;@1ab1d93d, true, 5, 0)	0.002s	passed
testMultipleOptionalArguments[1]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@6604f246, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@c1386b4, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@53d9af1], [Ljava.lang.String;@c89e263, true, 5, -0.3333)	0.004s	passed
testMultipleOptionalArguments[2]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@29db008c, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@1d008e61, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@191b44ca], [Ljava.lang.String;@5de243bb, false, 0, 0)	0.003s	passed
testMultipleOptionalArguments[3]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@67c2b55d, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@5db04bd2, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@6f921e32], [Ljava.lang.String;@31c5304f, true, 5, -0.2941)	0.003s	passed
testMultipleOptionalArguments[4]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@63d66761, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@434a8938, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@237cd264], [Ljava.lang.String;@51cd2d2, false, 0, -0.3333)	0.003s	passed
testMultipleOptionalArguments[5]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@134955bb, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@45b08b17, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@6723e6b3], [Ljava.lang.String;@3883b5e9, false, 0, -0.3333)	0.006s	passed
testMultipleOptionalArguments[6]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@6c19769c, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@434d001d, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@36453773], [Ljava.lang.String;@4db16677, true, 5, -0.2941)	0.004s	passed
testMultipleOptionalArguments[7]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@2b15ba1a], [Ljava.lang.String;@796fe2b5, false, 0, -0.2941)	0.007s	passed
testMultipleOptionalArguments[8]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@2b1a1a37], [Ljava.lang.String;@7d90764a, false, 0, 0)	0.005s	passed
testNoAnnotations	0.003s	passed
testOverridingInstancesWithGetInstance	0.001s	passed
testPossibleDeNovoAnnotationArguments	0.003s	passed
testToolDefaultAnnotationArgumentsOverridingFromCommandLine	0.006s	passed
testUseAllAnnotations	0.004s	passed
testUseAllAnnotationsDisableToolDefaultAnnotaiotns	0.004s	passed

Standard error

14:50:47.569 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
14:50:47.685 INFO  TestAnnotationsTool - ------------------------------------------------------------
14:50:47.687 INFO  TestAnnotationsTool - org.broadinstitute.hellbender.cmdline.GATKPlugin vUnavailable
14:50:47.687 INFO  TestAnnotationsTool - For support and documentation go to https://software.broadinstitute.org/gatk/
14:50:47.687 INFO  TestAnnotationsTool - Executing as runner@runnervmnay03 on Linux v6.14.0-1017-azure amd64
14:50:47.688 INFO  TestAnnotationsTool - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
14:50:47.688 INFO  TestAnnotationsTool - Start Date/Time: March 4, 2026 at 2:50:47 PM UTC
14:50:47.688 INFO  TestAnnotationsTool - ------------------------------------------------------------
14:50:47.688 INFO  TestAnnotationsTool - ------------------------------------------------------------
14:50:47.691 INFO  TestAnnotationsTool - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:50:47.692 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:50:47.692 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:50:47.692 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:50:47.692 INFO  TestAnnotationsTool - Deflater: IntelDeflater
14:50:47.692 INFO  TestAnnotationsTool - Inflater: IntelInflater
14:50:47.693 INFO  TestAnnotationsTool - GCS max retries/reopens: 20
14:50:47.693 INFO  TestAnnotationsTool - Requester pays: disabled
14:50:47.693 INFO  TestAnnotationsTool - Initializing engine
14:50:47.741 INFO  TestAnnotationsTool - Done initializing engine
14:50:47.741 INFO  ProgressMeter - Starting traversal
14:50:47.742 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
14:50:47.745 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
14:50:47.745 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:50:47.746 INFO  TestAnnotationsTool - Shutting down engine
[March 4, 2026 at 2:50:47 PM UTC] org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$TestAnnotationsTool done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=140509184
14:50:47.846 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
14:50:47.855 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
14:50:47.859 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
14:50:47.909 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
14:50:47.925 INFO  PedReader - Phenotype is other? false
14:50:47.926 INFO  PedReader - Phenotype is other? false
14:50:47.930 INFO  PedReader - Phenotype is other? false
14:50:47.931 INFO  PedReader - Phenotype is other? false
14:50:47.931 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 1:10 and possibly subsequent; at least 10 samples must have called genotypes
14:50:47.943 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
14:50:47.944 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default