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

all > org.broadinstitute.hellbender.cmdline.GATKPlugin > GATKAnnotationPluginDescriptorUnitTest
48

tests
0

failures
0

ignored
2.749s

duration
100%

successful

Tests

Test Duration Result
testAnnotationArguments 0.040s passed
testAnnotationGroupAdditive 0.016s passed
testConfigFileControlsAnnotationPackages 2.008s passed
testDanglingAnnotationArguments[0](InbreedingCoeff, --founder-id, s1) 0.015s passed
testGetAllowedValuesForDescriptorHelpGroups 0.013s passed
testGetAllowedValuesForDescriptorHelp[0]([]) 0.013s passed
testGetAllowedValuesForDescriptorHelp[1]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@47bae235]) 0.013s passed
testGetAllowedValuesForDescriptorHelp[2]([org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@1aee0f49, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@7a80ebcd]) 0.016s passed
testGetAllowedValuesForDescriptorHelp[3]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@37d50217, org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@3e9e7a70]) 0.020s passed
testGetClassForPluginHelpFromReflection 0.013s passed
testGetDefaultInstances 0.015s passed
testGroupHierarchyBehavior[0]([Ljava.lang.String;@63437af4, false, false) 0.015s passed
testGroupHierarchyBehavior[1]([Ljava.lang.String;@39adf4e6, true, true) 0.014s passed
testGroupHierarchyBehavior[2]([Ljava.lang.String;@5c7876e1, true, false) 0.013s passed
testGroupHierarchyBehavior[3]([Ljava.lang.String;@6f28a07e, true, true) 0.013s passed
testGroupHierarchyBehavior[4]([Ljava.lang.String;@7d44e3c7, true, true) 0.022s passed
testHierarchicalAnnotationDiscovery 0.002s passed
testIncludeAllExcludeIndividual 0.034s passed
testIncludeDefaultExcludeIndividual 0.013s passed
testIncludeDefaultGroupExcludeIndividual 0.013s passed
testIncludeUserGroupExcludeIndividual 0.013s passed
testInvalidRequestedAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality]) 0.015s passed
testInvalidRequestedAnnotationGroups[1]([interface org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, interface org.broadinstitute.hellbender.tools.walkers.annotator.Annotation]) 0.012s passed
testInvalidRequestedAnnotationGroups[2]([class java.lang.Object]) 0.021s 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]) 0.027s passed
testInvalidUserSpecifiedAnnotations[1]([-A, RMSMappingQuality, -A, RMSMappingQuality]) 0.032s passed
testInvalidUserSpecifiedAnnotations[2]([-A, RMSMappingQuality, -AX, RMSMappingQuality]) 0.022s passed
testInvalidUserSpecifiedAnnotations[3]([G, StandardAnnotation, -AX, RMSMappingQuality, -AX, RMSMappingQuality]) 0.012s passed
testInvalidUserSpecifiedAnnotations[4]([-A, foo]) 0.012s passed
testInvalidUserSpecifiedAnnotations[5]([-A, VariantAnnotator]) 0.012s passed
testMultipleOptionalArguments[0]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@758e6acd, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@10ecf244], [Ljava.lang.String;@28592982, true, 5, 0) 0.012s passed
testMultipleOptionalArguments[1]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@766ab25b, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@735d7b99, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@7c424dfe], [Ljava.lang.String;@3577e37c, true, 5, -0.3333) 0.013s passed
testMultipleOptionalArguments[2]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@48e1e18a, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@74997ca6, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@7a6078d], [Ljava.lang.String;@372c428, false, 0, 0) 0.012s passed
testMultipleOptionalArguments[3]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@11b234aa, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@1455a374, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@cfb462], [Ljava.lang.String;@54418834, true, 5, -0.2941) 0.018s passed
testMultipleOptionalArguments[4]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@65689000, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@441d3ddf, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@420c9959], [Ljava.lang.String;@7e584f3c, false, 0, -0.3333) 0.013s passed
testMultipleOptionalArguments[5]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@289d9f0d, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@39aaa7db, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@14a3a66c], [Ljava.lang.String;@1738d3b2, false, 0, -0.3333) 0.017s passed
testMultipleOptionalArguments[6]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@3299ee2c, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@542759f, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@68ac6e6e], [Ljava.lang.String;@6eb6750f, true, 5, -0.2941) 0.015s passed
testMultipleOptionalArguments[7]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@722e1bff], [Ljava.lang.String;@4cce889e, false, 0, -0.2941) 0.017s passed
testMultipleOptionalArguments[8]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@9203db8], [Ljava.lang.String;@64d0b8e3, false, 0, 0) 0.014s passed
testNoAnnotations 0.013s passed
testOverridingInstancesWithGetInstance 0s passed
testPossibleDeNovoAnnotationArguments 0.014s passed
testToolDefaultAnnotationArgumentsOverridingFromCommandLine 0.030s passed
testUseAllAnnotations 0.038s passed
testUseAllAnnotationsDisableToolDefaultAnnotaiotns 0.024s passed

Standard error

15:08:58.146 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4157897-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
15:08:58.255 INFO  TestAnnotationsTool - ------------------------------------------------------------
15:08:58.258 INFO  TestAnnotationsTool - The Genome Analysis Toolkit (GATK) v4157897-SNAPSHOT
15:08:58.258 INFO  TestAnnotationsTool - For support and documentation go to https://software.broadinstitute.org/gatk/
15:08:58.258 INFO  TestAnnotationsTool - Executing as root@265a0ba1256d on Linux v6.14.0-1017-azure amd64
15:08:58.258 INFO  TestAnnotationsTool - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
15:08:58.259 INFO  TestAnnotationsTool - Start Date/Time: March 4, 2026 at 3:08:58 PM GMT
15:08:58.259 INFO  TestAnnotationsTool - ------------------------------------------------------------
15:08:58.259 INFO  TestAnnotationsTool - ------------------------------------------------------------
15:08:58.262 INFO  TestAnnotationsTool - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:08:58.262 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:08:58.262 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:08:58.263 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:08:58.263 INFO  TestAnnotationsTool - Deflater: IntelDeflater
15:08:58.263 INFO  TestAnnotationsTool - Inflater: IntelInflater
15:08:58.263 INFO  TestAnnotationsTool - GCS max retries/reopens: 20
15:08:58.263 INFO  TestAnnotationsTool - Requester pays: disabled
15:08:58.264 INFO  TestAnnotationsTool - Initializing engine
15:08:58.336 INFO  TestAnnotationsTool - Done initializing engine
15:08:58.336 INFO  ProgressMeter - Starting traversal
15:08:58.337 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
15:08:58.340 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
15:08:58.340 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
15:08:58.340 INFO  TestAnnotationsTool - Shutting down engine
[March 4, 2026 at 3:08:58 PM GMT] org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$TestAnnotationsTool done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=134217728
15:08:58.602 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
15:08:58.642 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
15:08:58.655 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
15:08:58.897 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
15:08:58.947 INFO  PedReader - Phenotype is other? false
15:08:58.948 INFO  PedReader - Phenotype is other? false
15:08:58.962 INFO  PedReader - Phenotype is other? false
15:08:58.963 INFO  PedReader - Phenotype is other? false
15:08:58.963 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 1:10 and possibly subsequent; at least 10 samples must have called genotypes
15:08:59.019 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
15:08:59.020 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default