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

48

tests

0

failures

0

ignored

2.082s

duration

100%

successful

Tests

Test Duration Result
testAnnotationArguments 0.032s passed
testAnnotationGroupAdditive 0.006s passed
testConfigFileControlsAnnotationPackages 1.879s passed
testDanglingAnnotationArguments[0](InbreedingCoeff, --founder-id, s1) 0.005s passed
testGetAllowedValuesForDescriptorHelpGroups 0.003s passed
testGetAllowedValuesForDescriptorHelp[0]([]) 0.005s passed
testGetAllowedValuesForDescriptorHelp[1]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@3d57fb9e]) 0.004s passed
testGetAllowedValuesForDescriptorHelp[2]([org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@5a9051fd, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@7614378d]) 0.003s passed
testGetAllowedValuesForDescriptorHelp[3]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@5f8df69, org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@1ce6a9bd]) 0.003s passed
testGetClassForPluginHelpFromReflection 0.003s passed
testGetDefaultInstances 0.004s passed
testGroupHierarchyBehavior[0]([Ljava.lang.String;@111cbcda, false, false) 0.004s passed
testGroupHierarchyBehavior[1]([Ljava.lang.String;@3d9c8c3c, true, true) 0.004s passed
testGroupHierarchyBehavior[2]([Ljava.lang.String;@3636f2a7, true, false) 0.004s passed
testGroupHierarchyBehavior[3]([Ljava.lang.String;@30b9728f, true, true) 0.006s passed
testGroupHierarchyBehavior[4]([Ljava.lang.String;@b842275, true, true) 0.004s passed
testHierarchicalAnnotationDiscovery 0.003s passed
testIncludeAllExcludeIndividual 0.014s passed
testIncludeDefaultExcludeIndividual 0.003s passed
testIncludeDefaultGroupExcludeIndividual 0.003s passed
testIncludeUserGroupExcludeIndividual 0.004s passed
testInvalidRequestedAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality]) 0.003s 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]) 0.002s 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]) 0.002s passed
testInvalidUserSpecifiedAnnotations[5]([-A, VariantAnnotator]) 0.002s passed
testMultipleOptionalArguments[0]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@1b7a4930, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@591a4d25], [Ljava.lang.String;@4bfe83d, true, 5, 0) 0.002s passed
testMultipleOptionalArguments[1]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@5d77be8e, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@55a055cc, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@1ab1d93d], [Ljava.lang.String;@57167ccb, true, 5, -0.3333) 0.004s passed
testMultipleOptionalArguments[2]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@c89e263, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@4d5ea776, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@5d68be4f], [Ljava.lang.String;@34eb5d01, false, 0, 0) 0.003s passed
testMultipleOptionalArguments[3]([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, true, 5, -0.2941) 0.004s passed
testMultipleOptionalArguments[4]([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, false, 0, -0.3333) 0.004s passed
testMultipleOptionalArguments[5]([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) 0.007s passed
testMultipleOptionalArguments[6]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@195cbf5e, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@4cb82b09, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@49665f92], [Ljava.lang.String;@b68932b, true, 5, -0.2941) 0.004s passed
testMultipleOptionalArguments[7]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@6c19769c], [Ljava.lang.String;@434d001d, false, 0, -0.2941) 0.008s passed
testMultipleOptionalArguments[8]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@443dae2], [Ljava.lang.String;@8f09a02, false, 0, 0) 0.005s passed
testNoAnnotations 0.002s passed
testOverridingInstancesWithGetInstance 0s passed
testPossibleDeNovoAnnotationArguments 0.003s passed
testToolDefaultAnnotationArgumentsOverridingFromCommandLine 0.006s passed
testUseAllAnnotations 0.005s passed
testUseAllAnnotationsDisableToolDefaultAnnotaiotns 0.005s passed

Standard error

20:32:51.170 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.0/5ec646c7bf8c4f7681c2a59819384e5da469db31/gkl-0.9.0.jar!/com/intel/gkl/native/libgkl_compression.so
20:32:51.279 INFO  TestAnnotationsTool - ------------------------------------------------------------
20:32:51.282 INFO  TestAnnotationsTool - org.broadinstitute.hellbender.cmdline.GATKPlugin vUnavailable
20:32:51.282 INFO  TestAnnotationsTool - For support and documentation go to https://software.broadinstitute.org/gatk/
20:32:51.282 INFO  TestAnnotationsTool - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
20:32:51.282 INFO  TestAnnotationsTool - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:32:51.283 INFO  TestAnnotationsTool - Start Date/Time: July 15, 2025 at 8:32:51 PM UTC
20:32:51.283 INFO  TestAnnotationsTool - ------------------------------------------------------------
20:32:51.283 INFO  TestAnnotationsTool - ------------------------------------------------------------
20:32:51.286 INFO  TestAnnotationsTool - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:32:51.286 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:32:51.286 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:32:51.286 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:32:51.287 INFO  TestAnnotationsTool - Deflater: IntelDeflater
20:32:51.287 INFO  TestAnnotationsTool - Inflater: IntelInflater
20:32:51.287 INFO  TestAnnotationsTool - GCS max retries/reopens: 20
20:32:51.287 INFO  TestAnnotationsTool - Requester pays: disabled
20:32:51.287 INFO  TestAnnotationsTool - Initializing engine
20:32:51.332 INFO  TestAnnotationsTool - Done initializing engine
20:32:51.333 INFO  ProgressMeter - Starting traversal
20:32:51.334 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
20:32:51.337 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
20:32:51.337 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:32:51.337 INFO  TestAnnotationsTool - Shutting down engine
[July 15, 2025 at 8:32:51 PM UTC] org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$TestAnnotationsTool done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=140509184
20:32:51.443 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:32:51.453 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:32:51.456 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:32:51.506 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
20:32:51.524 INFO  PedReader - Phenotype is other? false
20:32:51.525 INFO  PedReader - Phenotype is other? false
20:32:51.530 INFO  PedReader - Phenotype is other? false
20:32:51.530 INFO  PedReader - Phenotype is other? false
20:32:51.531 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 1:10 and possibly subsequent; at least 10 samples must have called genotypes
20:32:51.544 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
20:32:51.544 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default