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

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

tests
0

failures
0

ignored
1.781s

duration
100%

successful

Tests

Test Duration Result
testAnnotationArguments 0.022s passed
testAnnotationGroupAdditive 0.004s passed
testConfigFileControlsAnnotationPackages 1.642s passed
testDanglingAnnotationArguments[0](InbreedingCoeff, --founder-id, s1) 0.005s passed
testGetAllowedValuesForDescriptorHelpGroups 0.002s passed
testGetAllowedValuesForDescriptorHelp[0]([]) 0.004s passed
testGetAllowedValuesForDescriptorHelp[1]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@626df173]) 0.002s passed
testGetAllowedValuesForDescriptorHelp[2]([org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@4535bdc6, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@23e86863]) 0.002s passed
testGetAllowedValuesForDescriptorHelp[3]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@1bcb8599, org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@b671dda]) 0.002s passed
testGetClassForPluginHelpFromReflection 0.002s passed
testGetDefaultInstances 0.002s passed
testGroupHierarchyBehavior[0]([Ljava.lang.String;@50734cea, false, false) 0.002s passed
testGroupHierarchyBehavior[1]([Ljava.lang.String;@24842b8e, true, true) 0.002s passed
testGroupHierarchyBehavior[2]([Ljava.lang.String;@54a5496f, true, false) 0.002s passed
testGroupHierarchyBehavior[3]([Ljava.lang.String;@29ccab93, true, true) 0.002s passed
testGroupHierarchyBehavior[4]([Ljava.lang.String;@dd9de63, true, true) 0.001s passed
testHierarchicalAnnotationDiscovery 0.001s passed
testIncludeAllExcludeIndividual 0.009s passed
testIncludeDefaultExcludeIndividual 0.002s passed
testIncludeDefaultGroupExcludeIndividual 0.003s passed
testIncludeUserGroupExcludeIndividual 0.003s 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]) 0.002s 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]) 0.001s passed
testInvalidUserSpecifiedAnnotations[0]([-A, StandardAnnotation]) 0.002s passed
testInvalidUserSpecifiedAnnotations[1]([-A, RMSMappingQuality, -A, RMSMappingQuality]) 0.002s passed
testInvalidUserSpecifiedAnnotations[2]([-A, RMSMappingQuality, -AX, RMSMappingQuality]) 0.002s 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$testChildAnnotation@eb695e8, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@7eebb316], [Ljava.lang.String;@45273d40, true, 5, 0) 0.002s passed
testMultipleOptionalArguments[1]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@10d49900, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@e645600, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@e7b3e54], [Ljava.lang.String;@78d61f17, true, 5, -0.3333) 0.003s passed
testMultipleOptionalArguments[2]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@39004e4f, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@5f0ca069, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@6a6a2fdd], [Ljava.lang.String;@552ffa44, false, 0, 0) 0.002s passed
testMultipleOptionalArguments[3]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@39685204, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@72d0196d, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@77cf329d], [Ljava.lang.String;@4067634b, true, 5, -0.2941) 0.002s passed
testMultipleOptionalArguments[4]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@7b2dd35d, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@405223e4, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@2d2133fd], [Ljava.lang.String;@58a7a58d, false, 0, -0.3333) 0.002s passed
testMultipleOptionalArguments[5]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@64f6dd19, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@3b8b5b40, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@5151accb], [Ljava.lang.String;@2e1ad7de, false, 0, -0.3333) 0.005s passed
testMultipleOptionalArguments[6]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@4e80960a, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@2a0c244e, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@2f60e66a], [Ljava.lang.String;@5bccef9f, true, 5, -0.2941) 0.003s passed
testMultipleOptionalArguments[7]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@18f8e2e0], [Ljava.lang.String;@28d56028, false, 0, -0.2941) 0.006s passed
testMultipleOptionalArguments[8]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@30a791a6], [Ljava.lang.String;@719bb60d, false, 0, 0) 0.005s passed
testNoAnnotations 0.002s passed
testOverridingInstancesWithGetInstance 0.001s passed
testPossibleDeNovoAnnotationArguments 0.002s passed
testToolDefaultAnnotationArgumentsOverridingFromCommandLine 0.004s passed
testUseAllAnnotations 0.003s passed
testUseAllAnnotationsDisableToolDefaultAnnotaiotns 0.003s passed

Standard error

17:37:23.613 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
17:37:23.626 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression18109222506539164691.so: /tmp/libgkl_compression18109222506539164691.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:23.631 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
17:37:23.635 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression2019020083148319395.so: /tmp/libgkl_compression2019020083148319395.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:23.727 INFO  TestAnnotationsTool - ------------------------------------------------------------
17:37:23.730 INFO  TestAnnotationsTool - org.broadinstitute.hellbender.cmdline.GATKPlugin vUnavailable
17:37:23.730 INFO  TestAnnotationsTool - For support and documentation go to https://software.broadinstitute.org/gatk/
17:37:23.730 INFO  TestAnnotationsTool - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:37:23.730 INFO  TestAnnotationsTool - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:37:23.730 INFO  TestAnnotationsTool - Start Date/Time: October 27, 2025 at 5:37:23 PM UTC
17:37:23.730 INFO  TestAnnotationsTool - ------------------------------------------------------------
17:37:23.730 INFO  TestAnnotationsTool - ------------------------------------------------------------
17:37:23.733 INFO  TestAnnotationsTool - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:37:23.733 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:37:23.733 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:37:23.733 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:37:23.733 INFO  TestAnnotationsTool - Deflater: JdkDeflater
17:37:23.734 INFO  TestAnnotationsTool - Inflater: JdkInflater
17:37:23.734 INFO  TestAnnotationsTool - GCS max retries/reopens: 20
17:37:23.734 INFO  TestAnnotationsTool - Requester pays: disabled
17:37:23.734 INFO  TestAnnotationsTool - Initializing engine
17:37:23.783 INFO  TestAnnotationsTool - Done initializing engine
17:37:23.783 INFO  ProgressMeter - Starting traversal
17:37:23.784 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
17:37:23.787 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
17:37:23.787 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:37:23.787 INFO  TestAnnotationsTool - Shutting down engine
[October 27, 2025 at 5:37:23 PM UTC] org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$TestAnnotationsTool done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=140509184
17:37:23.861 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
17:37:23.868 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
17:37:23.870 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
17:37:23.903 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
17:37:23.916 INFO  PedReader - Phenotype is other? false
17:37:23.918 INFO  PedReader - Phenotype is other? false
17:37:23.922 INFO  PedReader - Phenotype is other? false
17:37:23.923 INFO  PedReader - Phenotype is other? false
17:37:23.924 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 1:10 and possibly subsequent; at least 10 samples must have called genotypes
17:37:23.932 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
17:37:23.933 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default