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

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

tests
0

failures
0

ignored
2.813s

duration
100%

successful

Tests

Test Duration Result
testAnnotationArguments 0.055s passed
testAnnotationGroupAdditive 0.030s passed
testConfigFileControlsAnnotationPackages 1.938s passed
testDanglingAnnotationArguments[0](InbreedingCoeff, --founder-id, s1) 0.018s passed
testGetAllowedValuesForDescriptorHelpGroups 0.033s passed
testGetAllowedValuesForDescriptorHelp[0]([]) 0.038s passed
testGetAllowedValuesForDescriptorHelp[1]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@54519d74]) 0.039s passed
testGetAllowedValuesForDescriptorHelp[2]([org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@94f79a7, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@647d3279]) 0.038s passed
testGetAllowedValuesForDescriptorHelp[3]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@33aa4326, org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@125ed27]) 0.037s passed
testGetClassForPluginHelpFromReflection 0.027s passed
testGetDefaultInstances 0.029s passed
testGroupHierarchyBehavior[0]([Ljava.lang.String;@1af29a19, false, false) 0.033s passed
testGroupHierarchyBehavior[1]([Ljava.lang.String;@78fd1179, true, true) 0.028s passed
testGroupHierarchyBehavior[2]([Ljava.lang.String;@2e214d39, true, false) 0.026s passed
testGroupHierarchyBehavior[3]([Ljava.lang.String;@2f9d47a3, true, true) 0.014s passed
testGroupHierarchyBehavior[4]([Ljava.lang.String;@215efb16, true, true) 0.023s passed
testHierarchicalAnnotationDiscovery 0.003s passed
testIncludeAllExcludeIndividual 0.033s passed
testIncludeDefaultExcludeIndividual 0.012s passed
testIncludeDefaultGroupExcludeIndividual 0.013s passed
testIncludeUserGroupExcludeIndividual 0.013s passed
testInvalidRequestedAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality]) 0.013s passed
testInvalidRequestedAnnotationGroups[1]([interface org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, interface org.broadinstitute.hellbender.tools.walkers.annotator.Annotation]) 0.011s passed
testInvalidRequestedAnnotationGroups[2]([class java.lang.Object]) 0.012s 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]) 0.012s passed
testInvalidUserSpecifiedAnnotations[1]([-A, RMSMappingQuality, -A, RMSMappingQuality]) 0.011s passed
testInvalidUserSpecifiedAnnotations[2]([-A, RMSMappingQuality, -AX, RMSMappingQuality]) 0.012s passed
testInvalidUserSpecifiedAnnotations[3]([G, StandardAnnotation, -AX, RMSMappingQuality, -AX, RMSMappingQuality]) 0.011s passed
testInvalidUserSpecifiedAnnotations[4]([-A, foo]) 0.011s passed
testInvalidUserSpecifiedAnnotations[5]([-A, VariantAnnotator]) 0.011s passed
testMultipleOptionalArguments[0]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@1226ba98, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@79194b1c], [Ljava.lang.String;@7ec01440, true, 5, 0) 0.012s passed
testMultipleOptionalArguments[1]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@622c658d, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@3619bc9e, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@2e640411], [Ljava.lang.String;@5e609b42, true, 5, -0.3333) 0.013s passed
testMultipleOptionalArguments[2]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@53f18591, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@4dfbe8c2, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@2bb03136], [Ljava.lang.String;@78a46d7b, false, 0, 0) 0.019s passed
testMultipleOptionalArguments[3]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@5e572ad6, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@709353b9, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@69c53b72], [Ljava.lang.String;@768967cf, true, 5, -0.2941) 0.013s passed
testMultipleOptionalArguments[4]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@38816a6c, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@74727e41, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@16117d9], [Ljava.lang.String;@78977b59, false, 0, -0.3333) 0.013s passed
testMultipleOptionalArguments[5]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@1a557a52, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@4ab959e8, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@39d4f046], [Ljava.lang.String;@5f910283, false, 0, -0.3333) 0.016s passed
testMultipleOptionalArguments[6]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@30fffb53, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@738b93a8, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@1e8c9083], [Ljava.lang.String;@64547a83, true, 5, -0.2941) 0.015s passed
testMultipleOptionalArguments[7]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@7eb006bd], [Ljava.lang.String;@633dce39, false, 0, -0.2941) 0.018s passed
testMultipleOptionalArguments[8]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@6e43c01f], [Ljava.lang.String;@6567de86, false, 0, 0) 0.015s passed
testNoAnnotations 0.012s passed
testOverridingInstancesWithGetInstance 0s passed
testPossibleDeNovoAnnotationArguments 0.012s passed
testToolDefaultAnnotationArgumentsOverridingFromCommandLine 0.024s passed
testUseAllAnnotations 0.023s passed
testUseAllAnnotationsDisableToolDefaultAnnotaiotns 0.024s passed

Standard error

16:11:52.571 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-6e00a37-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
16:11:52.668 INFO  TestAnnotationsTool - ------------------------------------------------------------
16:11:52.670 INFO  TestAnnotationsTool - The Genome Analysis Toolkit (GATK) v6e00a37-SNAPSHOT
16:11:52.670 INFO  TestAnnotationsTool - For support and documentation go to https://software.broadinstitute.org/gatk/
16:11:52.670 INFO  TestAnnotationsTool - Executing as root@a34d5a30ed3f on Linux v6.11.0-1013-azure amd64
16:11:52.671 INFO  TestAnnotationsTool - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
16:11:52.671 INFO  TestAnnotationsTool - Start Date/Time: May 5, 2025 at 4:11:52 PM GMT
16:11:52.671 INFO  TestAnnotationsTool - ------------------------------------------------------------
16:11:52.671 INFO  TestAnnotationsTool - ------------------------------------------------------------
16:11:52.674 INFO  TestAnnotationsTool - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:11:52.674 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:11:52.674 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:11:52.674 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:11:52.675 INFO  TestAnnotationsTool - Deflater: IntelDeflater
16:11:52.675 INFO  TestAnnotationsTool - Inflater: IntelInflater
16:11:52.675 INFO  TestAnnotationsTool - GCS max retries/reopens: 20
16:11:52.675 INFO  TestAnnotationsTool - Requester pays: disabled
16:11:52.675 INFO  TestAnnotationsTool - Initializing engine
16:11:52.740 INFO  TestAnnotationsTool - Done initializing engine
16:11:52.741 INFO  ProgressMeter - Starting traversal
16:11:52.741 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
16:11:52.744 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
16:11:52.744 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
16:11:52.744 INFO  TestAnnotationsTool - Shutting down engine
[May 5, 2025 at 4:11:52 PM GMT] org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$TestAnnotationsTool done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=134217728
16:11:53.193 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
16:11:53.231 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
16:11:53.244 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
16:11:53.424 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
16:11:53.473 INFO  PedReader - Phenotype is other? false
16:11:53.474 INFO  PedReader - Phenotype is other? false
16:11:53.488 INFO  PedReader - Phenotype is other? false
16:11:53.489 INFO  PedReader - Phenotype is other? false
16:11:53.489 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 1:10 and possibly subsequent; at least 10 samples must have called genotypes
16:11:53.539 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
16:11:53.540 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default