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

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

tests
0

failures
0

ignored
2.930s

duration
100%

successful

Tests

Test Duration Result
testAnnotationArguments 0.035s passed
testAnnotationGroupAdditive 0.020s passed
testConfigFileControlsAnnotationPackages 2.182s passed
testDanglingAnnotationArguments[0](InbreedingCoeff, --founder-id, s1) 0.015s passed
testGetAllowedValuesForDescriptorHelpGroups 0.017s passed
testGetAllowedValuesForDescriptorHelp[0]([]) 0.014s passed
testGetAllowedValuesForDescriptorHelp[1]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@6b83ec49]) 0.014s passed
testGetAllowedValuesForDescriptorHelp[2]([org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@2b20caed, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@307eb95f]) 0.014s passed
testGetAllowedValuesForDescriptorHelp[3]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@6d028c7e, org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@2e5ff1d4]) 0.019s passed
testGetClassForPluginHelpFromReflection 0.018s passed
testGetDefaultInstances 0.018s passed
testGroupHierarchyBehavior[0]([Ljava.lang.String;@57f83dc7, false, false) 0.018s passed
testGroupHierarchyBehavior[1]([Ljava.lang.String;@515a2afd, true, true) 0.018s passed
testGroupHierarchyBehavior[2]([Ljava.lang.String;@54dc163a, true, false) 0.017s passed
testGroupHierarchyBehavior[3]([Ljava.lang.String;@36d7e8d2, true, true) 0.014s passed
testGroupHierarchyBehavior[4]([Ljava.lang.String;@73ccdfc1, true, true) 0.020s passed
testHierarchicalAnnotationDiscovery 0.002s passed
testIncludeAllExcludeIndividual 0.031s passed
testIncludeDefaultExcludeIndividual 0.012s passed
testIncludeDefaultGroupExcludeIndividual 0.013s passed
testIncludeUserGroupExcludeIndividual 0.012s passed
testInvalidRequestedAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality]) 0.018s passed
testInvalidRequestedAnnotationGroups[1]([interface org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, interface org.broadinstitute.hellbender.tools.walkers.annotator.Annotation]) 0.018s passed
testInvalidRequestedAnnotationGroups[2]([class java.lang.Object]) 0.024s 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]) 0.018s passed
testInvalidUserSpecifiedAnnotations[1]([-A, RMSMappingQuality, -A, RMSMappingQuality]) 0.013s 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]) 0.012s passed
testInvalidUserSpecifiedAnnotations[5]([-A, VariantAnnotator]) 0.012s passed
testMultipleOptionalArguments[0]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@7aff1db3, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@46374b8], [Ljava.lang.String;@29ceefb3, true, 5, 0) 0.022s passed
testMultipleOptionalArguments[1]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@24673720, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@2aadeb31, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@704ddfad], [Ljava.lang.String;@23973547, true, 5, -0.3333) 0.022s passed
testMultipleOptionalArguments[2]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@3509f32d, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@1f9a5d3b, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@440e2406], [Ljava.lang.String;@56adb75e, false, 0, 0) 0.027s passed
testMultipleOptionalArguments[3]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@7b8b755d, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@3bd5dff5, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@6df605f], [Ljava.lang.String;@68cc6fa4, true, 5, -0.2941) 0.018s passed
testMultipleOptionalArguments[4]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@2c914364, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@25c756f0, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@66c9aca2], [Ljava.lang.String;@18206382, false, 0, -0.3333) 0.015s passed
testMultipleOptionalArguments[5]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@6e5106fc, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@70199db0, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@274b0c2a], [Ljava.lang.String;@721f3526, false, 0, -0.3333) 0.016s passed
testMultipleOptionalArguments[6]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@487f025, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@7ef570be, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@39329d81], [Ljava.lang.String;@63574d76, true, 5, -0.2941) 0.015s passed
testMultipleOptionalArguments[7]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@6db64abf], [Ljava.lang.String;@34714012, false, 0, -0.2941) 0.018s passed
testMultipleOptionalArguments[8]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@5c883b3f], [Ljava.lang.String;@a47a011, false, 0, 0) 0.016s passed
testNoAnnotations 0.012s passed
testOverridingInstancesWithGetInstance 0s passed
testPossibleDeNovoAnnotationArguments 0.019s passed
testToolDefaultAnnotationArgumentsOverridingFromCommandLine 0.024s passed
testUseAllAnnotations 0.023s passed
testUseAllAnnotationsDisableToolDefaultAnnotaiotns 0.022s passed

Standard error

20:47:30.318 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-9eb1b78-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
20:47:30.435 INFO  TestAnnotationsTool - ------------------------------------------------------------
20:47:30.438 INFO  TestAnnotationsTool - The Genome Analysis Toolkit (GATK) v9eb1b78-SNAPSHOT
20:47:30.438 INFO  TestAnnotationsTool - For support and documentation go to https://software.broadinstitute.org/gatk/
20:47:30.439 INFO  TestAnnotationsTool - Executing as root@b6fedaba0a37 on Linux v6.11.0-1018-azure amd64
20:47:30.439 INFO  TestAnnotationsTool - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:47:30.439 INFO  TestAnnotationsTool - Start Date/Time: July 15, 2025 at 8:47:30 PM GMT
20:47:30.439 INFO  TestAnnotationsTool - ------------------------------------------------------------
20:47:30.439 INFO  TestAnnotationsTool - ------------------------------------------------------------
20:47:30.442 INFO  TestAnnotationsTool - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:47:30.442 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:47:30.443 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:47:30.443 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:47:30.443 INFO  TestAnnotationsTool - Deflater: IntelDeflater
20:47:30.443 INFO  TestAnnotationsTool - Inflater: IntelInflater
20:47:30.444 INFO  TestAnnotationsTool - GCS max retries/reopens: 20
20:47:30.444 INFO  TestAnnotationsTool - Requester pays: disabled
20:47:30.444 INFO  TestAnnotationsTool - Initializing engine
20:47:30.561 INFO  TestAnnotationsTool - Done initializing engine
20:47:30.562 INFO  ProgressMeter - Starting traversal
20:47:30.563 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
20:47:30.565 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
20:47:30.566 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:47:30.566 INFO  TestAnnotationsTool - Shutting down engine
[July 15, 2025 at 8:47:30 PM GMT] org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$TestAnnotationsTool done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=281018368
20:47:30.858 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:47:30.896 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:47:30.909 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:47:31.160 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
20:47:31.208 INFO  PedReader - Phenotype is other? false
20:47:31.209 INFO  PedReader - Phenotype is other? false
20:47:31.224 INFO  PedReader - Phenotype is other? false
20:47:31.225 INFO  PedReader - Phenotype is other? false
20:47:31.226 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 1:10 and possibly subsequent; at least 10 samples must have called genotypes
20:47:31.281 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
20:47:31.282 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default