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

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

tests

failures

ignored

2.767s

duration

100%

successful

Tests
Standard error

Tests

Test	Duration	Result
testAnnotationArguments	0.033s	passed
testAnnotationGroupAdditive	0.016s	passed
testConfigFileControlsAnnotationPackages	2.031s	passed
testDanglingAnnotationArguments[0](InbreedingCoeff, --founder-id, s1)	0.018s	passed
testGetAllowedValuesForDescriptorHelpGroups	0.018s	passed
testGetAllowedValuesForDescriptorHelp[0]([])	0.015s	passed
testGetAllowedValuesForDescriptorHelp[1]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@54519d74])	0.013s	passed
testGetAllowedValuesForDescriptorHelp[2]([org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@94f79a7, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@647d3279])	0.023s	passed
testGetAllowedValuesForDescriptorHelp[3]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@33aa4326, org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@125ed27])	0.015s	passed
testGetClassForPluginHelpFromReflection	0.017s	passed
testGetDefaultInstances	0.014s	passed
testGroupHierarchyBehavior[0]([Ljava.lang.String;@1af29a19, false, false)	0.014s	passed
testGroupHierarchyBehavior[1]([Ljava.lang.String;@78fd1179, true, true)	0.013s	passed
testGroupHierarchyBehavior[2]([Ljava.lang.String;@2e214d39, true, false)	0.013s	passed
testGroupHierarchyBehavior[3]([Ljava.lang.String;@2f9d47a3, true, true)	0.023s	passed
testGroupHierarchyBehavior[4]([Ljava.lang.String;@215efb16, true, true)	0.013s	passed
testHierarchicalAnnotationDiscovery	0.002s	passed
testIncludeAllExcludeIndividual	0.030s	passed
testIncludeDefaultExcludeIndividual	0.011s	passed
testIncludeDefaultGroupExcludeIndividual	0.013s	passed
testIncludeUserGroupExcludeIndividual	0.013s	passed
testInvalidRequestedAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality])	0.012s	passed
testInvalidRequestedAnnotationGroups[1]([interface org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, interface org.broadinstitute.hellbender.tools.walkers.annotator.Annotation])	0.026s	passed
testInvalidRequestedAnnotationGroups[2]([class java.lang.Object])	0.027s	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])	0.029s	passed
testInvalidUserSpecifiedAnnotations[1]([-A, RMSMappingQuality, -A, RMSMappingQuality])	0.027s	passed
testInvalidUserSpecifiedAnnotations[2]([-A, RMSMappingQuality, -AX, RMSMappingQuality])	0.014s	passed
testInvalidUserSpecifiedAnnotations[3]([G, StandardAnnotation, -AX, RMSMappingQuality, -AX, RMSMappingQuality])	0.011s	passed
testInvalidUserSpecifiedAnnotations[4]([-A, foo])	0.011s	passed
testInvalidUserSpecifiedAnnotations[5]([-A, VariantAnnotator])	0.012s	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)	0.013s	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)	0.014s	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)	0.025s	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)	0.014s	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)	0.012s	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)	0.014s	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)	0.012s	passed
testMultipleOptionalArguments[7]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@7eb006bd], [Ljava.lang.String;@633dce39, false, 0, -0.2941)	0.016s	passed
testMultipleOptionalArguments[8]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@6e43c01f], [Ljava.lang.String;@6567de86, false, 0, 0)	0.013s	passed
testNoAnnotations	0.012s	passed
testOverridingInstancesWithGetInstance	0s	passed
testPossibleDeNovoAnnotationArguments	0.011s	passed
testToolDefaultAnnotationArgumentsOverridingFromCommandLine	0.032s	passed
testUseAllAnnotations	0.029s	passed
testUseAllAnnotationsDisableToolDefaultAnnotaiotns	0.022s	passed

Standard error

22:03:19.917 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-fa08e16-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
22:03:20.041 INFO  TestAnnotationsTool - ------------------------------------------------------------
22:03:20.044 INFO  TestAnnotationsTool - The Genome Analysis Toolkit (GATK) vfa08e16-SNAPSHOT
22:03:20.044 INFO  TestAnnotationsTool - For support and documentation go to https://software.broadinstitute.org/gatk/
22:03:20.044 INFO  TestAnnotationsTool - Executing as root@f99bdcf77b66 on Linux v6.8.0-1021-azure amd64
22:03:20.044 INFO  TestAnnotationsTool - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
22:03:20.045 INFO  TestAnnotationsTool - Start Date/Time: April 22, 2025 at 10:03:19 PM GMT
22:03:20.045 INFO  TestAnnotationsTool - ------------------------------------------------------------
22:03:20.045 INFO  TestAnnotationsTool - ------------------------------------------------------------
22:03:20.049 INFO  TestAnnotationsTool - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:03:20.050 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:03:20.050 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:03:20.050 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:03:20.050 INFO  TestAnnotationsTool - Deflater: IntelDeflater
22:03:20.050 INFO  TestAnnotationsTool - Inflater: IntelInflater
22:03:20.051 INFO  TestAnnotationsTool - GCS max retries/reopens: 20
22:03:20.051 INFO  TestAnnotationsTool - Requester pays: disabled
22:03:20.051 INFO  TestAnnotationsTool - Initializing engine
22:03:20.138 INFO  TestAnnotationsTool - Done initializing engine
22:03:20.140 INFO  ProgressMeter - Starting traversal
22:03:20.140 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
22:03:20.143 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
22:03:20.144 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:03:20.144 INFO  TestAnnotationsTool - Shutting down engine
[April 22, 2025 at 10:03:20 PM GMT] org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$TestAnnotationsTool done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=226492416
22:03:20.419 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
22:03:20.455 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
22:03:20.468 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
22:03:20.724 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
22:03:20.766 INFO  PedReader - Phenotype is other? false
22:03:20.767 INFO  PedReader - Phenotype is other? false
22:03:20.780 INFO  PedReader - Phenotype is other? false
22:03:20.781 INFO  PedReader - Phenotype is other? false
22:03:20.781 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 1:10 and possibly subsequent; at least 10 samples must have called genotypes
22:03:20.837 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
22:03:20.837 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default