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

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

tests

failures

ignored

2.094s

duration

100%

successful

Tests
Standard error

Tests

Test	Duration	Result
testAnnotationArguments	0.035s	passed
testAnnotationGroupAdditive	0.005s	passed
testConfigFileControlsAnnotationPackages	1.854s	passed
testDanglingAnnotationArguments[0](InbreedingCoeff, --founder-id, s1)	0.006s	passed
testGetAllowedValuesForDescriptorHelpGroups	0.004s	passed
testGetAllowedValuesForDescriptorHelp[0]([])	0.005s	passed
testGetAllowedValuesForDescriptorHelp[1]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@6d7556a8])	0.004s	passed
testGetAllowedValuesForDescriptorHelp[2]([org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@626df173, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@4e030feb])	0.004s	passed
testGetAllowedValuesForDescriptorHelp[3]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@23e86863, org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@6df87ffd])	0.004s	passed
testGetClassForPluginHelpFromReflection	0.004s	passed
testGetDefaultInstances	0.004s	passed
testGroupHierarchyBehavior[0]([Ljava.lang.String;@4db568e1, false, false)	0.004s	passed
testGroupHierarchyBehavior[1]([Ljava.lang.String;@784212, true, true)	0.005s	passed
testGroupHierarchyBehavior[2]([Ljava.lang.String;@24842b8e, true, false)	0.004s	passed
testGroupHierarchyBehavior[3]([Ljava.lang.String;@54a5496f, true, true)	0.005s	passed
testGroupHierarchyBehavior[4]([Ljava.lang.String;@29ccab93, true, true)	0.004s	passed
testHierarchicalAnnotationDiscovery	0.002s	passed
testIncludeAllExcludeIndividual	0.015s	passed
testIncludeDefaultExcludeIndividual	0.004s	passed
testIncludeDefaultGroupExcludeIndividual	0.005s	passed
testIncludeUserGroupExcludeIndividual	0.004s	passed
testInvalidRequestedAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality])	0.004s	passed
testInvalidRequestedAnnotationGroups[1]([interface org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, interface org.broadinstitute.hellbender.tools.walkers.annotator.Annotation])	0.004s	passed
testInvalidRequestedAnnotationGroups[2]([class java.lang.Object])	0.004s	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])	0.003s	passed
testInvalidUserSpecifiedAnnotations[4]([-A, foo])	0.004s	passed
testInvalidUserSpecifiedAnnotations[5]([-A, VariantAnnotator])	0.004s	passed
testMultipleOptionalArguments[0]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@53df7e67, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@3d4b45b], [Ljava.lang.String;@4d0b276e, true, 5, 0)	0.004s	passed
testMultipleOptionalArguments[1]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@2a504ea7, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@10f397d0, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@33a3e5db], [Ljava.lang.String;@4f9213d2, true, 5, -0.3333)	0.006s	passed
testMultipleOptionalArguments[2]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@37d81587, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@7f3e9acc, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@47d4e28a], [Ljava.lang.String;@177068db, false, 0, 0)	0.004s	passed
testMultipleOptionalArguments[3]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@552ffa44, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@6e66b498, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@54d35ed5], [Ljava.lang.String;@6f7c9755, true, 5, -0.2941)	0.005s	passed
testMultipleOptionalArguments[4]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@4067634b, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@3b64f131, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@490d9c41], [Ljava.lang.String;@47d81427, false, 0, -0.3333)	0.005s	passed
testMultipleOptionalArguments[5]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@58a7a58d, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@4d8522ff, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@1c9975a8], [Ljava.lang.String;@3883031d, false, 0, -0.3333)	0.008s	passed
testMultipleOptionalArguments[6]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@134955bb, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@45b08b17, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@6723e6b3], [Ljava.lang.String;@3883b5e9, true, 5, -0.2941)	0.005s	passed
testMultipleOptionalArguments[7]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@5bccef9f], [Ljava.lang.String;@1136122a, false, 0, -0.2941)	0.010s	passed
testMultipleOptionalArguments[8]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@7b0525a8], [Ljava.lang.String;@4f2d8175, false, 0, 0)	0.006s	passed
testNoAnnotations	0.003s	passed
testOverridingInstancesWithGetInstance	0.001s	passed
testPossibleDeNovoAnnotationArguments	0.003s	passed
testToolDefaultAnnotationArgumentsOverridingFromCommandLine	0.008s	passed
testUseAllAnnotations	0.006s	passed
testUseAllAnnotationsDisableToolDefaultAnnotaiotns	0.006s	passed

Standard error

22:31:45.178 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.8.11/13f95ee601084b8bf047b2a37f6ea36cd588b96b/gkl-0.8.11.jar!/com/intel/gkl/native/libgkl_compression.so
22:31:45.299 INFO  TestAnnotationsTool - ------------------------------------------------------------
22:31:45.302 INFO  TestAnnotationsTool - org.broadinstitute.hellbender.cmdline.GATKPlugin vUnavailable
22:31:45.302 INFO  TestAnnotationsTool - For support and documentation go to https://software.broadinstitute.org/gatk/
22:31:45.302 INFO  TestAnnotationsTool - Executing as runner@fv-az1720-291 on Linux v6.8.0-1021-azure amd64
22:31:45.302 INFO  TestAnnotationsTool - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:31:45.303 INFO  TestAnnotationsTool - Start Date/Time: March 28, 2025 at 10:31:45 PM UTC
22:31:45.303 INFO  TestAnnotationsTool - ------------------------------------------------------------
22:31:45.303 INFO  TestAnnotationsTool - ------------------------------------------------------------
22:31:45.306 INFO  TestAnnotationsTool - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:31:45.307 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:31:45.307 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:31:45.307 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:31:45.308 INFO  TestAnnotationsTool - Deflater: IntelDeflater
22:31:45.308 INFO  TestAnnotationsTool - Inflater: IntelInflater
22:31:45.308 INFO  TestAnnotationsTool - GCS max retries/reopens: 20
22:31:45.308 INFO  TestAnnotationsTool - Requester pays: disabled
22:31:45.309 INFO  TestAnnotationsTool - Initializing engine
22:31:45.362 INFO  TestAnnotationsTool - Done initializing engine
22:31:45.363 INFO  ProgressMeter - Starting traversal
22:31:45.363 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
22:31:45.367 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
22:31:45.367 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
22:31:45.367 INFO  TestAnnotationsTool - Shutting down engine
[March 28, 2025 at 10:31:45 PM UTC] org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$TestAnnotationsTool done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=146800640
22:31:45.476 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
22:31:45.489 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
22:31:45.493 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
22:31:45.559 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
22:31:45.583 INFO  PedReader - Phenotype is other? false
22:31:45.584 INFO  PedReader - Phenotype is other? false
22:31:45.590 INFO  PedReader - Phenotype is other? false
22:31:45.591 INFO  PedReader - Phenotype is other? false
22:31:45.591 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 1:10 and possibly subsequent; at least 10 samples must have called genotypes
22:31:45.607 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
22:31:45.608 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default