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

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

tests

failures

ignored

1.877s

duration

100%

successful

Tests
Standard error

Tests

Test	Duration	Result
testAnnotationArguments	0.025s	passed
testAnnotationGroupAdditive	0.005s	passed
testConfigFileControlsAnnotationPackages	1.704s	passed
testDanglingAnnotationArguments[0](InbreedingCoeff, --founder-id, s1)	0.004s	passed
testGetAllowedValuesForDescriptorHelpGroups	0.004s	passed
testGetAllowedValuesForDescriptorHelp[0]([])	0.004s	passed
testGetAllowedValuesForDescriptorHelp[1]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@2c2e5e72])	0.004s	passed
testGetAllowedValuesForDescriptorHelp[2]([org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@7614378d, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@7028b5cc])	0.004s	passed
testGetAllowedValuesForDescriptorHelp[3]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@1ce6a9bd, org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@4a47bc9c])	0.003s	passed
testGetClassForPluginHelpFromReflection	0.003s	passed
testGetDefaultInstances	0.004s	passed
testGroupHierarchyBehavior[0]([Ljava.lang.String;@437c1a87, false, false)	0.003s	passed
testGroupHierarchyBehavior[1]([Ljava.lang.String;@2dc73024, true, true)	0.003s	passed
testGroupHierarchyBehavior[2]([Ljava.lang.String;@34652065, true, false)	0.004s	passed
testGroupHierarchyBehavior[3]([Ljava.lang.String;@6b899971, true, true)	0.003s	passed
testGroupHierarchyBehavior[4]([Ljava.lang.String;@33399052, true, true)	0.003s	passed
testHierarchicalAnnotationDiscovery	0.001s	passed
testIncludeAllExcludeIndividual	0.011s	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])	0.003s	passed
testInvalidRequestedAnnotationGroups[2]([class java.lang.Object])	0.002s	passed
testInvalidToolDefaultAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality])	0.001s	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])	0.003s	passed
testInvalidUserSpecifiedAnnotations[1]([-A, RMSMappingQuality, -A, RMSMappingQuality])	0.003s	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])	0.003s	passed
testInvalidUserSpecifiedAnnotations[5]([-A, VariantAnnotator])	0.002s	passed
testMultipleOptionalArguments[0]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@591a4d25, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@4bfe83d], [Ljava.lang.String;@5906ebfb, true, 5, 0)	0.002s	passed
testMultipleOptionalArguments[1]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@55a055cc, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@1ab1d93d, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@57167ccb], [Ljava.lang.String;@37753b69, true, 5, -0.3333)	0.003s	passed
testMultipleOptionalArguments[2]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@4d5ea776, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@5d68be4f, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@34eb5d01], [Ljava.lang.String;@77b22b05, false, 0, 0)	0.002s	passed
testMultipleOptionalArguments[3]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@1d008e61, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@191b44ca, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@5de243bb], [Ljava.lang.String;@2c4cf7eb, true, 5, -0.2941)	0.004s	passed
testMultipleOptionalArguments[4]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@5db04bd2, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@6f921e32, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@31c5304f], [Ljava.lang.String;@43df1377, false, 0, -0.3333)	0.003s	passed
testMultipleOptionalArguments[5]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@434a8938, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@237cd264, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@51cd2d2], [Ljava.lang.String;@5521407f, false, 0, -0.3333)	0.006s	passed
testMultipleOptionalArguments[6]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@4cb82b09, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@49665f92, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@b68932b], [Ljava.lang.String;@77b27b57, true, 5, -0.2941)	0.003s	passed
testMultipleOptionalArguments[7]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@434d001d], [Ljava.lang.String;@36453773, false, 0, -0.2941)	0.007s	passed
testMultipleOptionalArguments[8]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@8f09a02], [Ljava.lang.String;@5454be, false, 0, 0)	0.004s	passed
testNoAnnotations	0.002s	passed
testOverridingInstancesWithGetInstance	0.001s	passed
testPossibleDeNovoAnnotationArguments	0.002s	passed
testToolDefaultAnnotationArgumentsOverridingFromCommandLine	0.005s	passed
testUseAllAnnotations	0.005s	passed
testUseAllAnnotationsDisableToolDefaultAnnotaiotns	0.004s	passed

Standard error

19:47:55.406 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.0/5ec646c7bf8c4f7681c2a59819384e5da469db31/gkl-0.9.0.jar!/com/intel/gkl/native/libgkl_compression.so
19:47:55.518 INFO  TestAnnotationsTool - ------------------------------------------------------------
19:47:55.521 INFO  TestAnnotationsTool - org.broadinstitute.hellbender.cmdline.GATKPlugin vUnavailable
19:47:55.521 INFO  TestAnnotationsTool - For support and documentation go to https://software.broadinstitute.org/gatk/
19:47:55.521 INFO  TestAnnotationsTool - Executing as runner@pkrvmq0rgcvqdmg on Linux v6.11.0-1018-azure amd64
19:47:55.521 INFO  TestAnnotationsTool - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
19:47:55.522 INFO  TestAnnotationsTool - Start Date/Time: July 15, 2025 at 7:47:55 PM UTC
19:47:55.522 INFO  TestAnnotationsTool - ------------------------------------------------------------
19:47:55.522 INFO  TestAnnotationsTool - ------------------------------------------------------------
19:47:55.525 INFO  TestAnnotationsTool - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:47:55.525 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:47:55.525 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:47:55.525 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:47:55.525 INFO  TestAnnotationsTool - Deflater: IntelDeflater
19:47:55.526 INFO  TestAnnotationsTool - Inflater: IntelInflater
19:47:55.526 INFO  TestAnnotationsTool - GCS max retries/reopens: 20
19:47:55.526 INFO  TestAnnotationsTool - Requester pays: disabled
19:47:55.526 INFO  TestAnnotationsTool - Initializing engine
19:47:55.572 INFO  TestAnnotationsTool - Done initializing engine
19:47:55.572 INFO  ProgressMeter - Starting traversal
19:47:55.573 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
19:47:55.575 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
19:47:55.575 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
19:47:55.576 INFO  TestAnnotationsTool - Shutting down engine
[July 15, 2025 at 7:47:55 PM UTC] org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$TestAnnotationsTool done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=140509184
19:47:55.668 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
19:47:55.676 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
19:47:55.679 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
19:47:55.722 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
19:47:55.737 INFO  PedReader - Phenotype is other? false
19:47:55.738 INFO  PedReader - Phenotype is other? false
19:47:55.742 INFO  PedReader - Phenotype is other? false
19:47:55.743 INFO  PedReader - Phenotype is other? false
19:47:55.743 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 1:10 and possibly subsequent; at least 10 samples must have called genotypes
19:47:55.753 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
19:47:55.754 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default