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

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

tests

failures

ignored

2.931s

duration

100%

successful

Tests
Standard error

Tests

Test	Duration	Result
testAnnotationArguments	0.034s	passed
testAnnotationGroupAdditive	0.017s	passed
testConfigFileControlsAnnotationPackages	2.167s	passed
testDanglingAnnotationArguments[0](InbreedingCoeff, --founder-id, s1)	0.015s	passed
testGetAllowedValuesForDescriptorHelpGroups	0.019s	passed
testGetAllowedValuesForDescriptorHelp[0]([])	0.015s	passed
testGetAllowedValuesForDescriptorHelp[1]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@20a434a8])	0.014s	passed
testGetAllowedValuesForDescriptorHelp[2]([org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@5a86112a, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@3203ffa3])	0.015s	passed
testGetAllowedValuesForDescriptorHelp[3]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@234dfc8e, org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@18918ab9])	0.025s	passed
testGetClassForPluginHelpFromReflection	0.019s	passed
testGetDefaultInstances	0.020s	passed
testGroupHierarchyBehavior[0]([Ljava.lang.String;@33ccab9c, false, false)	0.018s	passed
testGroupHierarchyBehavior[1]([Ljava.lang.String;@6bbff652, true, true)	0.019s	passed
testGroupHierarchyBehavior[2]([Ljava.lang.String;@3ad5f99, true, false)	0.019s	passed
testGroupHierarchyBehavior[3]([Ljava.lang.String;@1af29a19, true, true)	0.015s	passed
testGroupHierarchyBehavior[4]([Ljava.lang.String;@b67b359, true, true)	0.013s	passed
testHierarchicalAnnotationDiscovery	0.003s	passed
testIncludeAllExcludeIndividual	0.042s	passed
testIncludeDefaultExcludeIndividual	0.013s	passed
testIncludeDefaultGroupExcludeIndividual	0.014s	passed
testIncludeUserGroupExcludeIndividual	0.014s	passed
testInvalidRequestedAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality])	0.015s	passed
testInvalidRequestedAnnotationGroups[1]([interface org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, interface org.broadinstitute.hellbender.tools.walkers.annotator.Annotation])	0.014s	passed
testInvalidRequestedAnnotationGroups[2]([class java.lang.Object])	0.013s	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])	0.013s	passed
testInvalidUserSpecifiedAnnotations[1]([-A, RMSMappingQuality, -A, RMSMappingQuality])	0.013s	passed
testInvalidUserSpecifiedAnnotations[2]([-A, RMSMappingQuality, -AX, RMSMappingQuality])	0.022s	passed
testInvalidUserSpecifiedAnnotations[3]([G, StandardAnnotation, -AX, RMSMappingQuality, -AX, RMSMappingQuality])	0.013s	passed
testInvalidUserSpecifiedAnnotations[4]([-A, foo])	0.013s	passed
testInvalidUserSpecifiedAnnotations[5]([-A, VariantAnnotator])	0.013s	passed
testMultipleOptionalArguments[0]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@5c940e28, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@56c39949], [Ljava.lang.String;@41f3f64, true, 5, 0)	0.012s	passed
testMultipleOptionalArguments[1]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@6b58a0f9, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@7b6c3b37, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@a8964c1], [Ljava.lang.String;@38320819, true, 5, -0.3333)	0.014s	passed
testMultipleOptionalArguments[2]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@46bbcb82, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@b91e024, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@309ac89e], [Ljava.lang.String;@2db0dd19, false, 0, 0)	0.012s	passed
testMultipleOptionalArguments[3]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@f14d079, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@d0456ad, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@12dd3501], [Ljava.lang.String;@4cb0e39e, true, 5, -0.2941)	0.013s	passed
testMultipleOptionalArguments[4]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@23973547, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@3ed4c822, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@7b6558aa], [Ljava.lang.String;@65cb50dc, false, 0, -0.3333)	0.016s	passed
testMultipleOptionalArguments[5]([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, -0.3333)	0.019s	passed
testMultipleOptionalArguments[6]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@18ada4e1, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@10cf3e4f, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@359f3401], [Ljava.lang.String;@242a3997, true, 5, -0.2941)	0.024s	passed
testMultipleOptionalArguments[7]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@52b2713a], [Ljava.lang.String;@54e39504, false, 0, -0.2941)	0.018s	passed
testMultipleOptionalArguments[8]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@592fbd8], [Ljava.lang.String;@354baab2, false, 0, 0)	0.016s	passed
testNoAnnotations	0.012s	passed
testOverridingInstancesWithGetInstance	0s	passed
testPossibleDeNovoAnnotationArguments	0.013s	passed
testToolDefaultAnnotationArgumentsOverridingFromCommandLine	0.026s	passed
testUseAllAnnotations	0.024s	passed
testUseAllAnnotationsDisableToolDefaultAnnotaiotns	0.053s	passed

Standard error

21:17:31.431 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-40db79c-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
SLF4J(W): Class path contains multiple SLF4J providers.
SLF4J(W): Found provider [org.apache.logging.slf4j.SLF4JServiceProvider@1109730f]
SLF4J(W): Found provider [ch.qos.logback.classic.spi.LogbackServiceProvider@1f42366]
SLF4J(W): See https://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J(I): Actual provider is of type [org.apache.logging.slf4j.SLF4JServiceProvider@1109730f]
21:17:31.542 INFO  TestAnnotationsTool - ------------------------------------------------------------
21:17:31.545 INFO  TestAnnotationsTool - The Genome Analysis Toolkit (GATK) v40db79c-SNAPSHOT
21:17:31.545 INFO  TestAnnotationsTool - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:31.545 INFO  TestAnnotationsTool - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:31.545 INFO  TestAnnotationsTool - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:31.546 INFO  TestAnnotationsTool - Start Date/Time: February 10, 2025 at 9:17:31 PM GMT
21:17:31.546 INFO  TestAnnotationsTool - ------------------------------------------------------------
21:17:31.546 INFO  TestAnnotationsTool - ------------------------------------------------------------
21:17:31.549 INFO  TestAnnotationsTool - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:31.549 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:31.549 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:31.550 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:31.550 INFO  TestAnnotationsTool - Deflater: IntelDeflater
21:17:31.550 INFO  TestAnnotationsTool - Inflater: IntelInflater
21:17:31.550 INFO  TestAnnotationsTool - GCS max retries/reopens: 20
21:17:31.550 INFO  TestAnnotationsTool - Requester pays: disabled
21:17:31.550 INFO  TestAnnotationsTool - Initializing engine
21:17:31.657 INFO  TestAnnotationsTool - Done initializing engine
21:17:31.658 INFO  ProgressMeter - Starting traversal
21:17:31.658 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
21:17:31.661 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
21:17:31.661 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
21:17:31.661 INFO  TestAnnotationsTool - Shutting down engine
[February 10, 2025 at 9:17:31 PM GMT] org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$TestAnnotationsTool done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=295698432
21:17:31.967 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
21:17:32.017 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
21:17:32.031 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
21:17:32.234 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
21:17:32.295 INFO  PedReader - Phenotype is other? false
21:17:32.296 INFO  PedReader - Phenotype is other? false
21:17:32.311 INFO  PedReader - Phenotype is other? false
21:17:32.312 INFO  PedReader - Phenotype is other? false
21:17:32.312 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 1:10 and possibly subsequent; at least 10 samples must have called genotypes
21:17:32.364 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
21:17:32.365 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default