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

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

tests
0

failures
0

ignored
2.947s

duration
100%

successful

Tests

Test Duration Result
testAnnotationArguments 0.037s passed
testAnnotationGroupAdditive 0.016s passed
testConfigFileControlsAnnotationPackages 1.966s passed
testDanglingAnnotationArguments[0](InbreedingCoeff, --founder-id, s1) 0.015s passed
testGetAllowedValuesForDescriptorHelpGroups 0.039s passed
testGetAllowedValuesForDescriptorHelp[0]([]) 0.017s passed
testGetAllowedValuesForDescriptorHelp[1]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@3d5b2c1e]) 0.019s passed
testGetAllowedValuesForDescriptorHelp[2]([org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@49231d79, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@25f67aea]) 0.018s passed
testGetAllowedValuesForDescriptorHelp[3]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@1315f1d5, org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality@3b32f0b4]) 0.044s passed
testGetClassForPluginHelpFromReflection 0.038s passed
testGetDefaultInstances 0.034s passed
testGroupHierarchyBehavior[0]([Ljava.lang.String;@6c89c92e, false, false) 0.029s passed
testGroupHierarchyBehavior[1]([Ljava.lang.String;@6a495d88, true, true) 0.028s passed
testGroupHierarchyBehavior[2]([Ljava.lang.String;@457dc809, true, false) 0.035s passed
testGroupHierarchyBehavior[3]([Ljava.lang.String;@23b02f37, true, true) 0.033s passed
testGroupHierarchyBehavior[4]([Ljava.lang.String;@130bd00e, true, true) 0.029s passed
testHierarchicalAnnotationDiscovery 0.001s passed
testIncludeAllExcludeIndividual 0.064s passed
testIncludeDefaultExcludeIndividual 0.028s passed
testIncludeDefaultGroupExcludeIndividual 0.028s passed
testIncludeUserGroupExcludeIndividual 0.028s passed
testInvalidRequestedAnnotationGroups[0]([class org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality]) 0.028s passed
testInvalidRequestedAnnotationGroups[1]([interface org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation, interface org.broadinstitute.hellbender.tools.walkers.annotator.Annotation]) 0.022s passed
testInvalidRequestedAnnotationGroups[2]([class java.lang.Object]) 0.012s 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]) 0.023s passed
testInvalidUserSpecifiedAnnotations[1]([-A, RMSMappingQuality, -A, RMSMappingQuality]) 0.015s passed
testInvalidUserSpecifiedAnnotations[2]([-A, RMSMappingQuality, -AX, RMSMappingQuality]) 0.018s passed
testInvalidUserSpecifiedAnnotations[3]([G, StandardAnnotation, -AX, RMSMappingQuality, -AX, RMSMappingQuality]) 0.012s passed
testInvalidUserSpecifiedAnnotations[4]([-A, foo]) 0.013s passed
testInvalidUserSpecifiedAnnotations[5]([-A, VariantAnnotator]) 0.012s passed
testMultipleOptionalArguments[0]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@41f3f64, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@454f6cc5], [Ljava.lang.String;@3956df0a, true, 5, 0) 0.018s passed
testMultipleOptionalArguments[1]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@a8964c1, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@38320819, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@16c3388e], [Ljava.lang.String;@cec1ce2, true, 5, -0.3333) 0.014s passed
testMultipleOptionalArguments[2]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@309ac89e, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@2db0dd19, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@354ff4f6], [Ljava.lang.String;@315bb2bb, false, 0, 0) 0.012s passed
testMultipleOptionalArguments[3]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@12dd3501, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@4cb0e39e, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@650e6569], [Ljava.lang.String;@4a10e65b, true, 5, -0.2941) 0.014s passed
testMultipleOptionalArguments[4]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@7b6558aa, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@65cb50dc, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@7fec6c2f], [Ljava.lang.String;@67e12e28, false, 0, -0.3333) 0.014s passed
testMultipleOptionalArguments[5]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@440e2406, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@56adb75e, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@2cc7b63d], [Ljava.lang.String;@6179551b, false, 0, -0.3333) 0.016s passed
testMultipleOptionalArguments[6]([org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testChildAnnotation@359f3401, org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$testParentAnnotation@242a3997, org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@51d50b5f], [Ljava.lang.String;@38816a6c, true, 5, -0.2941) 0.015s passed
testMultipleOptionalArguments[7]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@2bdf6c7c], [Ljava.lang.String;@13ac1657, false, 0, -0.2941) 0.021s passed
testMultipleOptionalArguments[8]([org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff@30be6a05], [Ljava.lang.String;@6812708d, false, 0, 0) 0.015s passed
testNoAnnotations 0.012s passed
testOverridingInstancesWithGetInstance 0s passed
testPossibleDeNovoAnnotationArguments 0.011s passed
testToolDefaultAnnotationArgumentsOverridingFromCommandLine 0.030s passed
testUseAllAnnotations 0.029s passed
testUseAllAnnotationsDisableToolDefaultAnnotaiotns 0.025s passed

Standard error

20:25:02.137 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-b2a05c7-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@1f42366]
SLF4J(W): Found provider [ch.qos.logback.classic.spi.LogbackServiceProvider@46c662f2]
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@1f42366]
20:25:02.250 INFO  TestAnnotationsTool - ------------------------------------------------------------
20:25:02.253 INFO  TestAnnotationsTool - The Genome Analysis Toolkit (GATK) vb2a05c7-SNAPSHOT
20:25:02.253 INFO  TestAnnotationsTool - For support and documentation go to https://software.broadinstitute.org/gatk/
20:25:02.253 INFO  TestAnnotationsTool - Executing as root@5a0ca63d86e8 on Linux v6.8.0-1020-azure amd64
20:25:02.253 INFO  TestAnnotationsTool - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
20:25:02.253 INFO  TestAnnotationsTool - Start Date/Time: February 10, 2025 at 8:25:02 PM GMT
20:25:02.253 INFO  TestAnnotationsTool - ------------------------------------------------------------
20:25:02.254 INFO  TestAnnotationsTool - ------------------------------------------------------------
20:25:02.256 INFO  TestAnnotationsTool - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:25:02.257 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:25:02.257 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:25:02.257 INFO  TestAnnotationsTool - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:25:02.257 INFO  TestAnnotationsTool - Deflater: IntelDeflater
20:25:02.257 INFO  TestAnnotationsTool - Inflater: IntelInflater
20:25:02.257 INFO  TestAnnotationsTool - GCS max retries/reopens: 20
20:25:02.258 INFO  TestAnnotationsTool - Requester pays: disabled
20:25:02.258 INFO  TestAnnotationsTool - Initializing engine
20:25:02.322 INFO  TestAnnotationsTool - Done initializing engine
20:25:02.323 INFO  ProgressMeter - Starting traversal
20:25:02.324 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
20:25:02.326 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
20:25:02.326 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
20:25:02.326 INFO  TestAnnotationsTool - Shutting down engine
[February 10, 2025 at 8:25:02 PM GMT] org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptorUnitTest$TestAnnotationsTool done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=140509184
20:25:02.785 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:25:02.872 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:25:02.899 WARN  GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
20:25:03.133 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
20:25:03.185 INFO  PedReader - Phenotype is other? false
20:25:03.186 INFO  PedReader - Phenotype is other? false
20:25:03.201 INFO  PedReader - Phenotype is other? false
20:25:03.201 INFO  PedReader - Phenotype is other? false
20:25:03.202 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 1:10 and possibly subsequent; at least 10 samples must have called genotypes
20:25:03.257 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default
20:25:03.257 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation (InbreedingCoeff) is enabled for this tool by default