Class org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers.varianteval > VariantEvalIntegrationTest
45

tests
0

failures
0

ignored
16.771s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.104s passed
testAlleleCountStratWithMLE 0.091s passed
testBadACValue 0.067s passed
testCompOverlap 0.137s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.357s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.321s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.307s passed
testEvalTrackWithoutGenotypes 0.362s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.098s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.076s passed
testFunctionClassWithSnpeff 0.688s passed
testFundamentalsCountVariantsNoCompRod 0.073s passed
testFundamentalsCountVariantsSNPsAndIndels 0.081s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.143s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.084s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.079s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.109s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.080s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.081s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.092s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.087s passed
testIncompatibleEvalAndStrat 0.083s passed
testIntervalStrat 0.073s passed
testMVEvalFamilyStrat 0.094s passed
testModernVCFWithLargeIndels 0.644s passed
testMultipleCompTracks 0.324s passed
testMultipleEvalTracksAlleleCountWithMerge 0.088s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.077s passed
testMultipleEvalTracksWithoutGenotypes 0.374s passed
testOutputFileCreation 0.085s passed
testPedigreeValidation[0](SILENT, false) 0.072s passed
testPedigreeValidation[1](STRICT, true) 0.069s passed
testPedigreeValidation[2](null, true) 0.066s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.153s passed
testPrintMissingComp 0.083s passed
testSelect1 9.282s passed
testStandardIndelEval 0.857s passed
testStratifySamplesAndExcludeMonomorphicSites 0.342s passed
testVEMendelianViolationEvaluator 0.070s passed
testValidationReport[0](sites-sites, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportEval.noGenotypes.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportComp.noGenotypes.vcf) 0.066s passed
testValidationReport[1](sites-genotypes, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportEval.noGenotypes.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportComp.vcf) 0.066s passed
testValidationReport[2](genotypes-sites, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportEval.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportComp.noGenotypes.vcf) 0.068s passed
testValidationReport[3](genotypes-genotypes, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportEval.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval/validationReportComp.vcf) 0.068s passed
testWithAC0 0.080s passed
testWithoutAC0 0.070s passed

Standard output

--------------------------------------------------------------------------------
[22:54:32] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
--------------------------------------------------------------------------------
[22:54:32] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
--------------------------------------------------------------------------------
[22:54:33] Executing test VariantEvalIntegrationTest:testBadACValue
--------------------------------------------------------------------------------
[22:54:33] Executing test VariantEvalIntegrationTest:testCompOverlap
--------------------------------------------------------------------------------
[22:54:33] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
--------------------------------------------------------------------------------
[22:54:33] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
--------------------------------------------------------------------------------
[22:54:33] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
--------------------------------------------------------------------------------
[22:54:34] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
--------------------------------------------------------------------------------
[22:54:34] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
--------------------------------------------------------------------------------
[22:54:34] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
--------------------------------------------------------------------------------
[22:54:34] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
--------------------------------------------------------------------------------
[22:54:35] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
--------------------------------------------------------------------------------
[22:54:35] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
--------------------------------------------------------------------------------
[22:54:35] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
--------------------------------------------------------------------------------
[22:54:35] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
--------------------------------------------------------------------------------
[22:54:35] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
--------------------------------------------------------------------------------
[22:54:35] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
--------------------------------------------------------------------------------
[22:54:36] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
--------------------------------------------------------------------------------
[22:54:36] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
--------------------------------------------------------------------------------
[22:54:36] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
--------------------------------------------------------------------------------
[22:54:36] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
--------------------------------------------------------------------------------
[22:54:36] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
--------------------------------------------------------------------------------
[22:54:36] Executing test VariantEvalIntegrationTest:testIntervalStrat
--------------------------------------------------------------------------------
[22:54:36] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
--------------------------------------------------------------------------------
[22:54:36] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
--------------------------------------------------------------------------------
[22:54:37] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
--------------------------------------------------------------------------------
[22:54:37] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
--------------------------------------------------------------------------------
[22:54:37] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
--------------------------------------------------------------------------------
[22:54:37] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
--------------------------------------------------------------------------------
[22:54:38] Executing test VariantEvalIntegrationTest:testPedigreeValidation
--------------------------------------------------------------------------------
[22:54:38] Executing test VariantEvalIntegrationTest:testPedigreeValidation
--------------------------------------------------------------------------------
[22:54:38] Executing test VariantEvalIntegrationTest:testPedigreeValidation
--------------------------------------------------------------------------------
[22:54:38] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
--------------------------------------------------------------------------------
[22:54:38] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
--------------------------------------------------------------------------------
[22:54:38] Executing test VariantEvalIntegrationTest:testPrintMissingComp
--------------------------------------------------------------------------------
[22:54:38] Executing test VariantEvalIntegrationTest:testSelect1
--------------------------------------------------------------------------------
[22:54:47] Executing test VariantEvalIntegrationTest:testStandardIndelEval
--------------------------------------------------------------------------------
[22:54:48] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
--------------------------------------------------------------------------------
[22:54:49] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
--------------------------------------------------------------------------------
[22:54:49] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
--------------------------------------------------------------------------------
[22:54:49] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
--------------------------------------------------------------------------------
[22:54:49] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
--------------------------------------------------------------------------------
[22:54:49] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
--------------------------------------------------------------------------------
[22:54:49] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
--------------------------------------------------------------------------------
[22:54:49] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[March 28, 2025 at 10:54:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424