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

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

tests
0

failures
0

ignored
17.766s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.343s passed
testAlleleCountStratWithMLE 0.113s passed
testBadACValue 0.098s passed
testCompOverlap 0.141s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.429s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.276s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.253s passed
testEvalTrackWithoutGenotypes 0.549s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.156s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.119s passed
testFunctionClassWithSnpeff 0.836s passed
testFundamentalsCountVariantsNoCompRod 0.094s passed
testFundamentalsCountVariantsSNPsAndIndels 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.116s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.096s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.104s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.126s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.088s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.088s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.096s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.093s passed
testIncompatibleEvalAndStrat 0.078s passed
testIntervalStrat 0.083s passed
testMVEvalFamilyStrat 0.112s passed
testModernVCFWithLargeIndels 0.802s passed
testMultipleCompTracks 0.380s passed
testMultipleEvalTracksAlleleCountWithMerge 0.142s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.122s passed
testMultipleEvalTracksWithoutGenotypes 0.440s passed
testOutputFileCreation 0.104s passed
testPedigreeValidation[0](SILENT, false) 0.078s passed
testPedigreeValidation[1](STRICT, true) 0.078s passed
testPedigreeValidation[2](null, true) 0.080s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.178s passed
testPrintMissingComp 0.101s passed
testSelect1 8.954s passed
testStandardIndelEval 0.758s passed
testStratifySamplesAndExcludeMonomorphicSites 0.380s passed
testVEMendelianViolationEvaluator 0.088s 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) 0.084s 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) 0.083s 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) 0.083s 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) 0.076s passed
testWithAC0 0.095s passed
testWithoutAC0 0.086s passed

Standard output

--------------------------------------------------------------------------------
[21:10:46] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
--------------------------------------------------------------------------------
[21:10:47] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
--------------------------------------------------------------------------------
[21:10:47] Executing test VariantEvalIntegrationTest:testBadACValue
--------------------------------------------------------------------------------
[21:10:47] Executing test VariantEvalIntegrationTest:testCompOverlap
--------------------------------------------------------------------------------
[21:10:47] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
--------------------------------------------------------------------------------
[21:10:47] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
--------------------------------------------------------------------------------
[21:10:48] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
--------------------------------------------------------------------------------
[21:10:48] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
--------------------------------------------------------------------------------
[21:10:48] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
--------------------------------------------------------------------------------
[21:10:49] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
--------------------------------------------------------------------------------
[21:10:49] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
--------------------------------------------------------------------------------
[21:10:50] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
--------------------------------------------------------------------------------
[21:10:50] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
--------------------------------------------------------------------------------
[21:10:50] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
--------------------------------------------------------------------------------
[21:10:50] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
--------------------------------------------------------------------------------
[21:10:50] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
--------------------------------------------------------------------------------
[21:10:50] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
--------------------------------------------------------------------------------
[21:10:50] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
--------------------------------------------------------------------------------
[21:10:50] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
--------------------------------------------------------------------------------
[21:10:50] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
--------------------------------------------------------------------------------
[21:10:50] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
--------------------------------------------------------------------------------
[21:10:51] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
--------------------------------------------------------------------------------
[21:10:51] Executing test VariantEvalIntegrationTest:testIntervalStrat
--------------------------------------------------------------------------------
[21:10:51] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
--------------------------------------------------------------------------------
[21:10:51] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
--------------------------------------------------------------------------------
[21:10:52] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
--------------------------------------------------------------------------------
[21:10:52] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
--------------------------------------------------------------------------------
[21:10:52] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
--------------------------------------------------------------------------------
[21:10:52] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
--------------------------------------------------------------------------------
[21:10:53] Executing test VariantEvalIntegrationTest:testPedigreeValidation
--------------------------------------------------------------------------------
[21:10:53] Executing test VariantEvalIntegrationTest:testPedigreeValidation
--------------------------------------------------------------------------------
[21:10:53] Executing test VariantEvalIntegrationTest:testPedigreeValidation
--------------------------------------------------------------------------------
[21:10:53] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
--------------------------------------------------------------------------------
[21:10:53] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
--------------------------------------------------------------------------------
[21:10:53] Executing test VariantEvalIntegrationTest:testPrintMissingComp
--------------------------------------------------------------------------------
[21:10:53] Executing test VariantEvalIntegrationTest:testSelect1
--------------------------------------------------------------------------------
[21:11:02] Executing test VariantEvalIntegrationTest:testStandardIndelEval
--------------------------------------------------------------------------------
[21:11:03] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
--------------------------------------------------------------------------------
[21:11:03] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
--------------------------------------------------------------------------------
[21:11:03] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
--------------------------------------------------------------------------------
[21:11:04] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
--------------------------------------------------------------------------------
[21:11:04] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
--------------------------------------------------------------------------------
[21:11:04] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
--------------------------------------------------------------------------------
[21:11:04] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
--------------------------------------------------------------------------------
[21:11:04] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[June 12, 2025 at 9:10:47 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:47 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:47 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:47 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:47 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:48 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:48 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:48 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:49 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:49 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:10:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760