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

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

tests
0

failures
0

ignored
17.514s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.345s passed
testAlleleCountStratWithMLE 0.128s passed
testBadACValue 0.107s passed
testCompOverlap 0.152s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.470s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.238s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.329s passed
testEvalTrackWithoutGenotypes 0.515s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.154s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.106s passed
testFunctionClassWithSnpeff 0.763s passed
testFundamentalsCountVariantsNoCompRod 0.087s passed
testFundamentalsCountVariantsSNPsAndIndels 0.093s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.123s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.090s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.095s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.114s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.088s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.090s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.103s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.094s passed
testIncompatibleEvalAndStrat 0.076s passed
testIntervalStrat 0.086s passed
testMVEvalFamilyStrat 0.099s passed
testModernVCFWithLargeIndels 0.703s passed
testMultipleCompTracks 0.400s passed
testMultipleEvalTracksAlleleCountWithMerge 0.103s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.095s passed
testMultipleEvalTracksWithoutGenotypes 0.506s passed
testOutputFileCreation 0.107s passed
testPedigreeValidation[0](SILENT, false) 0.084s passed
testPedigreeValidation[1](STRICT, true) 0.077s passed
testPedigreeValidation[2](null, true) 0.076s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.176s passed
testPrintMissingComp 0.099s passed
testSelect1 8.896s passed
testStandardIndelEval 0.731s passed
testStratifySamplesAndExcludeMonomorphicSites 0.362s passed
testVEMendelianViolationEvaluator 0.079s 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) 0.079s 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) 0.079s 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) 0.076s 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) 0.075s passed
testWithAC0 0.087s passed
testWithoutAC0 0.079s passed

Standard output

--------------------------------------------------------------------------------
[16:10:33] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
--------------------------------------------------------------------------------
[16:10:34] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
--------------------------------------------------------------------------------
[16:10:34] Executing test VariantEvalIntegrationTest:testBadACValue
--------------------------------------------------------------------------------
[16:10:34] Executing test VariantEvalIntegrationTest:testCompOverlap
--------------------------------------------------------------------------------
[16:10:34] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
--------------------------------------------------------------------------------
[16:10:35] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
--------------------------------------------------------------------------------
[16:10:35] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
--------------------------------------------------------------------------------
[16:10:35] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
--------------------------------------------------------------------------------
[16:10:36] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
--------------------------------------------------------------------------------
[16:10:36] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
--------------------------------------------------------------------------------
[16:10:36] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
--------------------------------------------------------------------------------
[16:10:37] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
--------------------------------------------------------------------------------
[16:10:37] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
--------------------------------------------------------------------------------
[16:10:37] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
--------------------------------------------------------------------------------
[16:10:37] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
--------------------------------------------------------------------------------
[16:10:37] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
--------------------------------------------------------------------------------
[16:10:37] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
--------------------------------------------------------------------------------
[16:10:37] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
--------------------------------------------------------------------------------
[16:10:37] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
--------------------------------------------------------------------------------
[16:10:38] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
--------------------------------------------------------------------------------
[16:10:38] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
--------------------------------------------------------------------------------
[16:10:38] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
--------------------------------------------------------------------------------
[16:10:38] Executing test VariantEvalIntegrationTest:testIntervalStrat
--------------------------------------------------------------------------------
[16:10:38] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
--------------------------------------------------------------------------------
[16:10:38] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
--------------------------------------------------------------------------------
[16:10:39] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
--------------------------------------------------------------------------------
[16:10:39] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
--------------------------------------------------------------------------------
[16:10:39] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
--------------------------------------------------------------------------------
[16:10:39] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
--------------------------------------------------------------------------------
[16:10:40] Executing test VariantEvalIntegrationTest:testPedigreeValidation
--------------------------------------------------------------------------------
[16:10:40] Executing test VariantEvalIntegrationTest:testPedigreeValidation
--------------------------------------------------------------------------------
[16:10:40] Executing test VariantEvalIntegrationTest:testPedigreeValidation
--------------------------------------------------------------------------------
[16:10:40] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
--------------------------------------------------------------------------------
[16:10:40] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
--------------------------------------------------------------------------------
[16:10:40] Executing test VariantEvalIntegrationTest:testPrintMissingComp
--------------------------------------------------------------------------------
[16:10:40] Executing test VariantEvalIntegrationTest:testSelect1
--------------------------------------------------------------------------------
[16:10:49] Executing test VariantEvalIntegrationTest:testStandardIndelEval
--------------------------------------------------------------------------------
[16:10:50] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
--------------------------------------------------------------------------------
[16:10:50] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
--------------------------------------------------------------------------------
[16:10:51] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
--------------------------------------------------------------------------------
[16:10:51] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
--------------------------------------------------------------------------------
[16:10:51] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
--------------------------------------------------------------------------------
[16:10:51] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
--------------------------------------------------------------------------------
[16:10:51] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
--------------------------------------------------------------------------------
[16:10:51] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[May 27, 2025 at 4:10:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:39 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:39 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:39 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:39 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:49 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:51 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168