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

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

tests
0

failures
0

ignored
17.356s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.377s passed
testAlleleCountStratWithMLE 0.121s passed
testBadACValue 0.102s passed
testCompOverlap 0.163s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.316s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.267s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.337s passed
testEvalTrackWithoutGenotypes 0.403s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.115s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.085s passed
testFunctionClassWithSnpeff 0.681s passed
testFundamentalsCountVariantsNoCompRod 0.088s passed
testFundamentalsCountVariantsSNPsAndIndels 0.094s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.125s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.101s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.095s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.122s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.094s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.089s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.103s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.108s passed
testIncompatibleEvalAndStrat 0.081s passed
testIntervalStrat 0.084s passed
testMVEvalFamilyStrat 0.096s passed
testModernVCFWithLargeIndels 0.555s passed
testMultipleCompTracks 0.261s passed
testMultipleEvalTracksAlleleCountWithMerge 0.101s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.093s passed
testMultipleEvalTracksWithoutGenotypes 0.458s passed
testOutputFileCreation 0.109s passed
testPedigreeValidation[0](SILENT, false) 0.089s passed
testPedigreeValidation[1](STRICT, true) 0.079s passed
testPedigreeValidation[2](null, true) 0.077s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.184s passed
testPrintMissingComp 0.103s passed
testSelect1 9.122s passed
testStandardIndelEval 0.927s passed
testStratifySamplesAndExcludeMonomorphicSites 0.372s passed
testVEMendelianViolationEvaluator 0.083s 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) 0.082s 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) 0.081s 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) 0.079s passed
testWithAC0 0.089s passed
testWithoutAC0 0.082s passed

Standard output

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[14:15:03] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[14:15:03] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[14:15:03] Executing test VariantEvalIntegrationTest:testBadACValue
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[14:15:04] Executing test VariantEvalIntegrationTest:testCompOverlap
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[14:15:04] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[14:15:04] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[14:15:04] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[14:15:05] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[14:15:05] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[14:15:05] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[14:15:05] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[14:15:06] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[14:15:06] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[14:15:06] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[14:15:06] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[14:15:06] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[14:15:06] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[14:15:07] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[14:15:07] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[14:15:07] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[14:15:07] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[14:15:07] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[14:15:07] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[14:15:07] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[14:15:07] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[14:15:08] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[14:15:08] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[14:15:08] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[14:15:08] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[14:15:09] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[14:15:09] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[14:15:09] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[14:15:09] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[14:15:09] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[14:15:09] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[14:15:09] Executing test VariantEvalIntegrationTest:testSelect1
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[14:15:18] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[14:15:19] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[14:15:20] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[14:15:20] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[14:15:20] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[14:15:20] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[14:15:20] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[14:15:20] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[14:15:20] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[May 27, 2025 at 2:15:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000