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

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

tests
0

failures
0

ignored
16.683s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.329s passed
testAlleleCountStratWithMLE 0.102s passed
testBadACValue 0.074s passed
testCompOverlap 0.144s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.315s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.274s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.274s passed
testEvalTrackWithoutGenotypes 0.354s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.108s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.080s passed
testFunctionClassWithSnpeff 0.683s passed
testFundamentalsCountVariantsNoCompRod 0.086s passed
testFundamentalsCountVariantsSNPsAndIndels 0.094s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.120s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.091s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.091s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.116s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.091s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.090s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.091s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.091s passed
testIncompatibleEvalAndStrat 0.084s passed
testIntervalStrat 0.081s passed
testMVEvalFamilyStrat 0.094s passed
testModernVCFWithLargeIndels 0.510s passed
testMultipleCompTracks 0.266s passed
testMultipleEvalTracksAlleleCountWithMerge 0.098s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.089s passed
testMultipleEvalTracksWithoutGenotypes 0.428s passed
testOutputFileCreation 0.112s passed
testPedigreeValidation[0](SILENT, false) 0.085s passed
testPedigreeValidation[1](STRICT, true) 0.078s passed
testPedigreeValidation[2](null, true) 0.076s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.174s passed
testPrintMissingComp 0.111s passed
testSelect1 8.817s passed
testStandardIndelEval 0.950s 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) 0.081s 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) 0.075s 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) 0.077s 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 0.089s passed
testWithoutAC0 0.080s passed

Standard output

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[15:22:09] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[15:22:10] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[15:22:10] Executing test VariantEvalIntegrationTest:testBadACValue
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[15:22:10] Executing test VariantEvalIntegrationTest:testCompOverlap
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[15:22:10] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[15:22:10] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[15:22:11] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[15:22:11] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[15:22:11] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[15:22:11] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[15:22:12] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[15:22:12] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[15:22:12] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[15:22:12] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[15:22:13] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[15:22:13] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[15:22:13] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[15:22:13] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[15:22:13] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[15:22:13] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[15:22:13] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[15:22:13] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[15:22:13] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[15:22:13] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[15:22:13] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[15:22:14] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[15:22:14] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[15:22:14] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[15:22:14] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[15:22:15] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[15:22:15] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[15:22:15] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[15:22:15] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[15:22:15] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[15:22:15] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[15:22:15] Executing test VariantEvalIntegrationTest:testSelect1
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[15:22:24] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[15:22:25] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[15:22:26] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[15:22:26] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[15:22:26] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[15:22:26] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[15:22:26] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[15:22:26] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[15:22:26] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[May 27, 2025 at 3:22:10 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:10 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:10 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:10 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:10 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:11 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:11 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:11 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:11 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:14 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:14 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:14 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:14 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 3:22:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000