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

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

tests
0

failures
0

ignored
16.105s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.105s passed
testAlleleCountStratWithMLE 0.090s passed
testBadACValue 0.068s passed
testCompOverlap 0.141s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.304s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.241s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.249s passed
testEvalTrackWithoutGenotypes 0.377s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.093s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.071s passed
testFunctionClassWithSnpeff 0.693s passed
testFundamentalsCountVariantsNoCompRod 0.077s passed
testFundamentalsCountVariantsSNPsAndIndels 0.081s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.122s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.085s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.085s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.115s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.082s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.082s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.088s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.097s passed
testIncompatibleEvalAndStrat 0.071s passed
testIntervalStrat 0.076s passed
testMVEvalFamilyStrat 0.085s passed
testModernVCFWithLargeIndels 0.468s passed
testMultipleCompTracks 0.257s passed
testMultipleEvalTracksAlleleCountWithMerge 0.089s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.080s passed
testMultipleEvalTracksWithoutGenotypes 0.398s passed
testOutputFileCreation 0.089s passed
testPedigreeValidation[0](SILENT, false) 0.074s passed
testPedigreeValidation[1](STRICT, true) 0.071s passed
testPedigreeValidation[2](null, true) 0.071s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.179s passed
testPrintMissingComp 0.086s passed
testSelect1 9.163s passed
testStandardIndelEval 0.611s passed
testStratifySamplesAndExcludeMonomorphicSites 0.378s passed
testVEMendelianViolationEvaluator 0.071s 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) 0.068s 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) 0.069s 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) 0.071s 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) 0.073s passed
testWithAC0 0.086s passed
testWithoutAC0 0.075s passed

Standard output

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[20:55:59] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[20:55:59] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[20:55:59] Executing test VariantEvalIntegrationTest:testBadACValue
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[20:55:59] Executing test VariantEvalIntegrationTest:testCompOverlap
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[20:55:59] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[20:56:00] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[20:56:00] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[20:56:00] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[20:56:01] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[20:56:01] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[20:56:01] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[20:56:02] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[20:56:02] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[20:56:02] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[20:56:02] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[20:56:02] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[20:56:02] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[20:56:02] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[20:56:02] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[20:56:02] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[20:56:02] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[20:56:02] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[20:56:03] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[20:56:03] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[20:56:03] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[20:56:03] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[20:56:03] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[20:56:03] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[20:56:04] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[20:56:04] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[20:56:04] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[20:56:04] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[20:56:04] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[20:56:04] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[20:56:04] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[20:56:05] Executing test VariantEvalIntegrationTest:testSelect1
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[20:56:14] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[20:56:14] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[20:56:15] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[20:56:15] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[20:56:15] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[20:56:15] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[20:56:15] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[20:56:15] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[20:56:15] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[June 12, 2025 at 8:55:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:55:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:55:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:55:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192