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

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

tests
0

failures
0

ignored
16.104s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.103s passed
testAlleleCountStratWithMLE 0.086s passed
testBadACValue 0.065s passed
testCompOverlap 0.135s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.287s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.214s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.242s passed
testEvalTrackWithoutGenotypes 0.389s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.089s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.069s passed
testFunctionClassWithSnpeff 0.695s passed
testFundamentalsCountVariantsNoCompRod 0.072s passed
testFundamentalsCountVariantsSNPsAndIndels 0.077s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.105s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.082s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.079s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.108s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.078s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.079s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.086s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.083s passed
testIncompatibleEvalAndStrat 0.067s passed
testIntervalStrat 0.068s passed
testMVEvalFamilyStrat 0.079s passed
testModernVCFWithLargeIndels 0.645s passed
testMultipleCompTracks 0.284s passed
testMultipleEvalTracksAlleleCountWithMerge 0.085s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.074s passed
testMultipleEvalTracksWithoutGenotypes 0.352s passed
testOutputFileCreation 0.091s passed
testPedigreeValidation[0](SILENT, false) 0.077s passed
testPedigreeValidation[1](STRICT, true) 0.066s passed
testPedigreeValidation[2](null, true) 0.062s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.143s passed
testPrintMissingComp 0.077s passed
testSelect1 9.049s passed
testStandardIndelEval 0.814s passed
testStratifySamplesAndExcludeMonomorphicSites 0.350s passed
testVEMendelianViolationEvaluator 0.072s 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) 0.070s 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) 0.068s 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) 0.069s 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) 0.069s passed
testWithAC0 0.078s passed
testWithoutAC0 0.072s passed

Standard output

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[18:25:08] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[18:25:08] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[18:25:08] Executing test VariantEvalIntegrationTest:testBadACValue
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[18:25:08] Executing test VariantEvalIntegrationTest:testCompOverlap
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[18:25:08] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[18:25:09] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[18:25:09] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[18:25:09] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[18:25:10] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[18:25:10] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[18:25:10] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[18:25:10] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[18:25:11] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[18:25:11] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[18:25:11] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[18:25:11] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[18:25:11] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[18:25:11] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[18:25:11] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[18:25:11] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[18:25:11] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[18:25:11] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[18:25:11] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[18:25:11] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[18:25:12] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[18:25:12] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[18:25:12] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[18:25:13] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[18:25:13] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[18:25:13] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[18:25:13] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[18:25:13] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[18:25:13] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[18:25:13] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[18:25:13] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[18:25:14] Executing test VariantEvalIntegrationTest:testSelect1
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[18:25:23] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[18:25:23] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[18:25:24] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[18:25:24] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[18:25:24] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[18:25:24] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[18:25:24] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[18:25:24] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[18:25:24] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[May 27, 2025 at 6:25:08 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:08 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:08 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:08 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:09 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:09 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:09 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:10 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:10 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:10 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:10 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:11 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:12 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728
[May 27, 2025 at 6:25:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1969225728