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

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

tests
0

failures
0

ignored
16.303s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.098s passed
testAlleleCountStratWithMLE 0.083s passed
testBadACValue 0.063s passed
testCompOverlap 0.132s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.299s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.273s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.337s passed
testEvalTrackWithoutGenotypes 0.339s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.089s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.070s passed
testFunctionClassWithSnpeff 0.671s passed
testFundamentalsCountVariantsNoCompRod 0.074s passed
testFundamentalsCountVariantsSNPsAndIndels 0.079s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.118s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.080s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.078s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.108s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.079s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.078s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.082s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.092s passed
testIncompatibleEvalAndStrat 0.066s passed
testIntervalStrat 0.068s passed
testMVEvalFamilyStrat 0.078s passed
testModernVCFWithLargeIndels 0.508s passed
testMultipleCompTracks 0.235s passed
testMultipleEvalTracksAlleleCountWithMerge 0.083s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.077s passed
testMultipleEvalTracksWithoutGenotypes 0.455s passed
testOutputFileCreation 0.092s passed
testPedigreeValidation[0](SILENT, false) 0.077s passed
testPedigreeValidation[1](STRICT, true) 0.068s passed
testPedigreeValidation[2](null, true) 0.061s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.144s passed
testPrintMissingComp 0.089s passed
testSelect1 9.359s passed
testStandardIndelEval 0.641s passed
testStratifySamplesAndExcludeMonomorphicSites 0.337s passed
testVEMendelianViolationEvaluator 0.066s 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) 0.096s 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) 0.083s 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) 0.072s 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) 0.072s passed
testWithAC0 0.076s passed
testWithoutAC0 0.078s passed

Standard output

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[15:07:29] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[15:07:29] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[15:07:29] Executing test VariantEvalIntegrationTest:testBadACValue
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[15:07:29] Executing test VariantEvalIntegrationTest:testCompOverlap
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[15:07:29] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[15:07:29] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[15:07:30] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[15:07:30] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[15:07:30] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[15:07:30] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[15:07:30] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[15:07:31] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[15:07:31] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[15:07:31] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[15:07:31] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[15:07:31] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[15:07:32] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[15:07:32] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[15:07:32] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[15:07:32] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[15:07:32] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[15:07:32] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[15:07:32] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[15:07:32] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[15:07:32] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[15:07:33] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[15:07:33] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[15:07:33] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[15:07:33] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[15:07:34] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[15:07:34] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[15:07:34] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[15:07:34] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[15:07:34] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[15:07:34] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[15:07:34] Executing test VariantEvalIntegrationTest:testSelect1
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[15:07:43] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[15:07:44] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[15:07:44] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[15:07:44] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[15:07:45] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[15:07:45] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[15:07:45] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[15:07:45] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[15:07:45] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[May 27, 2025 at 3:07:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304