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

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

tests
0

failures
0

ignored
16.640s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.109s passed
testAlleleCountStratWithMLE 0.114s passed
testBadACValue 0.090s passed
testCompOverlap 0.140s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.456s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.278s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.238s passed
testEvalTrackWithoutGenotypes 0.347s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.098s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.075s passed
testFunctionClassWithSnpeff 0.687s passed
testFundamentalsCountVariantsNoCompRod 0.079s passed
testFundamentalsCountVariantsSNPsAndIndels 0.084s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.124s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.091s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.120s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.084s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.082s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.085s passed
testIncompatibleEvalAndStrat 0.072s passed
testIntervalStrat 0.077s passed
testMVEvalFamilyStrat 0.084s passed
testModernVCFWithLargeIndels 0.603s passed
testMultipleCompTracks 0.373s passed
testMultipleEvalTracksAlleleCountWithMerge 0.122s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.107s passed
testMultipleEvalTracksWithoutGenotypes 0.428s passed
testOutputFileCreation 0.091s passed
testPedigreeValidation[0](SILENT, false) 0.069s passed
testPedigreeValidation[1](STRICT, true) 0.064s passed
testPedigreeValidation[2](null, true) 0.064s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.166s passed
testPrintMissingComp 0.092s passed
testSelect1 9.159s passed
testStandardIndelEval 0.627s passed
testStratifySamplesAndExcludeMonomorphicSites 0.389s passed
testVEMendelianViolationEvaluator 0.073s 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) 0.065s 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) 0.066s 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) 0.070s passed
testWithAC0 0.083s passed
testWithoutAC0 0.073s passed

Standard output

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[13:59:41] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[13:59:41] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[13:59:41] Executing test VariantEvalIntegrationTest:testBadACValue
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[13:59:41] Executing test VariantEvalIntegrationTest:testCompOverlap
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[13:59:41] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[13:59:42] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[13:59:42] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[13:59:42] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[13:59:43] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[13:59:43] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[13:59:43] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[13:59:43] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[13:59:43] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[13:59:44] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[13:59:44] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[13:59:44] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[13:59:44] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[13:59:44] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[13:59:44] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[13:59:44] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[13:59:44] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[13:59:44] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[13:59:44] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[13:59:44] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[13:59:45] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[13:59:45] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[13:59:46] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[13:59:46] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[13:59:46] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[13:59:46] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[13:59:46] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[13:59:46] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[13:59:46] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[13:59:47] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[13:59:47] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[13:59:47] Executing test VariantEvalIntegrationTest:testSelect1
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[13:59:56] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[13:59:57] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[13:59:57] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[13:59:57] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[13:59:57] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[13:59:57] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[13:59:57] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[13:59:57] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[13:59:57] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[May 27, 2025 at 1:59:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:56 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464
[May 27, 2025 at 1:59:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1220542464