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

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

tests
0

failures
0

ignored
17.214s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.292s passed
testAlleleCountStratWithMLE 0.101s passed
testBadACValue 0.074s passed
testCompOverlap 0.151s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.313s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.289s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.393s passed
testEvalTrackWithoutGenotypes 0.381s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.116s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.082s passed
testFunctionClassWithSnpeff 0.691s passed
testFundamentalsCountVariantsNoCompRod 0.086s passed
testFundamentalsCountVariantsSNPsAndIndels 0.092s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.126s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.091s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.096s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.117s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.090s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.100s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.138s passed
testIncompatibleEvalAndStrat 0.074s passed
testIntervalStrat 0.081s passed
testMVEvalFamilyStrat 0.110s passed
testModernVCFWithLargeIndels 0.711s passed
testMultipleCompTracks 0.371s passed
testMultipleEvalTracksAlleleCountWithMerge 0.134s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.093s passed
testMultipleEvalTracksWithoutGenotypes 0.508s passed
testOutputFileCreation 0.106s passed
testPedigreeValidation[0](SILENT, false) 0.082s passed
testPedigreeValidation[1](STRICT, true) 0.074s passed
testPedigreeValidation[2](null, true) 0.077s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.182s passed
testPrintMissingComp 0.101s passed
testSelect1 8.878s passed
testStandardIndelEval 0.789s passed
testStratifySamplesAndExcludeMonomorphicSites 0.369s passed
testVEMendelianViolationEvaluator 0.087s 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) 0.077s 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) 0.077s 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 0.090s passed
testWithoutAC0 0.085s passed

Standard output

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[17:00:00] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[17:00:00] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[17:00:00] Executing test VariantEvalIntegrationTest:testBadACValue
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[17:00:00] Executing test VariantEvalIntegrationTest:testCompOverlap
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[17:00:01] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[17:00:01] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[17:00:01] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[17:00:02] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[17:00:02] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[17:00:02] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[17:00:02] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[17:00:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[17:00:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[17:00:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[17:00:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[17:00:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[17:00:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[17:00:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[17:00:04] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[17:00:04] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[17:00:04] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[17:00:04] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[17:00:04] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[17:00:04] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[17:00:04] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[17:00:05] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[17:00:05] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[17:00:05] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[17:00:05] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[17:00:06] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[17:00:06] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[17:00:06] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[17:00:06] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[17:00:06] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[17:00:06] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[17:00:07] Executing test VariantEvalIntegrationTest:testSelect1
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[17:00:15] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[17:00:16] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[17:00:17] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[17:00:17] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[17:00:17] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[17:00:17] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[17:00:17] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[17:00:17] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[17:00:17] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[May 27, 2025 at 5:00:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 5:00:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000