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

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

tests
0

failures
0

ignored
16.650s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.109s passed
testAlleleCountStratWithMLE 0.090s passed
testBadACValue 0.069s passed
testCompOverlap 0.142s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.316s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.290s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.290s passed
testEvalTrackWithoutGenotypes 0.345s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.097s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.078s passed
testFunctionClassWithSnpeff 0.697s passed
testFundamentalsCountVariantsNoCompRod 0.080s passed
testFundamentalsCountVariantsSNPsAndIndels 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.115s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.084s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.090s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.151s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.089s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.083s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.086s passed
testIncompatibleEvalAndStrat 0.086s passed
testIntervalStrat 0.076s passed
testMVEvalFamilyStrat 0.097s passed
testModernVCFWithLargeIndels 0.726s passed
testMultipleCompTracks 0.296s passed
testMultipleEvalTracksAlleleCountWithMerge 0.089s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.080s passed
testMultipleEvalTracksWithoutGenotypes 0.381s passed
testOutputFileCreation 0.090s passed
testPedigreeValidation[0](SILENT, false) 0.086s passed
testPedigreeValidation[1](STRICT, true) 0.094s passed
testPedigreeValidation[2](null, true) 0.070s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.158s passed
testPrintMissingComp 0.085s passed
testSelect1 9.162s passed
testStandardIndelEval 0.697s passed
testStratifySamplesAndExcludeMonomorphicSites 0.368s passed
testVEMendelianViolationEvaluator 0.076s 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) 0.072s 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) 0.073s 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) 0.073s 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 0.085s passed
testWithoutAC0 0.082s passed

Standard output

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[15:54:44] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[15:54:44] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[15:54:44] Executing test VariantEvalIntegrationTest:testBadACValue
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[15:54:44] Executing test VariantEvalIntegrationTest:testCompOverlap
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[15:54:44] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[15:54:45] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[15:54:45] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[15:54:45] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[15:54:46] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[15:54:46] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[15:54:46] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[15:54:47] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[15:54:47] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[15:54:47] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[15:54:47] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[15:54:47] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[15:54:47] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[15:54:47] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[15:54:47] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[15:54:47] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[15:54:47] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[15:54:48] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[15:54:48] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[15:54:48] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[15:54:48] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[15:54:48] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[15:54:49] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[15:54:49] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[15:54:49] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[15:54:49] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[15:54:50] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[15:54:50] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[15:54:50] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[15:54:50] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[15:54:50] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[15:54:50] Executing test VariantEvalIntegrationTest:testSelect1
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[15:54:59] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[15:55:00] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[15:55:00] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[15:55:00] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[15:55:00] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[15:55:00] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[15:55:00] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[15:55:01] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[15:55:01] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[May 19, 2025 at 3:54:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:54:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848
[May 19, 2025 at 3:55:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1308622848