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

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

tests
0

failures
0

ignored
16.659s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.102s passed
testAlleleCountStratWithMLE 0.088s passed
testBadACValue 0.068s passed
testCompOverlap 0.127s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.287s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.234s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.227s passed
testEvalTrackWithoutGenotypes 0.359s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.086s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.070s passed
testFunctionClassWithSnpeff 0.681s passed
testFundamentalsCountVariantsNoCompRod 0.077s passed
testFundamentalsCountVariantsSNPsAndIndels 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.107s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.086s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.124s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.084s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.084s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.085s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.084s passed
testIncompatibleEvalAndStrat 0.073s passed
testIntervalStrat 0.074s passed
testMVEvalFamilyStrat 0.080s passed
testModernVCFWithLargeIndels 0.391s passed
testMultipleCompTracks 0.228s passed
testMultipleEvalTracksAlleleCountWithMerge 0.087s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.079s passed
testMultipleEvalTracksWithoutGenotypes 0.361s passed
testOutputFileCreation 0.084s passed
testPedigreeValidation[0](SILENT, false) 0.072s passed
testPedigreeValidation[1](STRICT, true) 0.073s passed
testPedigreeValidation[2](null, true) 0.073s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.162s passed
testPrintMissingComp 0.082s passed
testSelect1 10.011s passed
testStandardIndelEval 0.602s passed
testStratifySamplesAndExcludeMonomorphicSites 0.371s 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) 0.072s 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) 0.072s 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) 0.075s passed
testWithAC0 0.080s passed
testWithoutAC0 0.077s passed

Standard output

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[17:57:58] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[17:57:58] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[17:57:58] Executing test VariantEvalIntegrationTest:testBadACValue
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[17:57:58] Executing test VariantEvalIntegrationTest:testCompOverlap
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[17:57:59] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[17:57:59] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[17:57:59] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[17:57:59] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[17:58:00] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[17:58:00] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[17:58:00] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[17:58:01] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[17:58:01] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[17:58:01] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[17:58:01] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[17:58:01] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[17:58:01] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[17:58:01] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[17:58:01] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[17:58:01] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[17:58:01] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[17:58:01] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[17:58:02] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[17:58:02] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[17:58:02] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[17:58:02] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[17:58:02] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[17:58:02] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[17:58:02] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[17:58:03] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[17:58:03] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[17:58:03] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[17:58:03] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[17:58:03] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[17:58:03] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[17:58:03] Executing test VariantEvalIntegrationTest:testSelect1
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[17:58:13] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[17:58:14] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[17:58:14] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[17:58:14] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[17:58:15] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[17:58:15] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[17:58:15] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[17:58:15] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[17:58:15] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[October 27, 2025 at 5:57:58 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:57:58 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:57:58 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:57:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:57:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:57:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:57:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1677721600
[October 27, 2025 at 5:58:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=922746880
[October 27, 2025 at 5:58:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=922746880
[October 27, 2025 at 5:58:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=922746880
[October 27, 2025 at 5:58:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=922746880
[October 27, 2025 at 5:58:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=922746880
[October 27, 2025 at 5:58:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=922746880
[October 27, 2025 at 5:58:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=922746880
[October 27, 2025 at 5:58:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=922746880
[October 27, 2025 at 5:58:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=922746880
[October 27, 2025 at 5:58:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=922746880
[October 27, 2025 at 5:58:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=922746880
[October 27, 2025 at 5:58:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=922746880
[October 27, 2025 at 5:58:13 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.17 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:14 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784