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

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

tests
0

failures
0

ignored
17.037s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.347s passed
testAlleleCountStratWithMLE 0.121s passed
testBadACValue 0.078s passed
testCompOverlap 0.152s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.327s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.289s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.264s passed
testEvalTrackWithoutGenotypes 0.385s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.114s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.081s passed
testFunctionClassWithSnpeff 0.702s passed
testFundamentalsCountVariantsNoCompRod 0.091s passed
testFundamentalsCountVariantsSNPsAndIndels 0.093s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.132s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.090s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.093s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.113s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.092s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.091s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.095s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.089s passed
testIncompatibleEvalAndStrat 0.076s passed
testIntervalStrat 0.082s passed
testMVEvalFamilyStrat 0.097s passed
testModernVCFWithLargeIndels 0.503s passed
testMultipleCompTracks 0.274s passed
testMultipleEvalTracksAlleleCountWithMerge 0.100s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.094s passed
testMultipleEvalTracksWithoutGenotypes 0.432s passed
testOutputFileCreation 0.122s passed
testPedigreeValidation[0](SILENT, false) 0.083s passed
testPedigreeValidation[1](STRICT, true) 0.077s passed
testPedigreeValidation[2](null, true) 0.094s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.223s passed
testPrintMissingComp 0.127s passed
testSelect1 9.184s passed
testStandardIndelEval 0.656s passed
testStratifySamplesAndExcludeMonomorphicSites 0.369s passed
testVEMendelianViolationEvaluator 0.084s 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) 0.085s 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) 0.088s 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) 0.086s 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) 0.079s passed
testWithAC0 0.098s passed
testWithoutAC0 0.085s passed

Standard output

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[19:24:00] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[19:24:00] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[19:24:00] Executing test VariantEvalIntegrationTest:testBadACValue
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[19:24:00] Executing test VariantEvalIntegrationTest:testCompOverlap
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[19:24:00] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[19:24:01] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[19:24:01] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[19:24:01] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[19:24:02] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[19:24:02] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[19:24:02] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[19:24:02] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[19:24:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[19:24:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[19:24:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[19:24:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[19:24:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[19:24:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[19:24:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[19:24:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[19:24:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[19:24:03] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[19:24:04] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[19:24:04] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[19:24:04] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[19:24:04] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[19:24:04] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[19:24:05] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[19:24:05] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[19:24:05] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[19:24:05] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[19:24:05] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[19:24:05] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[19:24:06] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[19:24:06] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[19:24:06] Executing test VariantEvalIntegrationTest:testSelect1
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[19:24:15] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[19:24:16] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[19:24:16] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[19:24:16] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[19:24:16] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[19:24:16] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[19:24:16] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[19:24:16] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[19:24:17] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[May 19, 2025 at 7:24:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:15 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:16 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 7:24:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000