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

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

tests
0

failures
0

ignored
17.519s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.395s passed
testAlleleCountStratWithMLE 0.114s passed
testBadACValue 0.089s passed
testCompOverlap 0.157s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.341s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.267s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.270s passed
testEvalTrackWithoutGenotypes 0.379s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.112s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.092s passed
testFunctionClassWithSnpeff 0.728s passed
testFundamentalsCountVariantsNoCompRod 0.098s passed
testFundamentalsCountVariantsSNPsAndIndels 0.100s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.134s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.102s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.104s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.123s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.095s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.098s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.099s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.102s passed
testIncompatibleEvalAndStrat 0.085s passed
testIntervalStrat 0.088s passed
testMVEvalFamilyStrat 0.098s passed
testModernVCFWithLargeIndels 0.737s passed
testMultipleCompTracks 0.407s passed
testMultipleEvalTracksAlleleCountWithMerge 0.146s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.087s passed
testMultipleEvalTracksWithoutGenotypes 0.512s passed
testOutputFileCreation 0.136s passed
testPedigreeValidation[0](SILENT, false) 0.091s passed
testPedigreeValidation[1](STRICT, true) 0.082s passed
testPedigreeValidation[2](null, true) 0.087s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.188s passed
testPrintMissingComp 0.116s passed
testSelect1 8.956s passed
testStandardIndelEval 0.752s passed
testStratifySamplesAndExcludeMonomorphicSites 0.371s passed
testVEMendelianViolationEvaluator 0.085s 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) 0.081s 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) 0.080s 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) 0.080s 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 0.091s passed
testWithoutAC0 0.085s passed

Standard output

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[16:12:03] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[16:12:03] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[16:12:03] Executing test VariantEvalIntegrationTest:testBadACValue
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[16:12:03] Executing test VariantEvalIntegrationTest:testCompOverlap
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[16:12:03] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[16:12:04] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[16:12:04] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[16:12:04] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[16:12:05] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[16:12:05] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[16:12:05] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[16:12:05] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[16:12:06] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[16:12:06] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[16:12:06] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[16:12:06] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[16:12:06] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[16:12:06] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[16:12:06] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[16:12:06] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[16:12:06] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[16:12:07] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[16:12:07] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[16:12:07] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[16:12:07] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[16:12:08] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[16:12:08] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[16:12:08] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[16:12:08] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[16:12:09] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[16:12:09] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[16:12:09] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[16:12:09] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[16:12:09] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[16:12:09] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[16:12:09] Executing test VariantEvalIntegrationTest:testSelect1
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[16:12:18] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[16:12:19] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[16:12:19] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[16:12:20] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[16:12:20] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[16:12:20] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[16:12:20] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[16:12:20] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[16:12:20] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[May 19, 2025 at 4:12:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:09 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000