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

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

tests
0

failures
0

ignored
19.226s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.386s passed
testAlleleCountStratWithMLE 0.144s passed
testBadACValue 0.122s passed
testCompOverlap 0.184s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.495s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.323s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.351s passed
testEvalTrackWithoutGenotypes 0.594s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.171s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.137s passed
testFunctionClassWithSnpeff 0.848s passed
testFundamentalsCountVariantsNoCompRod 0.109s passed
testFundamentalsCountVariantsSNPsAndIndels 0.124s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.158s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.126s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.130s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.155s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.126s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.126s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.126s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.122s passed
testIncompatibleEvalAndStrat 0.105s passed
testIntervalStrat 0.118s passed
testMVEvalFamilyStrat 0.127s passed
testModernVCFWithLargeIndels 0.522s passed
testMultipleCompTracks 0.308s passed
testMultipleEvalTracksAlleleCountWithMerge 0.126s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.123s passed
testMultipleEvalTracksWithoutGenotypes 0.472s passed
testOutputFileCreation 0.149s passed
testPedigreeValidation[0](SILENT, false) 0.114s passed
testPedigreeValidation[1](STRICT, true) 0.106s passed
testPedigreeValidation[2](null, true) 0.104s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.229s passed
testPrintMissingComp 0.127s passed
testSelect1 9.421s passed
testStandardIndelEval 0.911s passed
testStratifySamplesAndExcludeMonomorphicSites 0.432s passed
testVEMendelianViolationEvaluator 0.110s 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) 0.093s 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) 0.094s 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) 0.092s passed
testWithAC0 0.105s passed
testWithoutAC0 0.096s passed

Standard output

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[18:42:54] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[18:42:54] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[18:42:54] Executing test VariantEvalIntegrationTest:testBadACValue
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[18:42:54] Executing test VariantEvalIntegrationTest:testCompOverlap
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[18:42:54] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[18:42:55] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[18:42:55] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[18:42:56] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[18:42:56] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[18:42:56] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[18:42:56] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[18:42:57] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[18:42:57] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[18:42:58] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[18:42:58] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[18:42:58] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[18:42:58] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[18:42:58] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[18:42:58] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[18:42:58] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[18:42:58] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[18:42:59] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[18:42:59] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[18:42:59] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[18:42:59] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[18:42:59] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[18:43:00] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[18:43:00] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[18:43:00] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[18:43:01] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[18:43:01] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[18:43:01] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[18:43:01] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[18:43:01] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[18:43:01] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[18:43:01] Executing test VariantEvalIntegrationTest:testSelect1
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[18:43:11] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[18:43:12] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[18:43:12] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[18:43:12] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[18:43:12] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[18:43:12] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[18:43:12] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[18:43:13] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[18:43:13] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[May 27, 2025 at 6:42:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:57 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:58 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:42:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:01 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:11 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.16 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600