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

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

tests
0

failures
0

ignored
16.992s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.102s passed
testAlleleCountStratWithMLE 0.090s passed
testBadACValue 0.067s passed
testCompOverlap 0.157s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.445s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.232s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.242s passed
testEvalTrackWithoutGenotypes 0.358s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.095s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.072s passed
testFunctionClassWithSnpeff 0.694s passed
testFundamentalsCountVariantsNoCompRod 0.080s passed
testFundamentalsCountVariantsSNPsAndIndels 0.081s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.115s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.083s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.080s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.111s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.084s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.079s passed
testIncompatibleEvalAndStrat 0.071s passed
testIntervalStrat 0.076s passed
testMVEvalFamilyStrat 0.084s passed
testModernVCFWithLargeIndels 0.768s passed
testMultipleCompTracks 0.375s passed
testMultipleEvalTracksAlleleCountWithMerge 0.120s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.075s passed
testMultipleEvalTracksWithoutGenotypes 0.388s passed
testOutputFileCreation 0.122s passed
testPedigreeValidation[0](SILENT, false) 0.102s passed
testPedigreeValidation[1](STRICT, true) 0.084s passed
testPedigreeValidation[2](null, true) 0.068s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.155s passed
testPrintMissingComp 0.085s passed
testSelect1 9.433s passed
testStandardIndelEval 0.690s passed
testStratifySamplesAndExcludeMonomorphicSites 0.347s passed
testVEMendelianViolationEvaluator 0.075s 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) 0.070s 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) 0.070s 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) 0.069s passed
testWithAC0 0.077s passed
testWithoutAC0 0.074s passed

Standard output

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[16:45:16] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[16:45:16] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[16:45:16] Executing test VariantEvalIntegrationTest:testBadACValue
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[16:45:16] Executing test VariantEvalIntegrationTest:testCompOverlap
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[16:45:16] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[16:45:17] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[16:45:17] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[16:45:17] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[16:45:17] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[16:45:18] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[16:45:18] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[16:45:18] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[16:45:18] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[16:45:18] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[16:45:19] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[16:45:19] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[16:45:19] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[16:45:19] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[16:45:19] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[16:45:19] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[16:45:19] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[16:45:19] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[16:45:19] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[16:45:19] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[16:45:19] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[16:45:20] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[16:45:21] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[16:45:21] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[16:45:21] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[16:45:21] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[16:45:21] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[16:45:21] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[16:45:22] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[16:45:22] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[16:45:22] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[16:45:22] Executing test VariantEvalIntegrationTest:testSelect1
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[16:45:31] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[16:45:32] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[16:45:32] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[16:45:32] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[16:45:32] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[16:45:32] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[16:45:33] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[16:45:33] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[16:45:33] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[May 27, 2025 at 4:45:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.16 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688