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

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

tests
0

failures
0

ignored
16.746s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.112s passed
testAlleleCountStratWithMLE 0.095s passed
testBadACValue 0.071s passed
testCompOverlap 0.145s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.317s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.267s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.244s passed
testEvalTrackWithoutGenotypes 0.358s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.097s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.076s passed
testFunctionClassWithSnpeff 0.679s passed
testFundamentalsCountVariantsNoCompRod 0.079s passed
testFundamentalsCountVariantsSNPsAndIndels 0.088s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.121s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.120s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.088s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.092s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.098s passed
testIncompatibleEvalAndStrat 0.075s passed
testIntervalStrat 0.078s passed
testMVEvalFamilyStrat 0.105s passed
testModernVCFWithLargeIndels 0.757s passed
testMultipleCompTracks 0.374s passed
testMultipleEvalTracksAlleleCountWithMerge 0.090s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.082s passed
testMultipleEvalTracksWithoutGenotypes 0.410s passed
testOutputFileCreation 0.099s passed
testPedigreeValidation[0](SILENT, false) 0.080s passed
testPedigreeValidation[1](STRICT, true) 0.079s passed
testPedigreeValidation[2](null, true) 0.071s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.165s passed
testPrintMissingComp 0.087s passed
testSelect1 9.080s passed
testStandardIndelEval 0.789s passed
testStratifySamplesAndExcludeMonomorphicSites 0.388s passed
testVEMendelianViolationEvaluator 0.074s 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) 0.076s 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) 0.072s passed
testWithAC0 0.087s passed
testWithoutAC0 0.075s passed

Standard output

--------------------------------------------------------------------------------
[15:55:19] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
--------------------------------------------------------------------------------
[15:55:20] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
--------------------------------------------------------------------------------
[15:55:20] Executing test VariantEvalIntegrationTest:testBadACValue
--------------------------------------------------------------------------------
[15:55:20] Executing test VariantEvalIntegrationTest:testCompOverlap
--------------------------------------------------------------------------------
[15:55:20] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
--------------------------------------------------------------------------------
[15:55:20] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
--------------------------------------------------------------------------------
[15:55:20] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
--------------------------------------------------------------------------------
[15:55:21] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
--------------------------------------------------------------------------------
[15:55:21] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
--------------------------------------------------------------------------------
[15:55:21] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
--------------------------------------------------------------------------------
[15:55:21] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
--------------------------------------------------------------------------------
[15:55:22] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
--------------------------------------------------------------------------------
[15:55:22] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
--------------------------------------------------------------------------------
[15:55:22] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
--------------------------------------------------------------------------------
[15:55:22] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
--------------------------------------------------------------------------------
[15:55:22] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
--------------------------------------------------------------------------------
[15:55:22] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
--------------------------------------------------------------------------------
[15:55:22] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
--------------------------------------------------------------------------------
[15:55:23] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
--------------------------------------------------------------------------------
[15:55:23] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
--------------------------------------------------------------------------------
[15:55:23] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
--------------------------------------------------------------------------------
[15:55:23] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
--------------------------------------------------------------------------------
[15:55:23] Executing test VariantEvalIntegrationTest:testIntervalStrat
--------------------------------------------------------------------------------
[15:55:23] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
--------------------------------------------------------------------------------
[15:55:23] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
--------------------------------------------------------------------------------
[15:55:24] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
--------------------------------------------------------------------------------
[15:55:24] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
--------------------------------------------------------------------------------
[15:55:24] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
--------------------------------------------------------------------------------
[15:55:24] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
--------------------------------------------------------------------------------
[15:55:25] Executing test VariantEvalIntegrationTest:testPedigreeValidation
--------------------------------------------------------------------------------
[15:55:25] Executing test VariantEvalIntegrationTest:testPedigreeValidation
--------------------------------------------------------------------------------
[15:55:25] Executing test VariantEvalIntegrationTest:testPedigreeValidation
--------------------------------------------------------------------------------
[15:55:25] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
--------------------------------------------------------------------------------
[15:55:25] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
--------------------------------------------------------------------------------
[15:55:25] Executing test VariantEvalIntegrationTest:testPrintMissingComp
--------------------------------------------------------------------------------
[15:55:25] Executing test VariantEvalIntegrationTest:testSelect1
--------------------------------------------------------------------------------
[15:55:34] Executing test VariantEvalIntegrationTest:testStandardIndelEval
--------------------------------------------------------------------------------
[15:55:35] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
--------------------------------------------------------------------------------
[15:55:36] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
--------------------------------------------------------------------------------
[15:55:36] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
--------------------------------------------------------------------------------
[15:55:36] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
--------------------------------------------------------------------------------
[15:55:36] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
--------------------------------------------------------------------------------
[15:55:36] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
--------------------------------------------------------------------------------
[15:55:36] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
--------------------------------------------------------------------------------
[15:55:36] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[May 27, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:35 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432
[May 27, 2025 at 3:55:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1606418432