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

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

tests
0

failures
0

ignored
16.505s

duration
100%

successful

Tests

Test Duration Result
testAlleleCountStrat 0.107s passed
testAlleleCountStratWithMLE 0.093s passed
testBadACValue 0.071s passed
testCompOverlap 0.148s passed
testContigStratWithUserSuppliedIntervals[0](1:1-1480226, testContigStratWithUserSuppliedIntervals) 0.303s passed
testContigStratWithUserSuppliedIntervals[1](1, testContigStratWithUserSuppliedIntervals2) 0.226s passed
testContigStratWithUserSuppliedIntervals[2](null, testContigStratWithUserSuppliedIntervals3) 0.252s passed
testEvalTrackWithoutGenotypes 0.343s passed
testEvalTrackWithoutGenotypesWithSampleFields 0.108s passed
testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef 0.078s passed
testFunctionClassWithSnpeff 0.748s passed
testFundamentalsCountVariantsNoCompRod 0.082s passed
testFundamentalsCountVariantsSNPsAndIndels 0.088s passed
testFundamentalsCountVariantsSNPsAndIndelsWithCpG 0.121s passed
testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy 0.089s passed
testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses 0.091s passed
testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression 0.125s passed
testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNovelty 0.087s passed
testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter 0.093s passed
testFundamentalsCountVariantsSNPsAndIndelsWithSample 0.089s passed
testIncompatibleEvalAndStrat 0.076s passed
testIntervalStrat 0.079s passed
testMVEvalFamilyStrat 0.090s passed
testModernVCFWithLargeIndels 0.496s passed
testMultipleCompTracks 0.263s passed
testMultipleEvalTracksAlleleCountWithMerge 0.091s passed
testMultipleEvalTracksAlleleCountWithoutMerge 0.084s passed
testMultipleEvalTracksWithoutGenotypes 0.432s passed
testOutputFileCreation 0.093s passed
testPedigreeValidation[0](SILENT, false) 0.083s passed
testPedigreeValidation[1](STRICT, true) 0.079s passed
testPedigreeValidation[2](null, true) 0.072s passed
testPerSampleAndSubsettedSampleHaveSameResults 0.162s passed
testPrintMissingComp 0.089s passed
testSelect1 9.328s passed
testStandardIndelEval 0.649s passed
testStratifySamplesAndExcludeMonomorphicSites 0.383s passed
testVEMendelianViolationEvaluator 0.077s 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) 0.072s 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) 0.071s 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) 0.071s 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) 0.073s passed
testWithAC0 0.083s passed
testWithoutAC0 0.080s passed

Standard output

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[14:32:00] Executing test VariantEvalIntegrationTest:testAlleleCountStrat
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[14:32:00] Executing test VariantEvalIntegrationTest:testAlleleCountStratWithMLE
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[14:32:00] Executing test VariantEvalIntegrationTest:testBadACValue
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[14:32:00] Executing test VariantEvalIntegrationTest:testCompOverlap
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[14:32:00] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals
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[14:32:01] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals2
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[14:32:01] Executing test VariantEvalIntegrationTest:testContigStratWithUserSuppliedIntervals3
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[14:32:01] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypes
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[14:32:02] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFields
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[14:32:02] Executing test VariantEvalIntegrationTest:testEvalTrackWithoutGenotypesWithSampleFieldsWrongRef
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[14:32:02] Executing test VariantEvalIntegrationTest:testFunctionClassWithSnpeff
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[14:32:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsNoCompRod
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[14:32:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndels
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[14:32:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithCpG
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[14:32:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy
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[14:32:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClass
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[14:32:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression
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[14:32:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions
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[14:32:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNovelty
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[14:32:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter
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[14:32:03] Executing test VariantEvalIntegrationTest:testFundamentalsCountVariantsSNPsAndIndelsWithSample
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[14:32:03] Executing test VariantEvalIntegrationTest:testIncompatibleEvalAndStrat
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[14:32:04] Executing test VariantEvalIntegrationTest:testIntervalStrat
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[14:32:04] Executing test VariantEvalIntegrationTest:testMVEvalFamilyStrat
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[14:32:04] Executing test VariantEvalIntegrationTest:testModernVCFWithLargeIndels
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[14:32:04] Executing test VariantEvalIntegrationTest:testMultipleCompTracks
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[14:32:04] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithMerge
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[14:32:05] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksAlleleCountWithoutMerge
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[14:32:05] Executing test VariantEvalIntegrationTest:testMultipleEvalTracksWithoutGenotypes
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[14:32:05] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[14:32:05] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[14:32:05] Executing test VariantEvalIntegrationTest:testPedigreeValidation
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[14:32:05] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-subset
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[14:32:06] Executing test VariantEvalIntegrationTest:testPerSampleAndSubsettedSampleHaveSameResults-Onesample
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[14:32:06] Executing test VariantEvalIntegrationTest:testPrintMissingComp
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[14:32:06] Executing test VariantEvalIntegrationTest:testSelect1
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[14:32:15] Executing test VariantEvalIntegrationTest:testStandardIndelEval
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[14:32:16] Executing test VariantEvalIntegrationTest:testStratifySamplesAndExcludeMonomorphicSites
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[14:32:16] Executing test VariantEvalIntegrationTest:testVEMendelianViolationEvaluator
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[14:32:16] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-sites
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[14:32:16] Executing test VariantEvalIntegrationTest:testValidationReportData-sites-genotypes
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[14:32:16] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-sites
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[14:32:16] Executing test VariantEvalIntegrationTest:testValidationReportData-genotypes-genotypes
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[14:32:16] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = true
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[14:32:16] Executing test VariantEvalIntegrationTest:testIncludingAC0 keep ac 0 = false

Standard error

[June 2, 2025 at 2:32:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:06 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:06 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:06 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:15 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:16 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392
[June 2, 2025 at 2:32:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1302331392