Class org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCFIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers.variantutils > ReblockGVCFIntegrationTest
32

tests
0

failures
0

ignored
11.781s

duration
100%

successful

Tests

Test Duration Result
testASAnnotationsAndSubsetting 3.171s passed
testAddedHcAsAnnotations 0.124s passed
testAggressiveQualFiltering 0.077s passed
testContiguityWithSpanningDels 0.367s passed
testDragenGvcfs 0.208s passed
testFilters 0.190s passed
testFirstPositionOnContigNotDropped 0.127s passed
testGVCFReblockingIsContiguous 4.364s passed
testHomRefCalls 0.197s passed
testLeftContigBoundary 0.124s passed
testMQHeadersAreUpdated 0.174s passed
testMixedSamples 0.147s passed
testMovingFilters 0.191s passed
testMultipleInputs 0.273s passed
testNewCompressionScheme 0.082s passed
testNoCallGenotypes 0.132s passed
testNoCallWhenGQ0InNonRefAllele 0.127s passed
testNonGVCFInput 0.073s passed
testNonRefADCorrection 0.072s passed
testOneSampleAsForGnomAD 0.073s passed
testOverlappingDeletions 0.208s passed
testPosteriorDisagreementNeedingSubset 0.136s passed
testRawMQInput 0.096s passed
testReReblocking 0.198s passed
testRemovingAnnotationFromEmptyAttributes 0.126s passed
testRemovingFormatAnnotations 0.171s passed
testSpanDelRegression 0.077s passed
testTreeScoreThreshold 0.073s passed
testTreeScoreWithNoAnnotation 0.070s passed
testWithExactComparison[0](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/gvcfForReblocking.g.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/testJustOneSample.expected.g.vcf, -L chr20:69771 -rgq-threshold 19, /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta) 0.072s passed
testWithExactComparison[1](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prodWgsInput.g.vcf , src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prodWgsOutput.g.vcf, -do-qual-approx --floor-blocks -GQB 20 -GQB 30 -GQB 40 , /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz) 0.135s passed
testWithExactComparison[2](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prodWesInput.g.vcf , src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF/prodWesOutput.g.vcf, -do-qual-approx --floor-blocks -GQB 20 -GQB 30 -GQB 40 , /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz) 0.126s passed

Standard output

--------------------------------------------------------------------------------
[20:56:19] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[20:56:19] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[20:56:22] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[20:56:29] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[20:56:29] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[20:56:29] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[20:56:29] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[20:56:30] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[20:56:30] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[20:56:30] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[20:56:31] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[June 12, 2025 at 8:56:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:23 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192
[June 12, 2025 at 8:56:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1616904192