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

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

tests
0

failures
0

ignored
13.042s

duration
100%

successful

Tests

Test Duration Result
testASAnnotationsAndSubsetting 3.301s passed
testAddedHcAsAnnotations 0.145s passed
testAggressiveQualFiltering 0.113s passed
testContiguityWithSpanningDels 0.415s passed
testDragenGvcfs 0.224s passed
testFilters 0.233s passed
testFirstPositionOnContigNotDropped 0.158s passed
testGVCFReblockingIsContiguous 4.546s passed
testHomRefCalls 0.167s passed
testLeftContigBoundary 0.185s passed
testMQHeadersAreUpdated 0.207s passed
testMixedSamples 0.164s passed
testMovingFilters 0.217s passed
testMultipleInputs 0.348s passed
testNewCompressionScheme 0.111s passed
testNoCallGenotypes 0.159s passed
testNoCallWhenGQ0InNonRefAllele 0.160s passed
testNonGVCFInput 0.104s passed
testNonRefADCorrection 0.102s passed
testOneSampleAsForGnomAD 0.102s passed
testOverlappingDeletions 0.267s passed
testPosteriorDisagreementNeedingSubset 0.162s passed
testRawMQInput 0.124s passed
testReReblocking 0.237s passed
testRemovingAnnotationFromEmptyAttributes 0.159s passed
testRemovingFormatAnnotations 0.200s passed
testSpanDelRegression 0.108s passed
testTreeScoreThreshold 0.104s passed
testTreeScoreWithNoAnnotation 0.099s 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, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta) 0.099s 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 , /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz) 0.166s 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 , /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz) 0.156s passed

Standard output

--------------------------------------------------------------------------------
[14:15:25] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[14:15:25] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[14:15:28] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[14:15:35] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[14:15:36] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[14:15:36] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[14:15:36] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[14:15:36] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[14:15:37] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[14:15:37] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[14:15:37] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[May 27, 2025 at 2:15:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:36 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:37 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 27, 2025 at 2:15:38 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000