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

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

tests
0

failures
0

ignored
13.985s

duration
100%

successful

Tests

Test Duration Result
testASAnnotationsAndSubsetting 3.593s passed
testAddedHcAsAnnotations 0.160s passed
testAggressiveQualFiltering 0.116s passed
testContiguityWithSpanningDels 0.507s passed
testDragenGvcfs 0.280s passed
testFilters 0.267s passed
testFirstPositionOnContigNotDropped 0.202s passed
testGVCFReblockingIsContiguous 4.371s passed
testHomRefCalls 0.196s passed
testLeftContigBoundary 0.188s passed
testMQHeadersAreUpdated 0.290s passed
testMixedSamples 0.207s passed
testMovingFilters 0.246s passed
testMultipleInputs 0.402s passed
testNewCompressionScheme 0.139s passed
testNoCallGenotypes 0.197s passed
testNoCallWhenGQ0InNonRefAllele 0.194s passed
testNonGVCFInput 0.139s passed
testNonRefADCorrection 0.117s passed
testOneSampleAsForGnomAD 0.122s passed
testOverlappingDeletions 0.296s passed
testPosteriorDisagreementNeedingSubset 0.183s passed
testRawMQInput 0.152s passed
testReReblocking 0.255s passed
testRemovingAnnotationFromEmptyAttributes 0.176s passed
testRemovingFormatAnnotations 0.225s passed
testSpanDelRegression 0.111s passed
testTreeScoreThreshold 0.106s passed
testTreeScoreWithNoAnnotation 0.104s 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) 0.102s 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) 0.174s 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) 0.168s passed

Standard output

--------------------------------------------------------------------------------
[18:43:18] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[18:43:18] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[18:43:21] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[18:43:29] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[18:43:29] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[18:43:29] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[18:43:30] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[18:43:30] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[18:43:31] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[18:43:31] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[18:43:31] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[May 27, 2025 at 6:43:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600
[May 27, 2025 at 6:43:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1153433600