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

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

tests
0

failures
0

ignored
11.929s

duration
100%

successful

Tests

Test Duration Result
testASAnnotationsAndSubsetting 2.915s passed
testAddedHcAsAnnotations 0.119s passed
testAggressiveQualFiltering 0.078s passed
testContiguityWithSpanningDels 0.392s passed
testDragenGvcfs 0.202s passed
testFilters 0.201s passed
testFirstPositionOnContigNotDropped 0.135s passed
testGVCFReblockingIsContiguous 4.605s passed
testHomRefCalls 0.139s passed
testLeftContigBoundary 0.131s passed
testMQHeadersAreUpdated 0.187s passed
testMixedSamples 0.141s passed
testMovingFilters 0.212s passed
testMultipleInputs 0.304s passed
testNewCompressionScheme 0.087s passed
testNoCallGenotypes 0.138s passed
testNoCallWhenGQ0InNonRefAllele 0.134s passed
testNonGVCFInput 0.080s passed
testNonRefADCorrection 0.075s passed
testOneSampleAsForGnomAD 0.079s passed
testOverlappingDeletions 0.221s passed
testPosteriorDisagreementNeedingSubset 0.135s passed
testRawMQInput 0.109s passed
testReReblocking 0.197s passed
testRemovingAnnotationFromEmptyAttributes 0.132s passed
testRemovingFormatAnnotations 0.186s passed
testSpanDelRegression 0.082s passed
testTreeScoreThreshold 0.079s passed
testTreeScoreWithNoAnnotation 0.077s 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) 0.078s 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) 0.147s 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) 0.132s passed

Standard output

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[17:58:18] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[17:58:18] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[17:58:21] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[17:58:28] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[17:58:28] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[17:58:29] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[17:58:29] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[17:58:29] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[17:58:30] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[17:58:30] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[17:58:30] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[October 27, 2025 at 5:58:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:22 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784
[October 27, 2025 at 5:58:30 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=769654784