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

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

tests
0

failures
0

ignored
11.782s

duration
100%

successful

Tests

Test Duration Result
testASAnnotationsAndSubsetting 3.582s passed
testAddedHcAsAnnotations 0.124s passed
testAggressiveQualFiltering 0.081s passed
testContiguityWithSpanningDels 0.367s passed
testDragenGvcfs 0.198s passed
testFilters 0.191s passed
testFirstPositionOnContigNotDropped 0.134s passed
testGVCFReblockingIsContiguous 4.063s passed
testHomRefCalls 0.133s passed
testLeftContigBoundary 0.135s passed
testMQHeadersAreUpdated 0.179s passed
testMixedSamples 0.130s passed
testMovingFilters 0.196s passed
testMultipleInputs 0.273s passed
testNewCompressionScheme 0.078s passed
testNoCallGenotypes 0.134s passed
testNoCallWhenGQ0InNonRefAllele 0.124s passed
testNonGVCFInput 0.070s passed
testNonRefADCorrection 0.071s passed
testOneSampleAsForGnomAD 0.069s passed
testOverlappingDeletions 0.197s passed
testPosteriorDisagreementNeedingSubset 0.124s passed
testRawMQInput 0.094s passed
testReReblocking 0.190s passed
testRemovingAnnotationFromEmptyAttributes 0.127s passed
testRemovingFormatAnnotations 0.172s passed
testSpanDelRegression 0.077s passed
testTreeScoreThreshold 0.070s passed
testTreeScoreWithNoAnnotation 0.068s 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) 0.068s 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) 0.139s 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) 0.124s passed

Standard output

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[22:54:53] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[22:54:53] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[22:54:56] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[22:55:02] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[22:55:03] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[22:55:03] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[22:55:03] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[22:55:03] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[22:55:04] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[22:55:04] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[22:55:04] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[March 28, 2025 at 10:54:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:56 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:56 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:56 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:54:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424
[March 28, 2025 at 10:55:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1178599424