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

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

tests
0

failures
0

ignored
11.858s

duration
100%

successful

Tests

Test Duration Result
testASAnnotationsAndSubsetting 3.568s passed
testAddedHcAsAnnotations 0.133s passed
testAggressiveQualFiltering 0.084s passed
testContiguityWithSpanningDels 0.355s passed
testDragenGvcfs 0.185s passed
testFilters 0.209s passed
testFirstPositionOnContigNotDropped 0.129s passed
testGVCFReblockingIsContiguous 4.128s passed
testHomRefCalls 0.131s passed
testLeftContigBoundary 0.132s passed
testMQHeadersAreUpdated 0.174s passed
testMixedSamples 0.136s passed
testMovingFilters 0.189s passed
testMultipleInputs 0.277s passed
testNewCompressionScheme 0.078s passed
testNoCallGenotypes 0.130s passed
testNoCallWhenGQ0InNonRefAllele 0.122s passed
testNonGVCFInput 0.073s passed
testNonRefADCorrection 0.074s passed
testOneSampleAsForGnomAD 0.070s passed
testOverlappingDeletions 0.197s passed
testPosteriorDisagreementNeedingSubset 0.131s passed
testRawMQInput 0.093s passed
testReReblocking 0.189s passed
testRemovingAnnotationFromEmptyAttributes 0.127s passed
testRemovingFormatAnnotations 0.173s passed
testSpanDelRegression 0.078s passed
testTreeScoreThreshold 0.073s passed
testTreeScoreWithNoAnnotation 0.072s 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) 0.076s 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) 0.145s 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) 0.127s passed

Standard output

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[16:45:37] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[16:45:37] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[16:45:40] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[16:45:47] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[16:45:47] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[16:45:47] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[16:45:47] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[16:45:47] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[16:45:48] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[16:45:48] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[16:45:48] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[May 27, 2025 at 4:45:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:45 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:48 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688
[May 27, 2025 at 4:45:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1140850688