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

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

tests
0

failures
0

ignored
12.584s

duration
100%

successful

Tests

Test Duration Result
testASAnnotationsAndSubsetting 3.647s passed
testAddedHcAsAnnotations 0.136s passed
testAggressiveQualFiltering 0.080s passed
testContiguityWithSpanningDels 0.404s passed
testDragenGvcfs 0.191s passed
testFilters 0.198s passed
testFirstPositionOnContigNotDropped 0.126s passed
testGVCFReblockingIsContiguous 4.641s passed
testHomRefCalls 0.197s passed
testLeftContigBoundary 0.130s passed
testMQHeadersAreUpdated 0.176s passed
testMixedSamples 0.132s passed
testMovingFilters 0.190s passed
testMultipleInputs 0.276s passed
testNewCompressionScheme 0.079s passed
testNoCallGenotypes 0.131s passed
testNoCallWhenGQ0InNonRefAllele 0.128s passed
testNonGVCFInput 0.075s passed
testNonRefADCorrection 0.082s passed
testOneSampleAsForGnomAD 0.077s passed
testOverlappingDeletions 0.213s passed
testPosteriorDisagreementNeedingSubset 0.126s passed
testRawMQInput 0.102s passed
testReReblocking 0.192s passed
testRemovingAnnotationFromEmptyAttributes 0.124s passed
testRemovingFormatAnnotations 0.180s passed
testSpanDelRegression 0.080s passed
testTreeScoreThreshold 0.072s passed
testTreeScoreWithNoAnnotation 0.069s 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) 0.071s 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) 0.136s 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) 0.123s passed

Standard output

--------------------------------------------------------------------------------
[19:09:43] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[19:09:43] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[19:09:46] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[19:09:53] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[19:09:54] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[19:09:54] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[19:09:54] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[19:09:54] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[19:09:55] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[19:09:55] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[19:09:55] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[May 19, 2025 at 7:09:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:47 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:54 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:54 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:54 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:54 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:54 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:54 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:54 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:54 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:54 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:55 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:55 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:55 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:55 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:55 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:55 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528
[May 19, 2025 at 7:09:55 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1497366528