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

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

tests
0

failures
0

ignored
11.719s

duration
100%

successful

Tests

Test Duration Result
testASAnnotationsAndSubsetting 3.523s passed
testAddedHcAsAnnotations 0.135s passed
testAggressiveQualFiltering 0.085s passed
testContiguityWithSpanningDels 0.345s passed
testDragenGvcfs 0.177s passed
testFilters 0.181s passed
testFirstPositionOnContigNotDropped 0.120s passed
testGVCFReblockingIsContiguous 4.129s passed
testHomRefCalls 0.131s passed
testLeftContigBoundary 0.131s passed
testMQHeadersAreUpdated 0.189s passed
testMixedSamples 0.142s passed
testMovingFilters 0.181s passed
testMultipleInputs 0.259s passed
testNewCompressionScheme 0.080s passed
testNoCallGenotypes 0.127s passed
testNoCallWhenGQ0InNonRefAllele 0.120s passed
testNonGVCFInput 0.069s passed
testNonRefADCorrection 0.068s passed
testOneSampleAsForGnomAD 0.071s passed
testOverlappingDeletions 0.184s passed
testPosteriorDisagreementNeedingSubset 0.123s passed
testRawMQInput 0.104s passed
testReReblocking 0.198s passed
testRemovingAnnotationFromEmptyAttributes 0.158s passed
testRemovingFormatAnnotations 0.168s passed
testSpanDelRegression 0.071s passed
testTreeScoreThreshold 0.068s passed
testTreeScoreWithNoAnnotation 0.064s 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) 0.067s 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) 0.133s 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) 0.118s passed

Standard output

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[15:07:48] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[15:07:49] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[15:07:52] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[15:07:58] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[15:07:59] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[15:07:59] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[15:07:59] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[15:07:59] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[15:08:00] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[15:08:00] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[15:08:00] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[May 27, 2025 at 3:07:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:52 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:53 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:56 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:58 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:58 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:58 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:58 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:58 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:58 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:58 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:07:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:08:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:08:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:08:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:08:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:08:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:08:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:08:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304
[May 27, 2025 at 3:08:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1839202304