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

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

tests
0

failures
0

ignored
11.863s

duration
100%

successful

Tests

Test Duration Result
testASAnnotationsAndSubsetting 3.423s passed
testAddedHcAsAnnotations 0.120s passed
testAggressiveQualFiltering 0.075s passed
testContiguityWithSpanningDels 0.351s passed
testDragenGvcfs 0.180s passed
testFilters 0.184s passed
testFirstPositionOnContigNotDropped 0.122s passed
testGVCFReblockingIsContiguous 4.388s passed
testHomRefCalls 0.131s passed
testLeftContigBoundary 0.171s passed
testMQHeadersAreUpdated 0.173s passed
testMixedSamples 0.129s passed
testMovingFilters 0.191s passed
testMultipleInputs 0.275s passed
testNewCompressionScheme 0.078s passed
testNoCallGenotypes 0.128s passed
testNoCallWhenGQ0InNonRefAllele 0.123s passed
testNonGVCFInput 0.071s passed
testNonRefADCorrection 0.068s passed
testOneSampleAsForGnomAD 0.065s passed
testOverlappingDeletions 0.187s passed
testPosteriorDisagreementNeedingSubset 0.126s passed
testRawMQInput 0.093s passed
testReReblocking 0.192s passed
testRemovingAnnotationFromEmptyAttributes 0.129s passed
testRemovingFormatAnnotations 0.165s passed
testSpanDelRegression 0.072s passed
testTreeScoreThreshold 0.067s 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) 0.065s 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) 0.135s 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) 0.122s passed

Standard output

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[18:25:28] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[18:25:28] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[18:25:31] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[18:25:38] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[18:25:38] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[18:25:38] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[18:25:38] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[18:25:39] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[18:25:39] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[18:25:39] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[18:25:40] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[May 27, 2025 at 6:25:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248
[May 27, 2025 at 6:25:40 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1728053248