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

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

tests

failures

ignored

13.611s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testASAnnotationsAndSubsetting	3.658s	passed
testAddedHcAsAnnotations	0.151s	passed
testAggressiveQualFiltering	0.117s	passed
testContiguityWithSpanningDels	0.429s	passed
testDragenGvcfs	0.216s	passed
testFilters	0.225s	passed
testFirstPositionOnContigNotDropped	0.156s	passed
testGVCFReblockingIsContiguous	4.701s	passed
testHomRefCalls	0.243s	passed
testLeftContigBoundary	0.166s	passed
testMQHeadersAreUpdated	0.204s	passed
testMixedSamples	0.166s	passed
testMovingFilters	0.221s	passed
testMultipleInputs	0.344s	passed
testNewCompressionScheme	0.111s	passed
testNoCallGenotypes	0.160s	passed
testNoCallWhenGQ0InNonRefAllele	0.153s	passed
testNonGVCFInput	0.105s	passed
testNonRefADCorrection	0.103s	passed
testOneSampleAsForGnomAD	0.101s	passed
testOverlappingDeletions	0.263s	passed
testPosteriorDisagreementNeedingSubset	0.160s	passed
testRawMQInput	0.134s	passed
testReReblocking	0.223s	passed
testRemovingAnnotationFromEmptyAttributes	0.159s	passed
testRemovingFormatAnnotations	0.203s	passed
testSpanDelRegression	0.111s	passed
testTreeScoreThreshold	0.110s	passed
testTreeScoreWithNoAnnotation	0.102s	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, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)	0.099s	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 , /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz)	0.165s	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 , /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz)	0.152s	passed

Standard output

--------------------------------------------------------------------------------
[21:11:08] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[21:11:08] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[21:11:12] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[21:11:19] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[21:11:20] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[21:11:20] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[21:11:20] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[21:11:20] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[21:11:21] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[21:11:21] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
--------------------------------------------------------------------------------
[21:11:22] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[June 12, 2025 at 9:11:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:21 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760
[June 12, 2025 at 9:11:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1059061760