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

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

tests

failures

ignored

13.317s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testASAnnotationsAndSubsetting	3.335s	passed
testAddedHcAsAnnotations	0.156s	passed
testAggressiveQualFiltering	0.124s	passed
testContiguityWithSpanningDels	0.442s	passed
testDragenGvcfs	0.238s	passed
testFilters	0.224s	passed
testFirstPositionOnContigNotDropped	0.156s	passed
testGVCFReblockingIsContiguous	4.647s	passed
testHomRefCalls	0.231s	passed
testLeftContigBoundary	0.188s	passed
testMQHeadersAreUpdated	0.218s	passed
testMixedSamples	0.174s	passed
testMovingFilters	0.237s	passed
testMultipleInputs	0.349s	passed
testNewCompressionScheme	0.107s	passed
testNoCallGenotypes	0.162s	passed
testNoCallWhenGQ0InNonRefAllele	0.154s	passed
testNonGVCFInput	0.105s	passed
testNonRefADCorrection	0.102s	passed
testOneSampleAsForGnomAD	0.101s	passed
testOverlappingDeletions	0.263s	passed
testPosteriorDisagreementNeedingSubset	0.154s	passed
testRawMQInput	0.116s	passed
testReReblocking	0.220s	passed
testRemovingAnnotationFromEmptyAttributes	0.154s	passed
testRemovingFormatAnnotations	0.207s	passed
testSpanDelRegression	0.112s	passed
testTreeScoreThreshold	0.102s	passed
testTreeScoreWithNoAnnotation	0.104s	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)	0.105s	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)	0.169s	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)	0.161s	passed

Standard output

--------------------------------------------------------------------------------
[14:46:14] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[14:46:14] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[14:46:18] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[14:46:25] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[14:46:25] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[14:46:25] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[14:46:26] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[14:46:26] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[14:46:27] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[14:46:27] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
--------------------------------------------------------------------------------
[14:46:27] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[June 2, 2025 at 2:46:14 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:14 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:19 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 2, 2025 at 2:46:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000