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

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

tests
0

failures
0

ignored
13.176s

duration
100%

successful

Tests

Test Duration Result
testASAnnotationsAndSubsetting 3.947s passed
testAddedHcAsAnnotations 0.144s passed
testAggressiveQualFiltering 0.117s passed
testContiguityWithSpanningDels 0.450s passed
testDragenGvcfs 0.230s passed
testFilters 0.222s passed
testFirstPositionOnContigNotDropped 0.151s passed
testGVCFReblockingIsContiguous 4.086s passed
testHomRefCalls 0.167s passed
testLeftContigBoundary 0.170s passed
testMQHeadersAreUpdated 0.202s passed
testMixedSamples 0.166s passed
testMovingFilters 0.219s passed
testMultipleInputs 0.344s passed
testNewCompressionScheme 0.110s passed
testNoCallGenotypes 0.156s passed
testNoCallWhenGQ0InNonRefAllele 0.156s passed
testNonGVCFInput 0.100s passed
testNonRefADCorrection 0.100s passed
testOneSampleAsForGnomAD 0.106s passed
testOverlappingDeletions 0.258s passed
testPosteriorDisagreementNeedingSubset 0.155s passed
testRawMQInput 0.132s passed
testReReblocking 0.222s passed
testRemovingAnnotationFromEmptyAttributes 0.153s passed
testRemovingFormatAnnotations 0.201s passed
testSpanDelRegression 0.106s passed
testTreeScoreThreshold 0.099s passed
testTreeScoreWithNoAnnotation 0.099s 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) 0.160s 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) 0.149s passed

Standard output

--------------------------------------------------------------------------------
[16:10:55] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting
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[16:10:55] Executing test ReblockGVCFIntegrationTest:testASAnnotationsAndSubsetting2
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[16:10:59] Executing test ReblockGVCFIntegrationTest:testVariantQualFiltering
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[16:11:05] Executing test ReblockGVCFIntegrationTest:testNewCompressionScheme
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[16:11:06] Executing test ReblockGVCFIntegrationTest:testNonRefADCorrection
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[16:11:06] Executing test ReblockGVCFIntegrationTest:testOneSampleDropLows
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[16:11:06] Executing test ReblockGVCFIntegrationTest:testOverlappingDeletions
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[16:11:07] Executing test ReblockGVCFIntegrationTest:testRawMQInput
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[16:11:08] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[16:11:08] Executing test ReblockGVCFIntegrationTest:testWithExactComparison
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[16:11:08] Executing test ReblockGVCFIntegrationTest:testWithExactComparison

Standard error

[May 27, 2025 at 4:10:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:55 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:10:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:00 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:05 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:06 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168
[May 27, 2025 at 4:11:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1119879168