Class org.broadinstitute.hellbender.tools.walkers.ValidateVariantsIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers > ValidateVariantsIntegrationTest
37

tests
0

failures
0

ignored
3.016s

duration
100%

successful

Tests

Test Duration Result
testBadAllele 0.071s passed
testBadAllele2 0.069s passed
testBadChrCount1 0.142s passed
testBadChrCount2 0.071s passed
testBadEverythingDefaultNoRefNoDBNSP 0.069s passed
testBadEverythingDefaultNoRefYesDBSNP 0.072s passed
testBadEverythingDefaultYesRefNoDBSNP 0.069s passed
testBadEverythingDefaultYesRefYesDBSNP 0.072s passed
testBadGvcfMissingNON_REF 0.080s passed
testBadGvcfOutOfOrder 0.077s passed
testBadGvcfOverlappingHomRefBlockAndVariant 0.118s passed
testBadGvcfOverlappingHomRefBlocks 0.118s passed
testBadGvcfRegions 0.073s passed
testBadID 0.070s passed
testBadID2_OKif_noDBSNPArgument 0.069s passed
testBadID2_OKif_notInDBSNP 0.071s passed
testBadID2_okIfIDnotInDBSNP_withoutDbDNParg 0.068s passed
testBadRefBase1 0.069s passed
testBadRefBase2 0.074s passed
testBadVariantsOrderThreeContigs 0.121s passed
testBadVariantsOrderTwoContigs 0.121s passed
testComplexEvents 0.070s passed
testComplexEventsDictError 0.070s passed
testGoodFile 0.070s passed
testGoodFile2 0.073s passed
testGoodGvcf 0.072s passed
testGoodGvcfExcludingAlleles 0.075s passed
testGoodVariantsOrderThreeContigs 0.131s passed
testGoodVariantsOrderTwoContigs 0.121s passed
testMissingReference 0.070s passed
testNoIntervalFullGenomeGVCF 0.069s passed
testNoIntervalShortenedHeaderDict 0.070s passed
testNoValidation 0.068s passed
testNonOverlappingRegions 0.071s passed
testNonOverlappingRegionsBP_RESOLUTION 0.076s passed
testUnusedAlleleError 0.074s passed
testUnusedAlleleFix 0.072s passed

Standard output

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[14:24:40] Executing test ValidateVariantsIntegrationTest:test bad alt allele
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[14:24:41] Executing test ValidateVariantsIntegrationTest:test bad ref allele in deletion
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[14:24:41] Executing test ValidateVariantsIntegrationTest:test bad chr counts #1
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[14:24:41] Executing test ValidateVariantsIntegrationTest:test bad chr counts with no ref and no validations specified
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[14:24:41] Executing test ValidateVariantsIntegrationTest:test bad chr counts #2
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[14:24:41] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/o dbsnp or ref files
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[14:24:41] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/o ref, w/ dbsnp
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[14:24:41] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/ ref, w/o dbsnp
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[14:24:41] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/ ref, w/ dbsnp
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[14:24:41] Executing test ValidateVariantsIntegrationTest:tests capture of missing NON_REF allele
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[14:24:41] Executing test ValidateVariantsIntegrationTest:tests capture of a gvcf missing a reference block
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[14:24:41] Executing test ValidateVariantsIntegrationTest:tests a gvcf with reference block overlapping variant and --no-overlaps arg
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[14:24:41] Executing test ValidateVariantsIntegrationTest:tests a gvcf with reference block overlapping variant and --no-overlaps arg
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[14:24:41] Executing test ValidateVariantsIntegrationTest:tests capture of a gvcf missing a reference block
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[14:24:42] Executing test ValidateVariantsIntegrationTest:test bad RS ID
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[14:24:42] Executing test ValidateVariantsIntegrationTest:test bad RS ID is OK if there's no dbsnp argument
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[14:24:42] Executing test ValidateVariantsIntegrationTest:test bad RS ID is OK when not in dbSNP even with dbsnp arg
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[14:24:42] Executing test ValidateVariantsIntegrationTest:test bad RS ID is OK when not in dbSNP when no dbsnp arg
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[14:24:42] Executing test ValidateVariantsIntegrationTest:test bad ref base #1
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[14:24:42] Executing test ValidateVariantsIntegrationTest:test bad ref base #2
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[14:24:42] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for an invalid file including three contigs
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[14:24:42] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for an invalid file including two contigs
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[14:24:42] Executing test ValidateVariantsIntegrationTest:test validating complex events
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[14:24:42] Executing test ValidateVariantsIntegrationTest:test validating complex events
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[14:24:42] Executing test ValidateVariantsIntegrationTest:test good file
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[14:24:42] Executing test ValidateVariantsIntegrationTest:test good file
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[14:24:42] Executing test ValidateVariantsIntegrationTest:tests correct gvcf
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[14:24:43] Executing test ValidateVariantsIntegrationTest:tests correct gvcf
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[14:24:43] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for a valid file including three contigs
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[14:24:43] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for a valid file including two contigs
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[14:24:43] Executing test ValidateVariantsIntegrationTest:test bad ref base #1
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[14:24:43] Executing test ValidateVariantsIntegrationTest:tests gvcf that doesnt cover full genome but doesnt give an interval
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[14:24:43] Executing test ValidateVariantsIntegrationTest:tests gvcf that has a header dictionary of just chr20 and doesn't give an interval
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[14:24:43] Executing test ValidateVariantsIntegrationTest:test no validation
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[14:24:43] Executing test ValidateVariantsIntegrationTest:tests capture of non-complete region
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[14:24:43] Executing test ValidateVariantsIntegrationTest:tests capture of non-complete region, on BP_RESOLUTION gvcf
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[14:24:43] Executing test ValidateVariantsIntegrationTest:test unused allele bug fix
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[14:24:43] Executing test ValidateVariantsIntegrationTest:test unused allele bug fix

Standard error

[June 2, 2025 at 2:24:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536
[June 2, 2025 at 2:24:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1663041536