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

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

tests
0

failures
0

ignored
2.757s

duration
100%

successful

Tests

Test Duration Result
testBadAllele 0.069s passed
testBadAllele2 0.061s passed
testBadChrCount1 0.115s passed
testBadChrCount2 0.064s passed
testBadEverythingDefaultNoRefNoDBNSP 0.062s passed
testBadEverythingDefaultNoRefYesDBSNP 0.066s passed
testBadEverythingDefaultYesRefNoDBSNP 0.066s passed
testBadEverythingDefaultYesRefYesDBSNP 0.064s passed
testBadGvcfMissingNON_REF 0.065s passed
testBadGvcfOutOfOrder 0.065s passed
testBadGvcfOverlappingHomRefBlockAndVariant 0.111s passed
testBadGvcfOverlappingHomRefBlocks 0.115s passed
testBadGvcfRegions 0.073s passed
testBadID 0.066s passed
testBadID2_OKif_noDBSNPArgument 0.064s passed
testBadID2_OKif_notInDBSNP 0.067s passed
testBadID2_okIfIDnotInDBSNP_withoutDbDNParg 0.068s passed
testBadRefBase1 0.068s passed
testBadRefBase2 0.062s passed
testBadVariantsOrderThreeContigs 0.117s passed
testBadVariantsOrderTwoContigs 0.118s passed
testComplexEvents 0.067s passed
testComplexEventsDictError 0.061s passed
testGoodFile 0.058s passed
testGoodFile2 0.062s passed
testGoodGvcf 0.061s passed
testGoodGvcfExcludingAlleles 0.060s passed
testGoodVariantsOrderThreeContigs 0.123s passed
testGoodVariantsOrderTwoContigs 0.117s passed
testMissingReference 0.068s passed
testNoIntervalFullGenomeGVCF 0.068s passed
testNoIntervalShortenedHeaderDict 0.070s passed
testNoValidation 0.059s passed
testNonOverlappingRegions 0.060s passed
testNonOverlappingRegionsBP_RESOLUTION 0.064s passed
testUnusedAlleleError 0.067s passed
testUnusedAlleleFix 0.066s passed

Standard output

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[22:47:41] Executing test ValidateVariantsIntegrationTest:test bad alt allele
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[22:47:41] Executing test ValidateVariantsIntegrationTest:test bad ref allele in deletion
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[22:47:41] Executing test ValidateVariantsIntegrationTest:test bad chr counts #1
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[22:47:41] Executing test ValidateVariantsIntegrationTest:test bad chr counts with no ref and no validations specified
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[22:47:41] Executing test ValidateVariantsIntegrationTest:test bad chr counts #2
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[22:47:42] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/o dbsnp or ref files
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[22:47:42] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/o ref, w/ dbsnp
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[22:47:42] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/ ref, w/o dbsnp
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[22:47:42] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/ ref, w/ dbsnp
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[22:47:42] Executing test ValidateVariantsIntegrationTest:tests capture of missing NON_REF allele
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[22:47:42] Executing test ValidateVariantsIntegrationTest:tests capture of a gvcf missing a reference block
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[22:47:42] Executing test ValidateVariantsIntegrationTest:tests a gvcf with reference block overlapping variant and --no-overlaps arg
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[22:47:42] Executing test ValidateVariantsIntegrationTest:tests a gvcf with reference block overlapping variant and --no-overlaps arg
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[22:47:42] Executing test ValidateVariantsIntegrationTest:tests capture of a gvcf missing a reference block
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[22:47:42] Executing test ValidateVariantsIntegrationTest:test bad RS ID
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[22:47:42] Executing test ValidateVariantsIntegrationTest:test bad RS ID is OK if there's no dbsnp argument
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[22:47:42] Executing test ValidateVariantsIntegrationTest:test bad RS ID is OK when not in dbSNP even with dbsnp arg
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[22:47:42] Executing test ValidateVariantsIntegrationTest:test bad RS ID is OK when not in dbSNP when no dbsnp arg
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[22:47:43] Executing test ValidateVariantsIntegrationTest:test bad ref base #1
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[22:47:43] Executing test ValidateVariantsIntegrationTest:test bad ref base #2
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[22:47:43] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for an invalid file including three contigs
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[22:47:43] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for an invalid file including two contigs
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[22:47:43] Executing test ValidateVariantsIntegrationTest:test validating complex events
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[22:47:43] Executing test ValidateVariantsIntegrationTest:test validating complex events
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[22:47:43] Executing test ValidateVariantsIntegrationTest:test good file
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[22:47:43] Executing test ValidateVariantsIntegrationTest:test good file
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[22:47:43] Executing test ValidateVariantsIntegrationTest:tests correct gvcf
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[22:47:43] Executing test ValidateVariantsIntegrationTest:tests correct gvcf
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[22:47:43] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for a valid file including three contigs
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[22:47:43] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for a valid file including two contigs
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[22:47:43] Executing test ValidateVariantsIntegrationTest:test bad ref base #1
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[22:47:44] Executing test ValidateVariantsIntegrationTest:tests gvcf that doesnt cover full genome but doesnt give an interval
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[22:47:44] Executing test ValidateVariantsIntegrationTest:tests gvcf that has a header dictionary of just chr20 and doesn't give an interval
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[22:47:44] Executing test ValidateVariantsIntegrationTest:test no validation
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[22:47:44] Executing test ValidateVariantsIntegrationTest:tests capture of non-complete region
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[22:47:44] Executing test ValidateVariantsIntegrationTest:tests capture of non-complete region, on BP_RESOLUTION gvcf
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[22:47:44] Executing test ValidateVariantsIntegrationTest:test unused allele bug fix
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[22:47:44] Executing test ValidateVariantsIntegrationTest:test unused allele bug fix

Standard error

[March 28, 2025 at 10:47:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:41 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008
[March 28, 2025 at 10:47:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1214251008