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

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

tests
0

failures
0

ignored
2.785s

duration
100%

successful

Tests

Test Duration Result
testBadAllele 0.072s passed
testBadAllele2 0.065s passed
testBadChrCount1 0.133s passed
testBadChrCount2 0.065s passed
testBadEverythingDefaultNoRefNoDBNSP 0.064s passed
testBadEverythingDefaultNoRefYesDBSNP 0.063s passed
testBadEverythingDefaultYesRefNoDBSNP 0.061s passed
testBadEverythingDefaultYesRefYesDBSNP 0.064s passed
testBadGvcfMissingNON_REF 0.070s passed
testBadGvcfOutOfOrder 0.070s passed
testBadGvcfOverlappingHomRefBlockAndVariant 0.111s passed
testBadGvcfOverlappingHomRefBlocks 0.122s passed
testBadGvcfRegions 0.072s passed
testBadID 0.067s passed
testBadID2_OKif_noDBSNPArgument 0.061s passed
testBadID2_OKif_notInDBSNP 0.066s passed
testBadID2_okIfIDnotInDBSNP_withoutDbDNParg 0.066s passed
testBadRefBase1 0.067s passed
testBadRefBase2 0.068s passed
testBadVariantsOrderThreeContigs 0.118s passed
testBadVariantsOrderTwoContigs 0.118s passed
testComplexEvents 0.068s passed
testComplexEventsDictError 0.061s passed
testGoodFile 0.057s passed
testGoodFile2 0.063s passed
testGoodGvcf 0.062s passed
testGoodGvcfExcludingAlleles 0.065s passed
testGoodVariantsOrderThreeContigs 0.117s passed
testGoodVariantsOrderTwoContigs 0.115s passed
testMissingReference 0.065s passed
testNoIntervalFullGenomeGVCF 0.062s passed
testNoIntervalShortenedHeaderDict 0.061s passed
testNoValidation 0.059s passed
testNonOverlappingRegions 0.061s passed
testNonOverlappingRegionsBP_RESOLUTION 0.068s passed
testUnusedAlleleError 0.069s passed
testUnusedAlleleFix 0.069s passed

Standard output

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[15:47:36] Executing test ValidateVariantsIntegrationTest:test bad alt allele
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[15:47:36] Executing test ValidateVariantsIntegrationTest:test bad ref allele in deletion
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[15:47:36] Executing test ValidateVariantsIntegrationTest:test bad chr counts #1
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[15:47:36] Executing test ValidateVariantsIntegrationTest:test bad chr counts with no ref and no validations specified
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[15:47:36] Executing test ValidateVariantsIntegrationTest:test bad chr counts #2
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[15:47:36] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/o dbsnp or ref files
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[15:47:36] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/o ref, w/ dbsnp
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[15:47:36] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/ ref, w/o dbsnp
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[15:47:37] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/ ref, w/ dbsnp
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[15:47:37] Executing test ValidateVariantsIntegrationTest:tests capture of missing NON_REF allele
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[15:47:37] Executing test ValidateVariantsIntegrationTest:tests capture of a gvcf missing a reference block
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[15:47:37] Executing test ValidateVariantsIntegrationTest:tests a gvcf with reference block overlapping variant and --no-overlaps arg
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[15:47:37] Executing test ValidateVariantsIntegrationTest:tests a gvcf with reference block overlapping variant and --no-overlaps arg
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[15:47:37] Executing test ValidateVariantsIntegrationTest:tests capture of a gvcf missing a reference block
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[15:47:37] Executing test ValidateVariantsIntegrationTest:test bad RS ID
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[15:47:37] Executing test ValidateVariantsIntegrationTest:test bad RS ID is OK if there's no dbsnp argument
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[15:47:37] Executing test ValidateVariantsIntegrationTest:test bad RS ID is OK when not in dbSNP even with dbsnp arg
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[15:47:37] Executing test ValidateVariantsIntegrationTest:test bad RS ID is OK when not in dbSNP when no dbsnp arg
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[15:47:37] Executing test ValidateVariantsIntegrationTest:test bad ref base #1
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[15:47:37] Executing test ValidateVariantsIntegrationTest:test bad ref base #2
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[15:47:37] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for an invalid file including three contigs
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[15:47:38] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for an invalid file including two contigs
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[15:47:38] Executing test ValidateVariantsIntegrationTest:test validating complex events
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[15:47:38] Executing test ValidateVariantsIntegrationTest:test validating complex events
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[15:47:38] Executing test ValidateVariantsIntegrationTest:test good file
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[15:47:38] Executing test ValidateVariantsIntegrationTest:test good file
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[15:47:38] Executing test ValidateVariantsIntegrationTest:tests correct gvcf
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[15:47:38] Executing test ValidateVariantsIntegrationTest:tests correct gvcf
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[15:47:38] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for a valid file including three contigs
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[15:47:38] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for a valid file including two contigs
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[15:47:38] Executing test ValidateVariantsIntegrationTest:test bad ref base #1
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[15:47:38] Executing test ValidateVariantsIntegrationTest:tests gvcf that doesnt cover full genome but doesnt give an interval
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[15:47:38] Executing test ValidateVariantsIntegrationTest:tests gvcf that has a header dictionary of just chr20 and doesn't give an interval
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[15:47:38] Executing test ValidateVariantsIntegrationTest:test no validation
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[15:47:39] Executing test ValidateVariantsIntegrationTest:tests capture of non-complete region
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[15:47:39] Executing test ValidateVariantsIntegrationTest:tests capture of non-complete region, on BP_RESOLUTION gvcf
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[15:47:39] Executing test ValidateVariantsIntegrationTest:test unused allele bug fix
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[15:47:39] Executing test ValidateVariantsIntegrationTest:test unused allele bug fix

Standard error

[May 19, 2025 at 3:47:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:37 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:38 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976
[May 19, 2025 at 3:47:39 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1337982976