Class org.broadinstitute.hellbender.tools.walkers.ValidateVariantsIntegrationTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testBadAllele | 0.086s | passed |
| testBadAllele2 | 0.089s | passed |
| testBadChrCount1 | 0.163s | passed |
| testBadChrCount2 | 0.082s | passed |
| testBadEverythingDefaultNoRefNoDBNSP | 0.084s | passed |
| testBadEverythingDefaultNoRefYesDBSNP | 0.087s | passed |
| testBadEverythingDefaultYesRefNoDBSNP | 0.082s | passed |
| testBadEverythingDefaultYesRefYesDBSNP | 0.086s | passed |
| testBadGvcfMissingNON_REF | 0.092s | passed |
| testBadGvcfOutOfOrder | 0.092s | passed |
| testBadGvcfOverlappingHomRefBlockAndVariant | 0.132s | passed |
| testBadGvcfOverlappingHomRefBlocks | 0.133s | passed |
| testBadGvcfRegions | 0.090s | passed |
| testBadID | 0.086s | passed |
| testBadID2_OKif_noDBSNPArgument | 0.084s | passed |
| testBadID2_OKif_notInDBSNP | 0.089s | passed |
| testBadID2_okIfIDnotInDBSNP_withoutDbDNParg | 0.086s | passed |
| testBadRefBase1 | 0.086s | passed |
| testBadRefBase2 | 0.084s | passed |
| testBadVariantsOrderThreeContigs | 0.145s | passed |
| testBadVariantsOrderTwoContigs | 0.178s | passed |
| testComplexEvents | 0.086s | passed |
| testComplexEventsDictError | 0.084s | passed |
| testGoodFile | 0.084s | passed |
| testGoodFile2 | 0.102s | passed |
| testGoodGvcf | 0.087s | passed |
| testGoodGvcfExcludingAlleles | 0.091s | passed |
| testGoodVariantsOrderThreeContigs | 0.149s | passed |
| testGoodVariantsOrderTwoContigs | 0.137s | passed |
| testMissingReference | 0.084s | passed |
| testNoIntervalFullGenomeGVCF | 0.084s | passed |
| testNoIntervalShortenedHeaderDict | 0.093s | passed |
| testNoValidation | 0.084s | passed |
| testNonOverlappingRegions | 0.085s | passed |
| testNonOverlappingRegionsBP_RESOLUTION | 0.097s | passed |
| testUnusedAlleleError | 0.112s | passed |
| testUnusedAlleleFix | 0.086s | passed |
Standard output
-------------------------------------------------------------------------------- [19:16:30] Executing test ValidateVariantsIntegrationTest:test bad alt allele -------------------------------------------------------------------------------- [19:16:30] Executing test ValidateVariantsIntegrationTest:test bad ref allele in deletion -------------------------------------------------------------------------------- [19:16:31] Executing test ValidateVariantsIntegrationTest:test bad chr counts #1 -------------------------------------------------------------------------------- [19:16:31] Executing test ValidateVariantsIntegrationTest:test bad chr counts with no ref and no validations specified -------------------------------------------------------------------------------- [19:16:31] Executing test ValidateVariantsIntegrationTest:test bad chr counts #2 -------------------------------------------------------------------------------- [19:16:31] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/o dbsnp or ref files -------------------------------------------------------------------------------- [19:16:31] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/o ref, w/ dbsnp -------------------------------------------------------------------------------- [19:16:31] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/ ref, w/o dbsnp -------------------------------------------------------------------------------- [19:16:31] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/ ref, w/ dbsnp -------------------------------------------------------------------------------- [19:16:31] Executing test ValidateVariantsIntegrationTest:tests capture of missing NON_REF allele -------------------------------------------------------------------------------- [19:16:31] Executing test ValidateVariantsIntegrationTest:tests capture of a gvcf missing a reference block -------------------------------------------------------------------------------- [19:16:31] Executing test ValidateVariantsIntegrationTest:tests a gvcf with reference block overlapping variant and --no-overlaps arg -------------------------------------------------------------------------------- [19:16:31] Executing test ValidateVariantsIntegrationTest:tests a gvcf with reference block overlapping variant and --no-overlaps arg -------------------------------------------------------------------------------- [19:16:32] Executing test ValidateVariantsIntegrationTest:tests capture of a gvcf missing a reference block -------------------------------------------------------------------------------- [19:16:32] Executing test ValidateVariantsIntegrationTest:test bad RS ID -------------------------------------------------------------------------------- [19:16:32] Executing test ValidateVariantsIntegrationTest:test bad RS ID is OK if there's no dbsnp argument -------------------------------------------------------------------------------- [19:16:32] Executing test ValidateVariantsIntegrationTest:test bad RS ID is OK when not in dbSNP even with dbsnp arg -------------------------------------------------------------------------------- [19:16:32] Executing test ValidateVariantsIntegrationTest:test bad RS ID is OK when not in dbSNP when no dbsnp arg -------------------------------------------------------------------------------- [19:16:32] Executing test ValidateVariantsIntegrationTest:test bad ref base #1 -------------------------------------------------------------------------------- [19:16:32] Executing test ValidateVariantsIntegrationTest:test bad ref base #2 -------------------------------------------------------------------------------- [19:16:32] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for an invalid file including three contigs -------------------------------------------------------------------------------- [19:16:32] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for an invalid file including two contigs -------------------------------------------------------------------------------- [19:16:33] Executing test ValidateVariantsIntegrationTest:test validating complex events -------------------------------------------------------------------------------- [19:16:33] Executing test ValidateVariantsIntegrationTest:test validating complex events -------------------------------------------------------------------------------- [19:16:33] Executing test ValidateVariantsIntegrationTest:test good file -------------------------------------------------------------------------------- [19:16:33] Executing test ValidateVariantsIntegrationTest:test good file -------------------------------------------------------------------------------- [19:16:33] Executing test ValidateVariantsIntegrationTest:tests correct gvcf -------------------------------------------------------------------------------- [19:16:33] Executing test ValidateVariantsIntegrationTest:tests correct gvcf -------------------------------------------------------------------------------- [19:16:33] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for a valid file including three contigs -------------------------------------------------------------------------------- [19:16:33] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for a valid file including two contigs -------------------------------------------------------------------------------- [19:16:33] Executing test ValidateVariantsIntegrationTest:test bad ref base #1 -------------------------------------------------------------------------------- [19:16:33] Executing test ValidateVariantsIntegrationTest:tests gvcf that doesnt cover full genome but doesnt give an interval -------------------------------------------------------------------------------- [19:16:33] Executing test ValidateVariantsIntegrationTest:tests gvcf that has a header dictionary of just chr20 and doesn't give an interval -------------------------------------------------------------------------------- [19:16:34] Executing test ValidateVariantsIntegrationTest:test no validation -------------------------------------------------------------------------------- [19:16:34] Executing test ValidateVariantsIntegrationTest:tests capture of non-complete region -------------------------------------------------------------------------------- [19:16:34] Executing test ValidateVariantsIntegrationTest:tests capture of non-complete region, on BP_RESOLUTION gvcf -------------------------------------------------------------------------------- [19:16:34] Executing test ValidateVariantsIntegrationTest:test unused allele bug fix -------------------------------------------------------------------------------- [19:16:34] Executing test ValidateVariantsIntegrationTest:test unused allele bug fix
Standard error
[May 19, 2025 at 7:16:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696 [May 19, 2025 at 7:16:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1306525696