Class org.broadinstitute.hellbender.tools.walkers.ValidateVariantsIntegrationTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testBadAllele | 0.064s | passed |
| testBadAllele2 | 0.060s | passed |
| testBadChrCount1 | 0.116s | passed |
| testBadChrCount2 | 0.066s | passed |
| testBadEverythingDefaultNoRefNoDBNSP | 0.058s | passed |
| testBadEverythingDefaultNoRefYesDBSNP | 0.058s | passed |
| testBadEverythingDefaultYesRefNoDBSNP | 0.060s | passed |
| testBadEverythingDefaultYesRefYesDBSNP | 0.059s | passed |
| testBadGvcfMissingNON_REF | 0.064s | passed |
| testBadGvcfOutOfOrder | 0.070s | passed |
| testBadGvcfOverlappingHomRefBlockAndVariant | 0.109s | passed |
| testBadGvcfOverlappingHomRefBlocks | 0.114s | passed |
| testBadGvcfRegions | 0.070s | passed |
| testBadID | 0.061s | passed |
| testBadID2_OKif_noDBSNPArgument | 0.056s | passed |
| testBadID2_OKif_notInDBSNP | 0.058s | passed |
| testBadID2_okIfIDnotInDBSNP_withoutDbDNParg | 0.058s | passed |
| testBadRefBase1 | 0.056s | passed |
| testBadRefBase2 | 0.061s | passed |
| testBadVariantsOrderThreeContigs | 0.109s | passed |
| testBadVariantsOrderTwoContigs | 0.122s | passed |
| testComplexEvents | 0.067s | passed |
| testComplexEventsDictError | 0.061s | passed |
| testGoodFile | 0.064s | passed |
| testGoodFile2 | 0.067s | passed |
| testGoodGvcf | 0.069s | passed |
| testGoodGvcfExcludingAlleles | 0.070s | passed |
| testGoodVariantsOrderThreeContigs | 0.124s | passed |
| testGoodVariantsOrderTwoContigs | 0.116s | passed |
| testMissingReference | 0.065s | passed |
| testNoIntervalFullGenomeGVCF | 0.059s | passed |
| testNoIntervalShortenedHeaderDict | 0.063s | passed |
| testNoValidation | 0.057s | passed |
| testNonOverlappingRegions | 0.060s | passed |
| testNonOverlappingRegionsBP_RESOLUTION | 0.066s | passed |
| testUnusedAlleleError | 0.068s | passed |
| testUnusedAlleleFix | 0.067s | passed |
Standard output
-------------------------------------------------------------------------------- [15:00:31] Executing test ValidateVariantsIntegrationTest:test bad alt allele -------------------------------------------------------------------------------- [15:00:31] Executing test ValidateVariantsIntegrationTest:test bad ref allele in deletion -------------------------------------------------------------------------------- [15:00:31] Executing test ValidateVariantsIntegrationTest:test bad chr counts #1 -------------------------------------------------------------------------------- [15:00:32] Executing test ValidateVariantsIntegrationTest:test bad chr counts with no ref and no validations specified -------------------------------------------------------------------------------- [15:00:32] Executing test ValidateVariantsIntegrationTest:test bad chr counts #2 -------------------------------------------------------------------------------- [15:00:32] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/o dbsnp or ref files -------------------------------------------------------------------------------- [15:00:32] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/o ref, w/ dbsnp -------------------------------------------------------------------------------- [15:00:32] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/ ref, w/o dbsnp -------------------------------------------------------------------------------- [15:00:32] Executing test ValidateVariantsIntegrationTest:test that validation occurs w/ ref, w/ dbsnp -------------------------------------------------------------------------------- [15:00:32] Executing test ValidateVariantsIntegrationTest:tests capture of missing NON_REF allele -------------------------------------------------------------------------------- [15:00:32] Executing test ValidateVariantsIntegrationTest:tests capture of a gvcf missing a reference block -------------------------------------------------------------------------------- [15:00:32] Executing test ValidateVariantsIntegrationTest:tests a gvcf with reference block overlapping variant and --no-overlaps arg -------------------------------------------------------------------------------- [15:00:32] Executing test ValidateVariantsIntegrationTest:tests a gvcf with reference block overlapping variant and --no-overlaps arg -------------------------------------------------------------------------------- [15:00:32] Executing test ValidateVariantsIntegrationTest:tests capture of a gvcf missing a reference block -------------------------------------------------------------------------------- [15:00:32] Executing test ValidateVariantsIntegrationTest:test bad RS ID -------------------------------------------------------------------------------- [15:00:32] Executing test ValidateVariantsIntegrationTest:test bad RS ID is OK if there's no dbsnp argument -------------------------------------------------------------------------------- [15:00:32] Executing test ValidateVariantsIntegrationTest:test bad RS ID is OK when not in dbSNP even with dbsnp arg -------------------------------------------------------------------------------- [15:00:33] Executing test ValidateVariantsIntegrationTest:test bad RS ID is OK when not in dbSNP when no dbsnp arg -------------------------------------------------------------------------------- [15:00:33] Executing test ValidateVariantsIntegrationTest:test bad ref base #1 -------------------------------------------------------------------------------- [15:00:33] Executing test ValidateVariantsIntegrationTest:test bad ref base #2 -------------------------------------------------------------------------------- [15:00:33] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for an invalid file including three contigs -------------------------------------------------------------------------------- [15:00:33] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for an invalid file including two contigs -------------------------------------------------------------------------------- [15:00:33] Executing test ValidateVariantsIntegrationTest:test validating complex events -------------------------------------------------------------------------------- [15:00:33] Executing test ValidateVariantsIntegrationTest:test validating complex events -------------------------------------------------------------------------------- [15:00:33] Executing test ValidateVariantsIntegrationTest:test good file -------------------------------------------------------------------------------- [15:00:33] Executing test ValidateVariantsIntegrationTest:test good file -------------------------------------------------------------------------------- [15:00:33] Executing test ValidateVariantsIntegrationTest:tests correct gvcf -------------------------------------------------------------------------------- [15:00:33] Executing test ValidateVariantsIntegrationTest:tests correct gvcf -------------------------------------------------------------------------------- [15:00:33] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for a valid file including three contigs -------------------------------------------------------------------------------- [15:00:33] Executing test ValidateVariantsIntegrationTest:tests the variants order validation for a valid file including two contigs -------------------------------------------------------------------------------- [15:00:34] Executing test ValidateVariantsIntegrationTest:test bad ref base #1 -------------------------------------------------------------------------------- [15:00:34] Executing test ValidateVariantsIntegrationTest:tests gvcf that doesnt cover full genome but doesnt give an interval -------------------------------------------------------------------------------- [15:00:34] Executing test ValidateVariantsIntegrationTest:tests gvcf that has a header dictionary of just chr20 and doesn't give an interval -------------------------------------------------------------------------------- [15:00:34] Executing test ValidateVariantsIntegrationTest:test no validation -------------------------------------------------------------------------------- [15:00:34] Executing test ValidateVariantsIntegrationTest:tests capture of non-complete region -------------------------------------------------------------------------------- [15:00:34] Executing test ValidateVariantsIntegrationTest:tests capture of non-complete region, on BP_RESOLUTION gvcf -------------------------------------------------------------------------------- [15:00:34] Executing test ValidateVariantsIntegrationTest:test unused allele bug fix -------------------------------------------------------------------------------- [15:00:34] Executing test ValidateVariantsIntegrationTest:test unused allele bug fix
Standard error
[May 27, 2025 at 3:00:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:32 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:33 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864 [May 27, 2025 at 3:00:34 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1902116864