Class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariantsIntegrationTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testLefAlignRequireReference[0](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf) | 0.092s | passed |
| testLeftAlignment[0](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf, ) | 0.105s | passed |
| testLeftAlignment[1](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf, --split-multi-allelics) | 0.102s | passed |
| testLeftAlignment[2](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf, --dont-trim-alleles) | 0.097s | passed |
| testLeftAlignment[3](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf, --no-trim --split-multi-allelics) | 0.098s | passed |
| testLeftAlignment[4](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf, --split-multi-allelics --keep-original-ac) | 0.102s | passed |
| testLeftAlignment[5](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf, --max-indel-length 296) | 0.101s | passed |
| testLeftAlignment[6](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf, /gatkCloneMountPoint/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta, src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf, --max-indel-length 342) | 0.094s | passed |
| testSplitAllelesWithASFilters | 0.098s | passed |
Standard output
-------------------------------------------------------------------------------- [21:11:07] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--requireReference -------------------------------------------------------------------------------- [21:11:07] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf -------------------------------------------------------------------------------- [21:11:07] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf -------------------------------------------------------------------------------- [21:11:07] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf -------------------------------------------------------------------------------- [21:11:08] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf -------------------------------------------------------------------------------- [21:11:08] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf -------------------------------------------------------------------------------- [21:11:08] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf -------------------------------------------------------------------------------- [21:11:08] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf -------------------------------------------------------------------------------- [21:11:08] Executing test LeftAlignAndTrimVariantsIntegrationTest:testSplitAllelesWithASFilters--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_split_with_AS_filters.vcf
Standard error
[June 12, 2025 at 9:11:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1059061760 [June 12, 2025 at 9:11:07 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1059061760 [June 12, 2025 at 9:11:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1059061760 [June 12, 2025 at 9:11:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1059061760 [June 12, 2025 at 9:11:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1059061760 [June 12, 2025 at 9:11:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1059061760 [June 12, 2025 at 9:11:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1059061760 [June 12, 2025 at 9:11:08 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1059061760