Class org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariantsIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers.variantutils > LeftAlignAndTrimVariantsIntegrationTest
9

tests
0

failures
0

ignored
1.124s

duration
100%

successful

Tests

Test Duration Result
testLefAlignRequireReference[0](src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf) 0.124s 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, ) 0.127s 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) 0.164s 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) 0.155s 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) 0.118s 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) 0.123s 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) 0.107s 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) 0.102s passed
testSplitAllelesWithASFilters 0.104s passed

Standard output

--------------------------------------------------------------------------------
[16:12:24] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--requireReference
--------------------------------------------------------------------------------
[16:12:24] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf
--------------------------------------------------------------------------------
[16:12:24] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf
--------------------------------------------------------------------------------
[16:12:24] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf
--------------------------------------------------------------------------------
[16:12:24] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf
--------------------------------------------------------------------------------
[16:12:24] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf
--------------------------------------------------------------------------------
[16:12:24] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf
--------------------------------------------------------------------------------
[16:12:24] Executing test LeftAlignAndTrimVariantsIntegrationTest:testLeftAlignment--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf
--------------------------------------------------------------------------------
[16:12:25] Executing test LeftAlignAndTrimVariantsIntegrationTest:testSplitAllelesWithASFilters--src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_split_with_AS_filters.vcf

Standard error

[May 19, 2025 at 4:12:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:24 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[May 19, 2025 at 4:12:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000