Class org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers.sv > SVAnnotateIntegrationTest
6

tests
0

failures
0

ignored
2.081s

duration
100%

successful

Tests

Test Duration Result
testSVAnnotate[0](--variant /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/sv/SVAnnotate/integration.vcf.gz --protein-coding-gtf /home/runner/work/gatk/gatk/src/test/resources/large/SVAnnotate/MANE.selected.GRCh38.v0.95.select_ensembl_genomic.gtf --non-coding-bed /home/runner/work/gatk/gatk/src/test/resources/large/SVAnnotate/noncoding.selected.hg38.bed.gz, ref_panel_1kg_v1_INV_chr21_1, {PREDICTED_INTRONIC=[APP], PREDICTED_NONCODING_BREAKPOINT=[Tommerup_TADanno]}) 0.879s passed
testSVAnnotate[1](--variant /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/sv/SVAnnotate/integration.vcf.gz --non-coding-bed /home/runner/work/gatk/gatk/src/test/resources/large/SVAnnotate/noncoding.selected.hg38.bed.gz, ref_panel_1kg_v1_INV_chr21_1, {PREDICTED_NONCODING_BREAKPOINT=[Tommerup_TADanno]}) 0.736s passed
testSVAnnotate[2](--variant /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/sv/SVAnnotate/integration.vcf.gz --protein-coding-gtf /home/runner/work/gatk/gatk/src/test/resources/large/SVAnnotate/MANE.selected.GRCh38.v0.95.select_ensembl_genomic.gtf, ref_panel_1kg_v1_BND_chr22_7, {PREDICTED_INTRONIC=[BCL2L13]}) 0.127s passed
testSVAnnotate[3](--variant /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/sv/SVAnnotate/integration.vcf.gz --protein-coding-gtf /home/runner/work/gatk/gatk/src/test/resources/large/SVAnnotate/MANE.selected.GRCh38.v0.95.select_ensembl_genomic.gtf --promoter-window-length 8000, ref_panel_1kg_v1_BND_chr22_7, {PREDICTED_INTRONIC=[BCL2L13], PREDICTED_PROMOTER=[ATP6V1E1]}) 0.127s passed
testSVAnnotate[4](--variant /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/sv/SVAnnotate/integration.vcf.gz --protein-coding-gtf /home/runner/work/gatk/gatk/src/test/resources/large/SVAnnotate/MANE.selected.GRCh38.v0.95.select_ensembl_genomic.gtf --max-breakend-as-cnv-length 12000, ref_panel_1kg_v1_BND_chr22_7, {PREDICTED_LOF=[BCL2L13]}) 0.135s passed
testSVAnnotate[5](--variant /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/sv/SVAnnotate/integration.vcf.gz, ref_panel_1kg_v1_BND_chr22_7, {}) 0.077s passed

Standard error

[March 28, 2025 at 10:53:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=736100352
[March 28, 2025 at 10:53:18 PM UTC] org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1063256064
[March 28, 2025 at 10:53:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1063256064
[March 28, 2025 at 10:53:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1063256064
[March 28, 2025 at 10:53:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1063256064
[March 28, 2025 at 10:53:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotate done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1063256064