Package org.broadinstitute.hellbender.tools.walkers.vqsr.scalable
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80%
successful |
Failed tests
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[0](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --model-backend PYTHON_IFOREST --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz)
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[1](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --model-backend PYTHON_IFOREST --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz --mode INDEL --resource:mills-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.1-5M.vcf.gz --resource:mills-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.5M-10M.vcf.gz)
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[2](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --python-script /tmp/isolation-forest.10380549983975128824.py --model-backend PYTHON_SCRIPT --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz)
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[3](extract.nonAS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --python-script /tmp/isolation-forest.10380549983975128824.py --model-backend PYTHON_SCRIPT --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz --mode INDEL --resource:mills-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.1-5M.vcf.gz --resource:mills-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.5M-10M.vcf.gz)
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[4](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --model-backend PYTHON_IFOREST --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz)
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[5](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --model-backend PYTHON_IFOREST --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz --mode INDEL --resource:mills-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.1-5M.vcf.gz --resource:mills-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.5M-10M.vcf.gz)
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[6](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snp, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --python-script /tmp/isolation-forest.10380549983975128824.py --model-backend PYTHON_SCRIPT --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz)
- ScoreVariantAnnotationsIntegrationTest. testValidInputs[7](extract.AS.snpIndel.posUn.train.snpIndel.posOnly.IF.score.snpIndel, --variant /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/input/small_callset_low_threshold.sites-only.chr1.1-10M.vcf --do-not-gzip-vcf-output --add-output-vcf-command-line false --python-script /tmp/isolation-forest.10380549983975128824.py --model-backend PYTHON_SCRIPT --mode SNP --resource:omni-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.1-5M.vcf.gz --resource:omni-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/1000G_omni2.5.hg38.chr1.5M-10M.vcf.gz --mode INDEL --resource:mills-training,training=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.1-5M.vcf.gz --resource:mills-calibration,calibration=true /gatkCloneMountPoint/src/test/resources/large/org/broadinstitute/hellbender/tools/walkers/vqsr/scalable/resources/Mills_and_1000G_gold_standard.indels.hg38.chr1.5M-10M.vcf.gz)
Classes
| Class | Tests | Failures | Ignored | Duration | Success rate |
|---|---|---|---|---|---|
| ExtractVariantAnnotationsIntegrationTest | 12 | 0 | 0 | 4.193s | 100% |
| ScoreVariantAnnotationsIntegrationTest | 12 | 8 | 0 | 21.302s | 33% |
| SystemCommandUtilsTest | 2 | 0 | 0 | 0.017s | 100% |
| TrainVariantAnnotationsModelIntegrationTest | 15 | 0 | 0 | 1m1.72s | 100% |