Test Summary
|
94%
successful |
Failed tests
- BwaMemIntegrationTest. loadIndex
- IntelInflaterDeflaterIntegrationTest. deflateInflateWithIntel
- IntelInflaterDeflaterIntegrationTest. testIntelDeflaterIsAvailable
- IntelInflaterDeflaterIntegrationTest. testIntelInflaterIsAvailable
- GenomicsDBIntegrationTest. testAsAuxiliaryVariants
- GenomicsDBIntegrationTest. testAsDrivingVariants
- GenomicsDBIntegrationTest. testRestrictingIntervals
- GenomicsDBIntegrationTest. testWithIntervalsAsAuxiliary
- GenomicsDBIntegrationTest. testWithIntervalsDriving
- BwaMemIndexImageCreatorIntegrationTest. testImageFileGeneration
- CollectReadCountsIntegrationTest. testHDF5Output[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/collect-read-counts-NA12878.bam, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/collect-read-counts-NA12878-expected.tsv)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[0](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[10](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 1, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[11](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 10, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[12](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[13](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[14](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[15](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[16](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[17](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[18](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[19](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[1](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[20](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[21](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --number-of-eigensamples 0, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[22](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --number-of-eigensamples 1, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[23](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --number-of-eigensamples 10, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[24](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[25](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[26](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[27](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[28](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[29](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[2](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[30](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[31](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[32](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[33](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 0, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[34](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 1, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[35](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 10, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[36](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[37](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[38](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[39](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[3](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[40](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[41](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[42](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[43](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[44](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[45](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --number-of-eigensamples 0, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[46](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --number-of-eigensamples 1, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[47](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --number-of-eigensamples 10, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[4](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[5](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[6](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[7](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[8](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv, true)
- DenoiseReadCountsIntegrationTest. testDenoiseReadCounts[9](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 0, true)
- ModelSegmentsIntegrationTest. testValidDataModesMultipleSamples[0](multiple-sample-cr-ac-nac, [/home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-denoised-copy-ratios-SM-74P4M-v1-chr20.denoisedCR.tsv, /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-2-denoised-copy-ratios-SM-74P4M-v1-chr20.denoisedCR.tsv], [/home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-allelic-counts-SM-74P4M-v1-chr20.allelicCounts.tsv, /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-2-allelic-counts-SM-74P4M-v1-chr20.allelicCounts.tsv], /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-normal-allelic-counts-SM-74NEG-v1-chr20.allelicCounts.tsv)
- ModelSegmentsIntegrationTest. testValidDataModesMultipleSamples[1](multiple-sample-cr-ac, [/home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-denoised-copy-ratios-SM-74P4M-v1-chr20.denoisedCR.tsv, /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-2-denoised-copy-ratios-SM-74P4M-v1-chr20.denoisedCR.tsv], [/home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-allelic-counts-SM-74P4M-v1-chr20.allelicCounts.tsv, /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-2-allelic-counts-SM-74P4M-v1-chr20.allelicCounts.tsv], null)
- ModelSegmentsIntegrationTest. testValidDataModesMultipleSamples[2](multiple-sample-ac-nac, null, [/home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-allelic-counts-SM-74P4M-v1-chr20.allelicCounts.tsv, /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-2-allelic-counts-SM-74P4M-v1-chr20.allelicCounts.tsv], /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-normal-allelic-counts-SM-74NEG-v1-chr20.allelicCounts.tsv)
- ModelSegmentsIntegrationTest. testValidDataModesMultipleSamples[4](multiple-sample-ac, null, [/home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-allelic-counts-SM-74P4M-v1-chr20.allelicCounts.tsv, /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-2-allelic-counts-SM-74P4M-v1-chr20.allelicCounts.tsv], null)
- ModelSegmentsIntegrationTest. testValidDataModesSingleSample[0](single-sample-cr-ac-nac, /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-denoised-copy-ratios-SM-74P4M-v1-chr20.denoisedCR.tsv, /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-allelic-counts-SM-74P4M-v1-chr20.allelicCounts.tsv, /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-normal-allelic-counts-SM-74NEG-v1-chr20.allelicCounts.tsv)
- ModelSegmentsIntegrationTest. testValidDataModesSingleSample[1](single-sample-cr-ac, /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-denoised-copy-ratios-SM-74P4M-v1-chr20.denoisedCR.tsv, /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-allelic-counts-SM-74P4M-v1-chr20.allelicCounts.tsv, null)
- ModelSegmentsIntegrationTest. testValidDataModesSingleSample[2](single-sample-ac-nac, null, /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-allelic-counts-SM-74P4M-v1-chr20.allelicCounts.tsv, /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-normal-allelic-counts-SM-74NEG-v1-chr20.allelicCounts.tsv)
- ModelSegmentsIntegrationTest. testValidDataModesSingleSample[4](single-sample-ac, null, /home/runner/work/gatk/gatk/src/test/resources/large/org/broadinstitute/hellbender/tools/copynumber/model-segments-wes-tumor-1-allelic-counts-SM-74P4M-v1-chr20.allelicCounts.tsv, null)
- CompareReferencesIntegrationTest. testFullAlignmentMode[0](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr2multiplesnps.fasta, hg19mini.fasta_hg19mini_chr2multiplesnps.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_chr2multiplesnps.fasta.vcf)
- CompareReferencesIntegrationTest. testFullAlignmentMode[1](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr1indel.fasta, hg19mini.fasta_hg19mini_chr1indel.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.testDeletion.hg19mini.fasta_hg19mini_chr1indel.fasta.vcf)
- CompareReferencesIntegrationTest. testFullAlignmentMode[2](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_chr1indel.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, hg19mini_chr1indel.fasta_hg19mini.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.testInsertion.hg19mini_chr1indel.fasta_hg19mini.fasta.vcf)
- CompareReferencesIntegrationTest. testFullAlignmentMode[3](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_snpsmultiplecontigs.fasta, hg19mini.fasta_hg19mini_snpsmultiplecontigs.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_snpsmultiplecontigs.fasta.vcf)
- CompareReferencesIntegrationTest. testFullAlignmentMode[4](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_snpandindel.fasta, hg19mini.fasta_hg19mini_snpandindel.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.SNPandINDEL.hg19mini.fasta_hg19mini_snpandindel.fasta.vcf)
- CompareReferencesIntegrationTest. testFullAlignmentMode[5](src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini.fasta, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/hg19mini_manySNPsINDELs.fasta, hg19mini.fasta_hg19mini_manySNPsINDELs.fasta.vcf, src/test/resources/org/broadinstitute/hellbender/tools/reference/CompareReferences/expected.hg19mini.fasta_hg19mini_manySNPsINDELs.fasta.vcf)
- BwaAndMarkDuplicatesPipelineSparkIntegrationTest. test
- BwaSparkIntegrationTest. testPairedEnd
- BwaSparkIntegrationTest. testSingleEnd
- PathSeqBwaSparkIntegrationTest. testBwaTool[0](basic_input.bam, basic_output.paired.bam)
- PathSeqFilterSparkIntegrationTest. testFilterTool[3](basic_input.bam, bwa_output.paired.bam, bwa_output.unpaired.bam, bwa_filter.metrics, false, true, false, false, true)
- PathSeqFilterSparkIntegrationTest. testFilterTool[5](basic_input.bam, all_output.paired.bam, all_output.unpaired.bam, all_filter.metrics, false, false, true, true, true)
- PathSeqPipelineSparkIntegrationTest. testPipelineTool[0](pipeline_input.bam, pipeline_output.bam, pipeline_output.txt, pipeline_output.filter.metrics, pipeline_output.score.metrics, false)
- PathSeqPipelineSparkIntegrationTest. testPipelineTool[1](pipeline_input_aligned.bam, pipeline_output_aligned.bam, pipeline_output_aligned.txt, pipeline_output_aligned.filter.metrics, pipeline_output_aligned.score.metrics, true)
- FindBreakpointEvidenceSparkIntegrationTest. testFindBreakpointRunnableLocal[0](FindBreakpointEvidenceSparkIntegrationTestArgs{bam-loc='/home/runner/work/gatk/gatk/src/test/resources/large//sv/SVIntegrationTest_hg19.bam', kmer-ignore-list-loc='src/test/resources/org/broadinstitute/hellbender/tools/spark/sv/integration/inputs/dummy.kill.kmers', aligner-ref-index-img-loc='/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.img', output-dir='/tmp/forNew2008707110744064124', bam-coverage='10.0'})
- FindBreakpointEvidenceSparkIntegrationTest. testFindBreakpointRunnableMiniCluster[0](FindBreakpointEvidenceSparkIntegrationTestArgs{bam-loc='/home/runner/work/gatk/gatk/src/test/resources/large//sv/SVIntegrationTest_hg19.bam', kmer-ignore-list-loc='src/test/resources/org/broadinstitute/hellbender/tools/spark/sv/integration/inputs/dummy.kill.kmers', aligner-ref-index-img-loc='/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.img', output-dir='/tmp/forNew3452413354981422584', bam-coverage='10.0'})
- StructuralVariationDiscoveryPipelineSparkIntegrationTest. testSVDiscoverPipelineRunnableLocal[0](StructuralVariationDiscoveryPipelineSparkIntegrationTestArgs{bam-loc='/home/runner/work/gatk/gatk/src/test/resources/large//sv/SVIntegrationTest_hg19.bam', kmer-ignore-list-loc='src/test/resources/org/broadinstitute/hellbender/tools/spark/sv/integration/inputs/dummy.kill.kmers', aligner-fef-index-img-loc='/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.img', cnv-calls-loc='src/test/resources/org/broadinstitute/hellbender/tools/spark/sv/integration/inputs/hg19_DEL_cnv_calls.vcf', output-dir='/tmp/new921381074256615202'})
- StructuralVariationDiscoveryPipelineSparkIntegrationTest. testSVDiscoverPipelineRunnableMiniCluster[0](StructuralVariationDiscoveryPipelineSparkIntegrationTestArgs{bam-loc='/home/runner/work/gatk/gatk/src/test/resources/large//sv/SVIntegrationTest_hg19.bam', kmer-ignore-list-loc='src/test/resources/org/broadinstitute/hellbender/tools/spark/sv/integration/inputs/dummy.kill.kmers', aligner-fef-index-img-loc='/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.img', cnv-calls-loc='src/test/resources/org/broadinstitute/hellbender/tools/spark/sv/integration/inputs/hg19_DEL_cnv_calls.vcf', output-dir='/tmp/new10220892705178568894'})
- GenotypeGVCFsIntegrationTest. assertMatchingAnnotationsFromGenomicsDB_newMQformat[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/expected.testGVCFMode.gatk4.g.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.singleSample.genotyped.vcf, 20:1-11000000, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
- GenotypeGVCFsIntegrationTest. assertMatchingGenotypesFromGenomicsDB[0](src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcf.basepairResolution.gvcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcf.basepairResolution.gatk3.7_30_ga4f720357.output.vcf, 20:1-11000000, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
- GenotypeGVCFsIntegrationTest. assertMatchingGenotypesFromGenomicsDB[2](/home/runner/work/gatk/gatk/src/test/resources/large/gvcfs/CEUTrio.20.21.gatk3.4.g.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.gatk3.7_30_ga4f720357.expected.vcf, 20:1-11000000, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
- GenotypeGVCFsIntegrationTest. assertMatchingGenotypesFromGenomicsDB[4](/home/runner/work/gatk/gatk/src/test/resources/large/gvcfs/CEUTrio.20.21.gatk3.4.g.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.21.gatk3.7_30_ga4f720357.expected.vcf, 21:1-11000000, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
- GenotypeGVCFsIntegrationTest. testGDBMaxAltsEqualsGGVCFsMaxAlts
- GenotypeGVCFsIntegrationTest. testGDBMaxAltsLessThanGGVCFsMaxAlts
- GenotypeGVCFsIntegrationTest. testGenotypeGVCFsMultiIntervalGDBQuery[0](/home/runner/work/gatk/gatk/src/test/resources/large/gvcfs/CEUTrio.20.21.gatk3.4.g.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/NA12878.mergedIntervals.vcf, [20:10000117-10000127, 20:10000137-10000147, 20:10000157-10000167, 20:10000177-10000187, 20:10000197-10000207, 20:10000217-10000227, 20:10000237-10000247, 20:10000257-10000267, 20:10000277-10000287, 20:10000297-10000307, 20:10000317-10000327, 20:10000337-10000347, 20:10000357-10000367, 20:10000377-10000387, 20:10000397-10000407, 20:10000417-10000427, 20:10000437-10000447, 20:10000457-10000467, 20:10000477-10000487, 20:10000497-10000507, 20:10000517-10000527, 20:10000537-10000547, 20:10000557-10000567, 20:10000577-10000587, 20:10000597-10000607, 20:10000617-10000627, 20:10000637-10000647, 20:10000657-10000667, 20:10000677-10000687, 20:10000697-10000707, 20:10000717-10000727, 20:10000737-10000747, 20:10000757-10000767, 20:10000777-10000787, 20:10000797-10000807, 20:10000817-10000827, 20:10000837-10000847, 20:10000857-10000867, 20:10000877-10000887, 20:10000897-10000907, 20:10000917-10000927, 20:10000937-10000947, 20:10000957-10000967, 20:10000977-10000987, 20:10000997-10001007, 20:10001017-10001027, 20:10001037-10001047, 20:10001057-10001067, 20:10001077-10001087, 20:10001097-10001107, 20:10001117-10001127, 20:10001137-10001147, 20:10001157-10001167, 20:10001177-10001187, 20:10001197-10001207, 20:10001217-10001227, 20:10001237-10001247, 20:10001257-10001267, 20:10001277-10001287, 20:10001297-10001307, 20:10001317-10001327, 20:10001337-10001347, 20:10001357-10001367, 20:10001377-10001387, 20:10001397-10001407, 20:10001417-10001427, 20:10001437-10001447, 20:10001457-10001467, 20:10001477-10001487, 20:10001497-10001507, 20:10001517-10001527, 20:10001537-10001547, 20:10001557-10001567, 20:10001577-10001587, 20:10001597-10001607, 20:10001617-10001627, 20:10001637-10001647, 20:10001657-10001667, 20:10001677-10001687, 20:10001697-10001707, 20:10001717-10001727, 20:10001737-10001747, 20:10001757-10001767, 20:10001777-10001787, 20:10001797-10001807, 20:10001817-10001827, 20:10001837-10001847, 20:10001857-10001867, 20:10001877-10001887, 20:10001897-10001907, 20:10001917-10001927, 20:10001937-10001947, 20:10001957-10001967, 20:10001977-10001987, 20:10001997-10002007, 20:10002017-10002027, 20:10002037-10002047, 20:10002057-10002067, 20:10002077-10002087, 20:10002097-10002107, 20:10002117-10002127, 20:10002137-10002147, 20:10002157-10002167, 20:10002177-10002187, 20:10002197-10002207, 20:10002217-10002227, 20:10002237-10002247, 20:10002257-10002267, 20:10002277-10002287, 20:10002297-10002307, 20:10002317-10002327, 20:10002337-10002347, 20:10002357-10002367, 20:10002377-10002387, 20:10002397-10002407, 20:10002417-10002427, 20:10002437-10002447, 20:10002457-10002467, 20:10002477-10002487, 20:10002497-10002507, 20:10002517-10002527, 20:10002537-10002547, 20:10002557-10002567, 20:10002577-10002587, 20:10002597-10002607, 20:10002617-10002627, 20:10002637-10002647, 20:10002657-10002667, 20:10002677-10002687, 20:10002697-10002707, 20:10002717-10002727, 20:10002737-10002747, 20:10002757-10002767, 20:10002777-10002787, 20:10002797-10002807, 20:10002817-10002827, 20:10002837-10002847, 20:10002857-10002867, 20:10002877-10002887, 20:10002897-10002907, 20:10002917-10002927, 20:10002937-10002947, 20:10002957-10002967, 20:10002977-10002987, 20:10002997-10003007, 20:10003017-10003027, 20:10003037-10003047, 20:10003057-10003067, 20:10003077-10003087, 20:10003097-10003107, 20:10003117-10003127, 20:10003137-10003147, 20:10003157-10003167, 20:10003177-10003187, 20:10003197-10003207, 20:10003217-10003227, 20:10003237-10003247, 20:10003257-10003267, 20:10003277-10003287, 20:10003297-10003307, 20:10003317-10003327, 20:10003337-10003347, 20:10003357-10003367, 20:10003377-10003387, 20:10003397-10003407, 20:10003417-10003427, 20:10003437-10003447, 20:10003457-10003467, 20:10003477-10003487, 20:10003497-10003507, 20:10003517-10003527, 20:10003537-10003547, 20:10003557-10003567, 20:10003577-10003587, 20:10003597-10003607, 20:10003617-10003627, 20:10003637-10003647, 20:10003657-10003667, 20:10003677-10003687, 20:10003697-10003707, 20:10003717-10003727, 20:10003737-10003747, 20:10003757-10003767, 20:10003777-10003787, 20:10003797-10003807, 20:10003817-10003827, 20:10003837-10003847, 20:10003857-10003867, 20:10003877-10003887, 20:10003897-10003907, 20:10003917-10003927, 20:10003937-10003947, 20:10003957-10003967, 20:10003977-10003987, 20:10003997-10004007, 20:10004017-10004027, 20:10004037-10004047, 20:10004057-10004067, 20:10004077-10004087, 20:10004097-10004107, 20:10004117-10004127, 20:10004137-10004147, 20:10004157-10004167, 20:10004177-10004187, 20:10004197-10004207, 20:10004217-10004227, 20:10004237-10004247, 20:10004257-10004267, 20:10004277-10004287, 20:10004297-10004307, 20:10004317-10004327, 20:10004337-10004347, 20:10004357-10004367, 20:10004377-10004387, 20:10004397-10004407, 20:10004417-10004427, 20:10004437-10004447, 20:10004457-10004467, 20:10004477-10004487, 20:10004497-10004507, 20:10004517-10004527, 20:10004537-10004547, 20:10004557-10004567, 20:10004577-10004587, 20:10004597-10004607, 20:10004617-10004627, 20:10004637-10004647, 20:10004657-10004667, 20:10004677-10004687, 20:10004697-10004707, 20:10004717-10004727, 20:10004737-10004747, 20:10004757-10004767, 20:10004777-10004787, 20:10004797-10004807, 20:10004817-10004827, 20:10004837-10004847, 20:10004857-10004867, 20:10004877-10004887, 20:10004897-10004907, 20:10004917-10004927, 20:10004937-10004947, 20:10004957-10004967, 20:10004977-10004987, 20:10004997-10005007, 20:10005017-10005027, 20:10005037-10005047, 20:10005057-10005067, 20:10005077-10005087, 20:10005097-10005107, 20:10005117-10005127, 20:10005137-10005147, 20:10005157-10005167, 20:10005177-10005187, 20:10005197-10005207, 20:10005217-10005227, 20:10005237-10005247, 20:10005257-10005267, 20:10005277-10005287, 20:10005297-10005307, 20:10005317-10005327, 20:10005337-10005347, 20:10005357-10005367, 20:10005377-10005387, 20:10005397-10005407, 20:10005417-10005427, 20:10005437-10005447, 20:10005457-10005467, 20:10005477-10005487, 20:10005497-10005507, 20:10005517-10005527, 20:10005537-10005547, 20:10005557-10005567, 20:10005577-10005587, 20:10005597-10005607, 20:10005617-10005627, 20:10005637-10005647, 20:10005657-10005667, 20:10005677-10005687, 20:10005697-10005707, 20:10005717-10005727, 20:10005737-10005747, 20:10005757-10005767, 20:10005777-10005787, 20:10005797-10005807, 20:10005817-10005827, 20:10005837-10005847, 20:10005857-10005867, 20:10005877-10005887, 20:10005897-10005907, 20:10005917-10005927, 20:10005937-10005947, 20:10005957-10005967, 20:10005977-10005987, 20:10005997-10006007, 20:10006017-10006027, 20:10006037-10006047, 20:10006057-10006067, 20:10006077-10006087, 20:10006097-10006107, 20:10006117-10006127, 20:10006137-10006147, 20:10006157-10006167, 20:10006177-10006187, 20:10006197-10006207, 20:10006217-10006227, 20:10006237-10006247, 20:10006257-10006267, 20:10006277-10006287, 20:10006297-10006307, 20:10006317-10006327, 20:10006337-10006347, 20:10006357-10006367, 20:10006377-10006387, 20:10006397-10006407, 20:10006417-10006427, 20:10006437-10006447, 20:10006457-10006467, 20:10006477-10006487, 20:10006497-10006507, 20:10006517-10006527, 20:10006537-10006547, 20:10006557-10006567, 20:10006577-10006587, 20:10006597-10006607, 20:10006617-10006627, 20:10006637-10006647, 20:10006657-10006667, 20:10006677-10006687, 20:10006697-10006707, 20:10006717-10006727, 20:10006737-10006747, 20:10006757-10006767, 20:10006777-10006787, 20:10006797-10006807, 20:10006817-10006827, 20:10006837-10006847, 20:10006857-10006867, 20:10006877-10006887, 20:10006897-10006907, 20:10006917-10006927, 20:10006937-10006947, 20:10006957-10006967, 20:10006977-10006987, 20:10006997-10007007, 20:10007017-10007027, 20:10007037-10007047, 20:10007057-10007067, 20:10007077-10007087, 20:10007097-10007107, 20:10007117-10007127, 20:10007137-10007147, 20:10007157-10007167, 20:10007177-10007187, 20:10007197-10007207, 20:10007217-10007227, 20:10007237-10007247, 20:10007257-10007267, 20:10007277-10007287, 20:10007297-10007307, 20:10007317-10007327, 20:10007337-10007347, 20:10007357-10007367, 20:10007377-10007387, 20:10007397-10007407, 20:10007417-10007427, 20:10007437-10007447, 20:10007457-10007467, 20:10007477-10007487, 20:10007497-10007507, 20:10007517-10007527, 20:10007537-10007547, 20:10007557-10007567, 20:10007577-10007587, 20:10007597-10007607, 20:10007617-10007627, 20:10007637-10007647, 20:10007657-10007667, 20:10007677-10007687, 20:10007697-10007707, 20:10007717-10007727, 20:10007737-10007747, 20:10007757-10007767, 20:10007777-10007787, 20:10007797-10007807, 20:10007817-10007827, 20:10007837-10007847, 20:10007857-10007867, 20:10007877-10007887, 20:10007897-10007907, 20:10007917-10007927, 20:10007937-10007947, 20:10007957-10007967, 20:10007977-10007987, 20:10007997-10008007, 20:10008017-10008027, 20:10008037-10008047, 20:10008057-10008067, 20:10008077-10008087, 20:10008097-10008107, 20:10008117-10008127, 20:10008137-10008147, 20:10008157-10008167, 20:10008177-10008187, 20:10008197-10008207, 20:10008217-10008227, 20:10008237-10008247, 20:10008257-10008267, 20:10008277-10008287, 20:10008297-10008307, 20:10008317-10008327, 20:10008337-10008347, 20:10008357-10008367, 20:10008377-10008387, 20:10008397-10008407, 20:10008417-10008427, 20:10008437-10008447, 20:10008457-10008467, 20:10008477-10008487, 20:10008497-10008507, 20:10008517-10008527, 20:10008537-10008547, 20:10008557-10008567, 20:10008577-10008587, 20:10008597-10008607, 20:10008617-10008627, 20:10008637-10008647, 20:10008657-10008667, 20:10008677-10008687, 20:10008697-10008707, 20:10008717-10008727, 20:10008737-10008747, 20:10008757-10008767, 20:10008777-10008787, 20:10008797-10008807, 20:10008817-10008827, 20:10008837-10008847, 20:10008857-10008867, 20:10008877-10008887, 20:10008897-10008907, 20:10008917-10008927, 20:10008937-10008947, 20:10008957-10008967, 20:10008977-10008987, 20:10008997-10009007, 20:10009017-10009027, 20:10009037-10009047, 20:10009057-10009067, 20:10009077-10009087, 20:10009097-10009107, 20:10009117-10009127, 20:10009137-10009147, 20:10009157-10009167, 20:10009177-10009187, 20:10009197-10009207, 20:10009217-10009227, 20:10009237-10009247, 20:10009257-10009267, 20:10009277-10009287, 20:10009297-10009307, 20:10009317-10009327, 20:10009337-10009347, 20:10009357-10009367, 20:10009377-10009387, 20:10009397-10009407, 20:10009417-10009427, 20:10009437-10009447, 20:10009457-10009467, 20:10009477-10009487, 20:10009497-10009507, 20:10009517-10009527, 20:10009537-10009547, 20:10009557-10009567, 20:10009577-10009587, 20:10009597-10009607, 20:10009617-10009627, 20:10009637-10009647, 20:10009657-10009667, 20:10009677-10009687, 20:10009697-10009707, 20:10009717-10009727, 20:10009737-10009747, 20:10009757-10009767, 20:10009777-10009787, 20:10009797-10009807, 20:10009817-10009827, 20:10009837-10009847, 20:10009857-10009867, 20:10009877-10009887, 20:10009897-10009907, 20:10009917-10009927, 20:10009937-10009947, 20:10009957-10009967, 20:10009977-10009987, 20:10009997-10010007, 20:10010017-10010027, 20:10010037-10010047, 20:10010057-10010067, 20:10010077-10010087, 20:10010097-10010107, 20:10010117-10010127, 20:10010137-10010147, 20:10010157-10010167, 20:10010177-10010187, 20:10010197-10010207, 20:10010217-10010227, 20:10010237-10010247, 20:10010257-10010267, 20:10010277-10010287, 20:10010297-10010307, 20:10010317-10010327, 20:10010337-10010347, 20:10010357-10010367, 20:10010377-10010387, 20:10010397-10010407, 20:10010417-10010427, 20:10010437-10010447, 20:10010457-10010467, 20:10010477-10010487, 20:10010497-10010507, 20:10010517-10010527, 20:10010537-10010547, 20:10010557-10010567, 20:10010577-10010587, 20:10010597-10010607, 20:10010617-10010627, 20:10010637-10010647, 20:10010657-10010667, 20:10010677-10010687, 20:10010697-10010707, 20:10010717-10010727, 20:10010737-10010747, 20:10010757-10010767, 20:10010777-10010787, 20:10010797-10010807, 20:10010817-10010827, 20:10010837-10010847, 20:10010857-10010867, 20:10010877-10010887, 20:10010897-10010907, 20:10010917-10010927, 20:10010937-10010947, 20:10010957-10010967, 20:10010977-10010987, 20:10010997-10011007, 20:10011017-10011027, 20:10011037-10011047, 20:10011057-10011067, 20:10011077-10011087, 20:10011097-10011107, 20:10011117-10011127, 20:10011137-10011147, 20:10011157-10011167, 20:10011177-10011187, 20:10011197-10011207, 20:10011217-10011227, 20:10011237-10011247, 20:10011257-10011267, 20:10011277-10011287, 20:10011297-10011307, 20:10011317-10011327, 20:10011337-10011347, 20:10011357-10011367, 20:10011377-10011387, 20:10011397-10011407, 20:10011417-10011427, 20:10011437-10011447, 20:10011457-10011467, 20:10011477-10011487, 20:10011497-10011507, 20:10011517-10011527, 20:10011537-10011547, 20:10011557-10011567, 20:10011577-10011587, 20:10011597-10011607, 20:10011617-10011627, 20:10011637-10011647, 20:10011657-10011667, 20:10011677-10011687, 20:10011697-10011707, 20:10011717-10011727, 20:10011737-10011747, 20:10011757-10011767, 20:10011777-10011787, 20:10011797-10011807, 20:10011817-10011827, 20:10011837-10011847, 20:10011857-10011867, 20:10011877-10011887, 20:10011897-10011907, 20:10011917-10011927, 20:10011937-10011947, 20:10011957-10011967, 20:10011977-10011987, 20:10011997-10012007, 20:10012017-10012027, 20:10012037-10012047, 20:10012057-10012067, 20:10012077-10012087, 20:10012097-10012107, 20:10012117-10012127, 20:10012137-10012147, 20:10012157-10012167, 20:10012177-10012187, 20:10012197-10012207, 20:10012217-10012227, 20:10012237-10012247, 20:10012257-10012267, 20:10012277-10012287, 20:10012297-10012307, 20:10012317-10012327, 20:10012337-10012347, 20:10012357-10012367, 20:10012377-10012387, 20:10012397-10012407, 20:10012417-10012427, 20:10012437-10012447, 20:10012457-10012467, 20:10012477-10012487, 20:10012497-10012507, 20:10012517-10012527, 20:10012537-10012547, 20:10012557-10012567, 20:10012577-10012587, 20:10012597-10012607, 20:10012617-10012627, 20:10012637-10012647, 20:10012657-10012667, 20:10012677-10012687, 20:10012697-10012707, 20:10012717-10012727, 20:10012737-10012747, 20:10012757-10012767, 20:10012777-10012787, 20:10012797-10012807, 20:10012817-10012827, 20:10012837-10012847, 20:10012857-10012867, 20:10012877-10012887, 20:10012897-10012907, 20:10012917-10012927, 20:10012937-10012947, 20:10012957-10012967, 20:10012977-10012987, 20:10012997-10013007, 20:10013017-10013027, 20:10013037-10013047, 20:10013057-10013067, 20:10013077-10013087, 20:10013097-10013107, 20:10013117-10013127, 20:10013137-10013147, 20:10013157-10013167, 20:10013177-10013187, 20:10013197-10013207, 20:10013217-10013227, 20:10013237-10013247, 20:10013257-10013267, 20:10013277-10013287, 20:10013297-10013307, 20:10013317-10013327, 20:10013337-10013347, 20:10013357-10013367, 20:10013377-10013387, 20:10013397-10013407, 20:10013417-10013427, 20:10013437-10013447, 20:10013457-10013467, 20:10013477-10013487, 20:10013497-10013507, 20:10013517-10013527, 20:10013537-10013547, 20:10013557-10013567, 20:10013577-10013587, 20:10013597-10013607, 20:10013617-10013627, 20:10013637-10013647, 20:10013657-10013667, 20:10013677-10013687, 20:10013697-10013707, 20:10013717-10013727, 20:10013737-10013747, 20:10013757-10013767, 20:10013777-10013787, 20:10013797-10013807, 20:10013817-10013827, 20:10013837-10013847, 20:10013857-10013867, 20:10013877-10013887, 20:10013897-10013907, 20:10013917-10013927, 20:10013937-10013947, 20:10013957-10013967, 20:10013977-10013987, 20:10013997-10014007, 20:10014017-10014027, 20:10014037-10014047, 20:10014057-10014067, 20:10014077-10014087, 20:10014097-10014107, 20:10014117-10014127, 20:10014137-10014147, 20:10014157-10014167, 20:10014177-10014187, 20:10014197-10014207, 20:10014217-10014227, 20:10014237-10014247, 20:10014257-10014267, 20:10014277-10014287, 20:10014297-10014307, 20:10014317-10014327, 20:10014337-10014347, 20:10014357-10014367, 20:10014377-10014387, 20:10014397-10014407, 20:10014417-10014427, 20:10014437-10014447, 20:10014457-10014467, 20:10014477-10014487, 20:10014497-10014507, 20:10014517-10014527, 20:10014537-10014547, 20:10014557-10014567, 20:10014577-10014587, 20:10014597-10014607, 20:10014617-10014627, 20:10014637-10014647, 20:10014657-10014667, 20:10014677-10014687, 20:10014697-10014707, 20:10014717-10014727, 20:10014737-10014747, 20:10014757-10014767, 20:10014777-10014787, 20:10014797-10014807, 20:10014817-10014827, 20:10014837-10014847, 20:10014857-10014867, 20:10014877-10014887, 20:10014897-10014907, 20:10014917-10014927, 20:10014937-10014947, 20:10014957-10014967, 20:10014977-10014987, 20:10014997-10015007, 20:10015017-10015027, 20:10015037-10015047, 20:10015057-10015067, 20:10015077-10015087, 20:10015097-10015107, 20:10015117-10015127, 20:10015137-10015147, 20:10015157-10015167, 20:10015177-10015187, 20:10015197-10015207, 20:10015217-10015227, 20:10015237-10015247, 20:10015257-10015267, 20:10015277-10015287, 20:10015297-10015307, 20:10015317-10015327, 20:10015337-10015347, 20:10015357-10015367, 20:10015377-10015387, 20:10015397-10015407, 20:10015417-10015427, 20:10015437-10015447, 20:10015457-10015467, 20:10015477-10015487, 20:10015497-10015507, 20:10015517-10015527, 20:10015537-10015547, 20:10015557-10015567, 20:10015577-10015587, 20:10015597-10015607, 20:10015617-10015627, 20:10015637-10015647, 20:10015657-10015667, 20:10015677-10015687, 20:10015697-10015707, 20:10015717-10015727, 20:10015737-10015747, 20:10015757-10015767, 20:10015777-10015787, 20:10015797-10015807, 20:10015817-10015827, 20:10015837-10015847, 20:10015857-10015867, 20:10015877-10015887, 20:10015897-10015907, 20:10015917-10015927, 20:10015937-10015947, 20:10015957-10015967, 20:10015977-10015987, 20:10015997-10016007, 20:10016017-10016027, 20:10016037-10016047, 20:10016057-10016067, 20:10016077-10016087, 20:10016097-10016107, 20:10016117-10016127, 20:10016137-10016147, 20:10016157-10016167, 20:10016177-10016187, 20:10016197-10016207, 20:10016217-10016227, 20:10016237-10016247, 20:10016257-10016267, 20:10016277-10016287, 20:10016297-10016307, 20:10016317-10016327, 20:10016337-10016347, 20:10016357-10016367, 20:10016377-10016387, 20:10016397-10016407, 20:10016417-10016427, 20:10016437-10016447, 20:10016457-10016467, 20:10016477-10016487, 20:10016497-10016507, 20:10016517-10016527, 20:10016537-10016547, 20:10016557-10016567, 20:10016577-10016587, 20:10016597-10016607, 20:10016617-10016627, 20:10016637-10016647, 20:10016657-10016667, 20:10016677-10016687, 20:10016697-10016707, 20:10016717-10016727, 20:10016737-10016747, 20:10016757-10016767, 20:10016777-10016787, 20:10016797-10016807, 20:10016817-10016827, 20:10016837-10016847, 20:10016857-10016867, 20:10016877-10016887, 20:10016897-10016907, 20:10016917-10016927, 20:10016937-10016947, 20:10016957-10016967, 20:10016977-10016987, 20:10016997-10017007, 20:10017017-10017027, 20:10017037-10017047, 20:10017057-10017067, 20:10017077-10017087, 20:10017097-10017107, 20:10017117-10017127, 20:10017137-10017147, 20:10017157-10017167, 20:10017177-10017187, 20:10017197-10017207, 20:10017217-10017227, 20:10017237-10017247, 20:10017257-10017267, 20:10017277-10017287, 20:10017297-10017307, 20:10017317-10017327, 20:10017337-10017347, 20:10017357-10017367, 20:10017377-10017387, 20:10017397-10017407, 20:10017417-10017427, 20:10017437-10017447, 20:10017457-10017467, 20:10017477-10017487, 20:10017497-10017507, 20:10017517-10017527, 20:10017537-10017547, 20:10017557-10017567, 20:10017577-10017587, 20:10017597-10017607, 20:10017617-10017627, 20:10017637-10017647, 20:10017657-10017667, 20:10017677-10017687, 20:10017697-10017707, 20:10017717-10017727, 20:10017737-10017747, 20:10017757-10017767, 20:10017777-10017787, 20:10017797-10017807, 20:10017817-10017827, 20:10017837-10017847, 20:10017857-10017867, 20:10017877-10017887, 20:10017897-10017907, 20:10017917-10017927, 20:10017937-10017947, 20:10017957-10017967, 20:10017977-10017987, 20:10017997-10018007, 20:10018017-10018027, 20:10018037-10018047, 20:10018057-10018067, 20:10018077-10018087, 20:10018097-10018107, 20:10018117-10018127, 20:10018137-10018147, 20:10018157-10018167, 20:10018177-10018187, 20:10018197-10018207, 20:10018217-10018227, 20:10018237-10018247, 20:10018257-10018267, 20:10018277-10018287, 20:10018297-10018307, 20:10018317-10018327, 20:10018337-10018347, 20:10018357-10018367, 20:10018377-10018387, 20:10018397-10018407, 20:10018417-10018427, 20:10018437-10018447, 20:10018457-10018467, 20:10018477-10018487, 20:10018497-10018507, 20:10018517-10018527, 20:10018537-10018547, 20:10018557-10018567, 20:10018577-10018587, 20:10018597-10018607, 20:10018617-10018627, 20:10018637-10018647, 20:10018657-10018667, 20:10018677-10018687, 20:10018697-10018707, 20:10018717-10018727, 20:10018737-10018747, 20:10018757-10018767, 20:10018777-10018787, 20:10018797-10018807, 20:10018817-10018827, 20:10018837-10018847, 20:10018857-10018867, 20:10018877-10018887, 20:10018897-10018907, 20:10018917-10018927, 20:10018937-10018947, 20:10018957-10018967, 20:10018977-10018987, 20:10018997-10019007, 20:10019017-10019027, 20:10019037-10019047, 20:10019057-10019067, 20:10019077-10019087, 20:10019097-10019107, 20:10019117-10019127, 20:10019137-10019147, 20:10019157-10019167, 20:10019177-10019187, 20:10019197-10019207, 20:10019217-10019227, 20:10019237-10019247, 20:10019257-10019267, 20:10019277-10019287, 20:10019297-10019307, 20:10019317-10019327, 20:10019337-10019347, 20:10019357-10019367, 20:10019377-10019387, 20:10019397-10019407, 20:10019417-10019427, 20:10019437-10019447, 20:10019457-10019467, 20:10019477-10019487, 20:10019497-10019507, 20:10019517-10019527, 20:10019537-10019547, 20:10019557-10019567, 20:10019577-10019587, 20:10019597-10019607, 20:10019617-10019627, 20:10019637-10019647, 20:10019657-10019667, 20:10019677-10019687, 20:10019697-10019707, 20:10019717-10019727, 20:10019737-10019747, 20:10019757-10019767, 20:10019777-10019787, 20:10019797-10019807, 20:10019817-10019827, 20:10019837-10019847, 20:10019857-10019867, 20:10019877-10019887, 20:10019897-10019907, 20:10019917-10019927, 20:10019937-10019947, 20:10019957-10019967, 20:10019977-10019987, 20:10019997-10020007, 20:10020017-10020027, 20:10020037-10020047, 20:10020057-10020067, 20:10020077-10020087, 20:10020097-10020107], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
- GenotypeGVCFsIntegrationTest. testMaxAltsToCombineInGenomicsDB
- GenotypeGVCFsIntegrationTest. testMixHaploidDiploidHighAltSite
- GenotypeGVCFsIntegrationTest. testNoReadsOutputAsNoCall
- GenotypeGVCFsIntegrationTest. testNoReadsReblockedOutputAsNoCall
- GnarlyGenotyperIntegrationTest. gnarlyHomRefNullPLs
- GnarlyGenotyperIntegrationTest. testNoReadsOutputAsNoCall
- GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[0]([Ljava.io.File;@999e3ea, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/haploidPlusDiploid.expected.vcf, null, [chrX:1000000-5000000], [--merge-input-intervals, --variant-output-filtering, STARTS_IN], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)
- GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[1]([Ljava.io.File;@760799e1, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/lotsOfAltsNoPLs.vcf, null, [chr20:257008-257008], [--merge-input-intervals, --variant-output-filtering, STARTS_IN], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)
- GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[2]([Ljava.io.File;@569945cc, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/lotsOfAltsYesPLs.vcf, null, [chr20:257008-257008], [--merge-input-intervals, --variant-output-filtering, STARTS_IN], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)
- GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[3]([Ljava.io.File;@10fd833b, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/fiveSampleTest.vcf, null, [chr20:251370-252000, chr20:263000-265600], [--merge-input-intervals, --variant-output-filtering, STARTS_IN], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)
- GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[4]([Ljava.io.File;@6957cbef, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/fiveSampleTest.vcf, null, [chr20:251370-252000, chr20:263000-265600], [--merge-input-intervals, --variant-output-filtering, STARTS_IN, --genomicsdb-use-bcf-codec], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)
- GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[5]([Ljava.io.File;@478bc828, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/fiveSampleTest.lowerCallThreshold.vcf, null, [chr20:250865-348163], [-stand-call-conf 10], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)
- GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[6]([Ljava.io.File;@6967b531, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/fiveSampleTest.lowerCallThreshold.vcf, null, [chr20:250865-348163], [-stand-call-conf 10, --genomicsdb-use-bcf-codec], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)
- GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[7]([Ljava.io.File;@9fe6edc, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/twoSampleAS.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/twoSampleASDB.vcf, [20:1-2147483647], [], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
- GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[8]([Ljava.io.File;@66d208c5, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/twoSampleAS.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/twoSampleASDB.vcf, [20:1-2147483647], [--genomicsdb-use-bcf-codec], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
- GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[9]([Ljava.io.File;@2f228a1, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/noGTCount.expected.chr20snippet.vcf, null, [chr20:1-2147483647], [], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz)
- DirichletAlleleDepthAndFractionIntegrationTest. testVCFModeIsConsistentWithPastResults[0](/home/runner/work/gatk/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
- DirichletAlleleDepthAndFractionIntegrationTest. testVCFModeIsConsistentWithPastResults[1](/home/runner/work/gatk/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
- GatherBQSRReportsIntegrationTest. testCombine5Reports
- GatherBQSRReportsIntegrationTest. testCombineReportsFromTwoChrs
- FlowBasedAlignmentIntegrationTest. testMatrix
- FilterAlignmentArtifactsIntegrationTest. testDreamTruthData
- HaplotypeBasedVariantRecallerIntegrationTest. testBasic
- ExtractVariantAnnotationsIntegrationTest. testNoResourcesAndExtractUnlabeled
- TrainVariantAnnotationsModelIntegrationTest. testPositiveAndUnlabeledAnnotationNamesAreNotIdentical