Package org.broadinstitute.hellbender.tools.copynumber

Failed tests

• 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)

Ignored tests

• CreateReadCountPanelOfNormalsIntegrationTest. test
• CreateReadCountPanelOfNormalsIntegrationTest. testSingleSample
• CreateReadCountPanelOfNormalsIntegrationTest. testZeroEigensamples

Classes