├── .github └── workflows │ └── ci.yml ├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── README.md ├── cwas ├── __init__.py ├── __main__.py ├── annotation.py ├── argparser.py ├── binomial_test.py ├── burden_shift.py ├── burden_test.py ├── categorization.py ├── cli.py ├── configuration.py ├── core │ ├── __init__.py │ ├── annotation │ │ ├── __init__.py │ │ ├── bed.py │ │ └── vep.py │ ├── burden_test │ │ ├── __init__.py │ │ └── binomial.py │ ├── categorization │ │ ├── __init__.py │ │ ├── categorizer.py │ │ ├── category.py │ │ ├── parser.py │ │ └── utils.py │ ├── common.py │ ├── configuration │ │ ├── __init__.py │ │ ├── create.py │ │ └── settings.py │ ├── dawn │ │ ├── __init__.py │ │ ├── clustering.py │ │ └── supernodeWGS.py │ └── preparation │ │ ├── __init__.py │ │ ├── annotation.py │ │ └── bedreader.py ├── correlation.py ├── dawn.py ├── effective_num_test.py ├── env.py ├── extract_variant.py ├── factory.py ├── permutation_test.py ├── preparation.py ├── risk_score.py ├── runnable.py ├── start.py └── utils │ ├── __init__.py │ ├── check.py │ ├── cmd.py │ └── log.py ├── docs ├── Makefile ├── conf.py ├── config │ └── configuration.rst ├── faq │ └── faq.rst ├── index.rst ├── install │ └── installation.rst ├── make.bat ├── quickstart │ ├── advanced_tutorial.rst │ └── quick_tutorial.rst ├── required │ ├── annotations.rst │ └── input.rst ├── requirements.txt ├── steps │ ├── annotation.rst │ ├── burden.rst │ ├── burdenshift.rst │ ├── categorization.rst │ ├── correlation.rst │ ├── dawn.rst │ ├── effective_num_test.rst │ └── risk_score.rst └── utils │ └── extract_variants.rst ├── environment.yml ├── images ├── CWAS_workflow.jpg ├── de_novo_variants.burden_test.volcano_plot.png └── de_novo_variants.lasso_histogram_thres_3.png ├── oryx-build-commands.txt ├── poetry.lock ├── pyproject.toml ├── setup.cfg └── tests ├── __init__.py ├── conftest.py ├── core ├── __init__.py ├── annotation │ ├── __init__.py │ └── test_vep.py ├── categorization │ ├── __init__.py │ ├── test_category.py │ ├── test_parser.py │ └── test_utils.py ├── configuration │ ├── __init__.py │ └── test_create.py ├── dawn │ ├── __init__.py │ ├── test_clustering.py │ └── test_supernodeWGS.py ├── preparation │ ├── __init__.py │ ├── test_annotation.py │ └── test_bedreader.py └── test_common.py ├── test_annotation.py ├── test_binomial_test.py ├── test_configuration.py ├── test_env.py ├── test_factory.py ├── test_file ├── adj_factors.txt ├── adj_factors_other.txt ├── sample.txt ├── sample_other.txt ├── test.burden_test.volcano_plot.pdf ├── test.categorization_result.zarr │ ├── .zgroup │ ├── data │ │ ├── .zarray │ │ └── 0.0 │ └── metadata │ │ ├── .zattrs │ │ └── .zgroup ├── test.category_counts.txt ├── test.category_info.txt └── test_annotated.vcf.gz ├── test_preparation.py ├── test_restart.py ├── test_runnable.py ├── test_start.py └── utils ├── test_check.py ├── test_cmd.py └── test_log.py /.github/workflows/ci.yml: -------------------------------------------------------------------------------- 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