├── .coveragerc ├── .github └── workflows │ └── deploydocs.yml ├── .gitignore ├── .isort.cfg ├── .pre-commit-config.yaml ├── LICENSE.txt ├── README.md ├── data ├── AFR.covar ├── AFR.gwas ├── AFR.ld ├── AFR.pheno ├── EAS.covar ├── EAS.gwas ├── EAS.ld ├── EAS.pheno ├── EUR.covar ├── EUR.gwas ├── EUR.ld ├── EUR.pheno ├── all.ancestry.index ├── all.covar ├── all.pheno ├── bgen │ ├── AFR.bgen │ ├── AFR.sample │ ├── EAS.bgen │ ├── EAS.sample │ ├── EUR.bgen │ └── EUR.sample ├── keep.subject ├── make_example.py ├── plink │ ├── AFR.bed │ ├── AFR.bim │ ├── AFR.fam │ ├── EAS.bed │ ├── EAS.bim │ ├── EAS.fam │ ├── EUR.bed │ ├── EUR.bim │ ├── EUR.fam │ ├── all.bed │ ├── all.bim │ └── all.fam ├── prior_weights └── vcf │ ├── AFR.vcf │ ├── EAS.vcf │ └── EUR.vcf ├── docs ├── Makefile ├── _static │ └── images │ │ ├── dna.png │ │ └── favicon.ico ├── api │ ├── cli.rst │ ├── infer.rst │ ├── io.rst │ └── utils.rst ├── authors.rst ├── conduct.rst ├── conf.py ├── contributing.rst ├── files.rst ├── index.rst ├── license.rst ├── manual.rst ├── model.rst ├── readme.rst └── version.rst ├── misc ├── make_FUSION.R └── run_sushie.sh ├── mypy.ini ├── pyproject.toml ├── requirements.txt ├── requirements_dev.txt ├── setup.cfg ├── setup.py ├── sushie ├── __init__.py ├── cli.py ├── infer.py ├── infer_ss.py ├── io.py ├── log.py └── utils.py ├── tests ├── conftest.py └── test_infer.py └── tox.ini /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mancusolab/sushie/HEAD/.coveragerc -------------------------------------------------------------------------------- /.github/workflows/deploydocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mancusolab/sushie/HEAD/.github/workflows/deploydocs.yml -------------------------------------------------------------------------------- /.gitignore: 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