├── .github └── workflows │ └── python-package.yml ├── .gitignore ├── .pyup.yml ├── .travis.yml ├── Dockerfile ├── MANIFEST.in ├── README.md ├── fixture ├── deep.bam ├── deep.bam.bai ├── gc.txt ├── longcontignames.bam ├── longcontignames.bam.bai ├── ref.fa ├── ref.fa.fai ├── ref.upper.fa ├── ref.upper.fa.fai ├── regression.npz ├── rna.bam ├── rna.bam.bai ├── test.bam └── test.bam.bai ├── performance.py ├── pyproject.toml ├── pysamstats ├── __init__.py ├── binned.py ├── config.py ├── io.py ├── opt.c ├── opt.pyx ├── pileup.py ├── test │ ├── __init__.py │ ├── test_binned.py │ ├── test_io.py │ ├── test_pileup.py │ ├── test_regression.py │ └── util.py └── util.py ├── release.txt ├── requirements.txt ├── requirements_dev.txt ├── sandbox.ipynb ├── scripts └── pysamstats └── setup.py /.github/workflows/python-package.yml: -------------------------------------------------------------------------------- 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