├── .github └── workflows │ └── pythonpackage.yml ├── .gitignore ├── .readthedocs.yml ├── LICENSE ├── README.md ├── docs ├── Makefile ├── api.rst ├── conf.py ├── index.rst └── release_notes.rst ├── flake8.cfg ├── mypy.ini ├── poetry.lock ├── pyproject.toml └── samwell ├── __init__.py ├── dnautils.py ├── itertools.py ├── overlap_detector.py ├── sam ├── __init__.py ├── bwa_mem.py ├── clipping.py ├── sambuilder.py └── tests │ ├── __init__.py │ ├── data │ └── valid.sam │ ├── test_bwa_mem.py │ ├── test_clipping.py │ ├── test_sam.py │ └── test_sambuilder.py └── tests ├── __init__.py ├── test_dnautils.py ├── test_itertools.py └── test_overlap_detector.py /.github/workflows/pythonpackage.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/myriad-opensource/samwell/HEAD/.github/workflows/pythonpackage.yml -------------------------------------------------------------------------------- /.gitignore: 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