├── .coveragerc ├── .github └── workflows │ ├── publish-pypi.yml │ └── run-tests.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── AUTHORS.md ├── CHANGELOG.md ├── CONTRIBUTING.md ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── _static │ └── .gitignore ├── authors.md ├── changelog.md ├── conf.py ├── contributing.md ├── index.md ├── license.md ├── readme.md ├── requirements.txt └── tutorial.md ├── perf ├── README.md ├── genomicranges.ipynb └── gr.R ├── pyproject.toml ├── setup.cfg ├── setup.py ├── src └── genomicranges │ ├── GenomicRanges.py │ ├── GenomicRangesList.py │ ├── SeqInfo.py │ ├── __init__.py │ ├── io │ ├── __init__.py │ ├── gtf.py │ └── ucsc.py │ └── utils.py ├── tests ├── R-checks │ ├── granges.R │ ├── overlaps.R │ ├── search.R │ └── setops.R ├── conftest.py ├── test_SeqInfo.py ├── test_gr_basic.py ├── test_gr_binnedAvg.py ├── test_gr_comparisons.py ├── test_gr_coverage.py ├── test_gr_flank.py ├── test_gr_initialize.py ├── test_gr_initialize_pandas.py ├── test_gr_initialize_polars.py ├── test_gr_interrange.py ├── test_gr_misc.py ├── test_gr_other.py ├── test_gr_overlaps.py ├── test_gr_resize.py ├── test_gr_search.py ├── test_gr_seqInfo_trim.py ├── test_gr_set_ops.py ├── test_gr_subtract.py ├── test_gr_tiling.py ├── test_gr_to_grl.py ├── test_grl_initialize.py ├── test_grl_methods.py └── test_ucsc.py └── tox.ini /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BiocPy/GenomicRanges/HEAD/.coveragerc -------------------------------------------------------------------------------- /.github/workflows/publish-pypi.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BiocPy/GenomicRanges/HEAD/.github/workflows/publish-pypi.yml -------------------------------------------------------------------------------- /.github/workflows/run-tests.yml: 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