/d4utils

Python utilities to work with d4 coverage files

Primary LanguagePythonMIT LicenseMIT

D4Utils

PyPI Status Python Version License

Read the documentation at https://d4utils.readthedocs.io/ Tests Codecov

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Features

D4Utils summarizes per-base coverages from multiple D4 files in parallel.

sum

Sum per-base coverages over all files to generate a global coverage distribution for setting coverage-based accessibility mask thresholds.

count

Count files with coverages within a user-defined range for setting accessibility mask thresholds based on number of individuals with sufficient coverage.

Requirements

  • click
  • pyd4
  • tqdm
  • pandas

Installation

You can install D4Utils via pip from the GitHub repository:

$ pip install git+https://github.com/percyfal/d4utils

Usage

Please see the Command-line Reference for details.

Contributing

Contributions are very welcome. To learn more, see the Contributor Guide.

License

Distributed under the terms of the MIT license, D4Utils is free and open source software.

Issues

If you encounter any problems, please file an issue along with a detailed description.

Credits

This project was generated from @cjolowicz's Hypermodern Python Cookiecutter template.