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This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

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dlaehnemann and tedil committed 08e4eeb Jul 13, 2020
* Add stats::probs::cdf runtime complexities.

* Apply suggestions from code review

Changes to `stats::probs::cdf` runtime complexities as suggested by @tedil.

Co-authored-by: Till Hartmann <till.hartmann@udo.edu>

* Fix width of credible interval description to fraction.

* Fix `CDF::total_prob()` time complexity to `O(1)`.

* Fix `CDF::from_pmf()` runtime complexity to `O(n log n)` in `src/stats/probs/cdf.rs`

Thanks @tedil.

Co-authored-by: Till Hartmann <till.hartmann@udo.edu>

Co-authored-by: Till Hartmann <till.hartmann@udo.edu>

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README.md

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Rust-Bio, a bioinformatics library for Rust.

This library provides Rust implementations of algorithms and data structures useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

Please see the API documentation for available features and examples of how to use them.

When using Rust-Bio, please cite the following article:

Köster, J. (2016). Rust-Bio: a fast and safe bioinformatics library. Bioinformatics, 32(3), 444-446.

Further, you can cite the used versions via DOIs:

Rust-Bio: DOI

Contribute

Any contributions are welcome, from a simple bug report to full-blown new modules:

If you find a bug and don't have the time or in-depth knowledge to fix it, just check if you can add info to an existing issue and otherwise file a bug report with as many infos as possible. If you want to contribute fixes, documentation or new code, please open a pull request. You have two options to do this:

  1. For one-time contributions, simply fork the repository, apply your changes to a branch in your fork and then open a pull request.
  2. If you plan on contributing more than once, become a contributor by saying hi in the Join the team! issue, we'll add you to the team. Then, you don't have to create a fork, but can simply push new branches into the main repository and open pull requests there.

If you want to contribute and don't know where to start, have a look at the roadmap.

Documentation guidelines

Every public function and module should have documentation comments. Check out which types of comments to use where. In rust-bio, documentation comments should:

  • explain functionality
  • give at least one useful example of how to use it (best as doctests, that run during testing)
  • describe time and memory complexity listed (where applicable)
  • cite and link sources and explanations for data structures, algorithms or code (where applicable)

For extra credit, feel free to familiarize yourself with:

Contributors

Main author:

Other contributors:

License

Licensed under the MIT license http://opensource.org/licenses/MIT. This project may not be copied, modified, or distributed except according to those terms.

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This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

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