millironx/SequenceVariation.jl
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WIP - biological sequence variation
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Thomas A. Christensen II adbf0ce7f1 Refactor reconstruct! to use the built-in reference sequence 
reconstruct! previously allow changing of _any_ sequence to match a
haplotype, with no check to see if that sequence is compatible with the
reference sequence the haplotype is based on. Change that to only allow
reconstructing sequences from the reference sequence itself, making this a
non-mutating function.
2023-01-10 11:22:06 -06:00
.github Add linting workflow for PRs 2023-01-04 11:56:45 -06:00
docs Update documentation wording to reflect new type names 2023-01-05 11:58:29 -06:00
src Refactor reconstruct! to use the built-in reference sequence 2023-01-10 11:22:06 -06:00
test Rename Variant type to Haplotype 2023-01-05 11:58:29 -06:00
.gitignore Add Julia gitignore 2022-07-05 09:19:06 -05:00
.JuliaFormatter.toml Declare Blue style formatting for all new documents 2023-01-04 11:56:45 -06:00
CHANGELOG.md Update CHANGELOG 2023-01-05 11:58:29 -06:00
LICENSE Add license 2022-07-11 13:25:28 -05:00
Project.toml Add Aqua tests 2023-01-04 11:56:45 -06:00
README.md Add Aqua tests 2023-01-04 11:56:45 -06:00

README.md

SequenceVariation

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public. Latest Release MIT license Stable documentation Latest documentation

This project follows the semver pro forma and uses the OneFlow branching model.

Description

SequenceVariation provides a Julia vocabulary for comparing genetic mutations within biological sequences.

Installation

You can install SequenceVariation from the Julia REPL. Press ] to enter pkg mode, and enter the following:

add SequenceVariation

Testing

SequenceVariation is tested against Julia 1.X on Linux, OS X, and Windows.

Latest build status:

Unit Tests Documentation codecov Aqua QA

Contributing

We appreciate contributions from users including reporting bugs, fixing issues, improving performance and adding new features.

Take a look at the contributing files for detailed contributor and maintainer guidelines, and code of conduct.

Financial contributions

We also welcome financial contributions in full transparency on our open collective. Anyone can file an expense. If the expense makes sense for the development the core contributors and the person who filed the expense will be reimbursed.

Backers & Sponsors

Thank you to all our backers and sponsors!

Love our work and community? Become a backer.

backers

Does your company use BioJulia? Help keep BioJulia feature rich and healthy by sponsoring the project. Your logo will show up here with a link to your website.

Questions?

If you have a question about contributing or using BioJulia software, come on over and chat to us on the Julia Slack workspace, or you can try the Bio category of the Julia discourse site.