# XAM.jl [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![Latest Release](https://img.shields.io/github/release/BioJulia/XAM.jl.svg)](https://github.com/BioJulia/XAM.jl/releases/latest) [![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/XAM.jl/blob/master/LICENSE) [![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/XAM.jl/stable) [![Latest documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/XAM.jl/dev/) [![Join the chat at https://gitter.im/BioJulia/XAM.jl](https://badges.gitter.im/BioJulia/XAM.jl.svg)](https://gitter.im/BioJulia/XAM.jl) > This project follows the [semver](http://semver.org) pro forma and uses the [git-flow branching model](https://nvie.com/posts/a-successful-git-branching-model/ "original blog post"). ## Description XAM provides I/O and utilities for manipulating SAM and BAM formatted alignment map files. ## Installation The latest version of XAM is made available to install through BioJulia's package registry. By default, Julia's package manager only includes the "General" package registry. To add the BioJulia registry from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/), press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command: ```julia registry add https://github.com/BioJulia/BioJuliaRegistry.git ``` Once the registry is added to your configuration, you can install XAM while in [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/) with the following: ```julia add XAM ``` If you are interested in the cutting edge of the development, please check out the [develop branch](https://github.com/BioJulia/XAM.jl/tree/develop) to try new features before release. ## Testing XAM is tested against Julia `1.X` on Linux, OS X, and Windows. **Latest build status:** [![Unit tests](https://github.com/BioJulia/XAM.jl/workflows/Unit%20tests/badge.svg?branch=master)](https://github.com/BioJulia/XAM.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster) [![Documentation](https://github.com/BioJulia/XAM.jl/workflows/Documentation/badge.svg?branch=master)](https://github.com/BioJulia/XAM.jl/actions?query=workflow%3ADocumentation+branch%3Amaster) [![codecov](https://codecov.io/gh/BioJulia/XAM.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/XAM.jl) ## Contributing We appreciate [contributions](https://github.com/BioJulia/XAM.jl/graphs/contributors) from users including reporting bugs, fixing issues, improving performance and adding new features. Take a look at the [contributing files](https://github.com/BioJulia/Contributing) detailed contributor and maintainer guidelines, and code of conduct. ### Financial contributions We also welcome financial contributions in full transparency on our [open collective](https://opencollective.com/biojulia). 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](https://opencollective.com/biojulia#backer). [![backers](https://opencollective.com/biojulia/backers.svg?width=890)](https://opencollective.com/biojulia#backers) Does your company use BioJulia? Help keep BioJulia feature rich and healthy by [sponsoring the project](https://opencollective.com/biojulia#sponsor). Your logo will show up here with a link to your website. [![](https://opencollective.com/biojulia/sponsor/0/avatar.svg)](https://opencollective.com/biojulia/sponsor/0/website) [![](https://opencollective.com/biojulia/sponsor/1/avatar.svg)](https://opencollective.com/biojulia/sponsor/1/website) [![](https://opencollective.com/biojulia/sponsor/2/avatar.svg)](https://opencollective.com/biojulia/sponsor/2/website) [![](https://opencollective.com/biojulia/sponsor/3/avatar.svg)](https://opencollective.com/biojulia/sponsor/3/website) [![](https://opencollective.com/biojulia/sponsor/4/avatar.svg)](https://opencollective.com/biojulia/sponsor/4/website) [![](https://opencollective.com/biojulia/sponsor/5/avatar.svg)](https://opencollective.com/biojulia/sponsor/5/website) [![](https://opencollective.com/biojulia/sponsor/6/avatar.svg)](https://opencollective.com/biojulia/sponsor/6/website) [![](https://opencollective.com/biojulia/sponsor/7/avatar.svg)](https://opencollective.com/biojulia/sponsor/7/website) [![](https://opencollective.com/biojulia/sponsor/8/avatar.svg)](https://opencollective.com/biojulia/sponsor/8/website) [![](https://opencollective.com/biojulia/sponsor/9/avatar.svg)](https://opencollective.com/biojulia/sponsor/9/website) ## Questions? If you have a question about contributing or using BioJulia software, come on over and chat to us on [Gitter](https://gitter.im/BioJulia/General), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).