# XAM.jl

[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
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> 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/).

## 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)
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[![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).

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## 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).