https://github.com/biojulia/xam.jl

Parse and process SAM and BAM formatted files
https://github.com/biojulia/xam.jl

bam bam-files bam-format bioinformatics biojulia sam sam-files sam-format

Last synced: 14 days ago
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Parse and process SAM and BAM formatted files

• Host: GitHub
• URL: https://github.com/biojulia/xam.jl
• Owner: BioJulia
• License: mit
• Created: 2019-08-12T04:31:09.000Z (over 5 years ago)
• Default Branch: develop
• Last Pushed: 2024-07-30T09:31:25.000Z (5 months ago)
• Last Synced: 2024-10-30T01:36:59.410Z (about 2 months ago)
• Topics: bam, bam-files, bam-format, bioinformatics, biojulia, sam, sam-files, sam-format
• Language: Julia
• Homepage:
• Size: 2.59 MB
• Stars: 27
• Watchers: 12
• Forks: 13
• Open Issues: 27
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Funding: .github/FUNDING.yml
  • License: LICENSE

Awesome Lists containing this project

README

        
#  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)

[![DOI](https://zenodo.org/badge/201858041.svg)](https://zenodo.org/badge/latestdoi/201858041)

[![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/)

> 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

The XAM package provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.

## Installation

You can install the XAM package 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

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/actions/workflows/UnitTests.yml/badge.svg?branch=develop)](https://github.com/BioJulia/XAM.jl/actions/workflows/UnitTests.yml)

[![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)

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## Questions?

If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.slack.com/channels/biology), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).