11# BioAlignments
22
3- [ ![ latest release] ( https://img.shields.io/github/release/BioJulia/BioAlignments.jl.svg?style=flat-square )] ( https://github.com/BioJulia/BioAlignments.jl/releases/latest )
3+ [ ![ Latest release] ( https://img.shields.io/github/release/BioJulia/BioAlignments.jl.svg?style=flat-square )] ( https://github.com/BioJulia/BioAlignments.jl/releases/latest )
44[ ![ MIT license] ( https://img.shields.io/badge/license-MIT-green.svg?style=flat-square )] ( https://github.com/BioJulia/BioAlignments.jl/blob/master/LICENSE )
5- [ ![ stable documentation] ( https://img.shields.io/badge/docs-stable-blue.svg?style=flat-square )] ( https://biojulia.github.io/BioAlignments.jl/stable )
6- [ ![ latest documentation] ( https://img.shields.io/badge/docs-latest-blue.svg?style=flat-square )] ( https://biojulia.github.io/BioAlignments.jl/latest/ )
7- ![ lifecycle ] ( https://img.shields.io/badge/lifecycle-maturing-blue.svg?style=flat-square )
5+ [ ![ Stable documentation] ( https://img.shields.io/badge/docs-stable-blue.svg?style=flat-square )] ( https://biojulia.github.io/BioAlignments.jl/stable )
6+ [ ![ Latest documentation] ( https://img.shields.io/badge/docs-latest-blue.svg?style=flat-square )] ( https://biojulia.github.io/BioAlignments.jl/latest/ )
7+ ![ Lifecycle ] ( https://img.shields.io/badge/lifecycle-maturing-blue.svg?style=flat-square )
88[ ![ Chat on Discord] ( https://img.shields.io/badge/discord-chat-blue.svg?style=flat-square&logo=discord&colorB=%237289DA )] ( https://discord.gg/z73YNFz )
9+ [ ![ Backers on Open Collective] ( oc-backers-img )] ( #backers )
10+ [ ![ Sponsors on Open Collective] ( oc-sponsors-img )] ( #sponsors )
11+
912
1013## Description
1114
1215BioAlignments provides alignment algorithms, data structures, and I/O
1316tools for SAM and BAM file formats.
1417
18+
1519## Installation
1620
1721Install BioAlignments from the Julia REPL:
@@ -25,23 +29,62 @@ add("BioAlignments")
2529If you are interested in the cutting edge of the development, please
2630check out the master branch to try new features before release.
2731
32+
2833## Testing
2934
3035BioAlignments is tested against julia ` 0.6 ` and current ` 0.7-dev ` on
3136Linux, OS X, and Windows.
3237
3338| ** Latest release** | ** Latest build status** |
3439| :------------------:| :-----------------------:|
35- | [ ![ julia06] ( http://pkg.julialang.org/badges/BioAlignments_0.6.svg?style=flat-square )] ( http://pkg.julialang.org/?pkg=BioAlignments ) [ ![ julia07] ( http://pkg.julialang.org/badges/BioAlignments_0.7.svg?style=flat-square )] ( http://pkg.julialang.org/?pkg=BioAlignments ) | [ ![ travis] ( https://img.shields.io/travis/BioJulia/BioAlignments.jl/master.svg?label=Linux+/+macOS )] ( https://travis-ci.org/BioJulia/BioAlignments.jl ) [ ![ appveyor] ( https://ci.appveyor.com/api/projects/status/klkynmkr1tgd30gq/branch/master?svg=true )] ( https://ci.appveyor.com/project/Ward9250/bioalignments-jl/branch/master ) [ ![ coverage] ( http://codecov.io/github/BioJulia/BioAlignments.jl/coverage.svg?branch=master )] ( http://codecov.io/github/BioJulia/BioAlignments.jl?branch=master ) |
40+ | [ ![ julia06] ( http://pkg.julialang.org/badges/BioAlignments_0.6.svg )] ( http://pkg.julialang.org/?pkg=BioAlignments ) [ ![ julia07] ( http://pkg.julialang.org/badges/BioAlignments_0.7.svg )] ( http://pkg.julialang.org/?pkg=BioAlignments ) | [ ![ travis] ( https://img.shields.io/travis/BioJulia/BioAlignments.jl/master.svg?label=Linux+/+macOS )] ( https://travis-ci.org/BioJulia/BioAlignments.jl ) [ ![ appveyor] ( https://ci.appveyor.com/api/projects/status/klkynmkr1tgd30gq/branch/master?svg=true )] ( https://ci.appveyor.com/project/Ward9250/bioalignments-jl/branch/master ) [ ![ coverage] ( http://codecov.io/github/BioJulia/BioAlignments.jl/coverage.svg?branch=master )] ( http://codecov.io/github/BioJulia/BioAlignments.jl?branch=master ) |
41+
3642
37- ## Contributing and Questions
43+ ## Contributing
3844
3945We appreciate contributions from users including reporting bugs, fixing
4046issues, improving performance and adding new features.
4147
4248Take a look at the [ CONTRIBUTING] ( CONTRIBUTING.md ) file provided with
43- this package for detailed contributor and maintainer guidelines.
49+ every BioJulia package package for detailed contributor and maintainer
50+ guidelines.
51+
52+
53+ ### Financial contributions
54+
55+ We also welcome financial contributions in full transparency on our
56+ [ open collective] ( https://opencollective.com/biojulia ) .
57+ Anyone can file an expense. If the expense makes sense for the development
58+ of the community, it will be "merged" in the ledger of our open collective by
59+ the core contributors and the person who filed the expense will be reimbursed.
60+
61+
62+ ## Backers & Sponsors
63+
64+ Thank you to all our backers and sponsors!
65+
66+ Love our work and community? [ Become a backer] ( https://opencollective.com/biojulia#backer ) .
67+
68+ [ ![ backers] ( https://opencollective.com/biojulia/backers.svg?width=890 )] ( https://opencollective.com/biojulia#backers )
69+
70+ Does your company use BioJulia? Help keep BioJulia feature rich and healthy by
71+ [ sponsoring the project] ( https://opencollective.com/biojulia#sponsor )
72+ Your logo will show up here with a link to your website.
73+
74+ [ ![ ] ( https://opencollective.com/biojulia/sponsor/0/avatar.svg )] ( https://opencollective.com/biojulia/sponsor/0/website )
75+ [ ![ ] ( https://opencollective.com/biojulia/sponsor/1/avatar.svg )] ( https://opencollective.com/biojulia/sponsor/1/website )
76+ [ ![ ] ( https://opencollective.com/biojulia/sponsor/2/avatar.svg )] ( https://opencollective.com/biojulia/sponsor/2/website )
77+ [ ![ ] ( https://opencollective.com/biojulia/sponsor/3/avatar.svg )] ( https://opencollective.com/biojulia/sponsor/3/website )
78+ [ ![ ] ( https://opencollective.com/biojulia/sponsor/4/avatar.svg )] ( https://opencollective.com/biojulia/sponsor/4/website )
79+ [ ![ ] ( https://opencollective.com/biojulia/sponsor/5/avatar.svg )] ( https://opencollective.com/biojulia/sponsor/5/website )
80+ [ ![ ] ( https://opencollective.com/biojulia/sponsor/6/avatar.svg )] ( https://opencollective.com/biojulia/sponsor/6/website )
81+ [ ![ ] ( https://opencollective.com/biojulia/sponsor/7/avatar.svg )] ( https://opencollective.com/biojulia/sponsor/7/website )
82+ [ ![ ] ( https://opencollective.com/biojulia/sponsor/8/avatar.svg )] ( https://opencollective.com/biojulia/sponsor/8/website )
83+ [ ![ ] ( https://opencollective.com/biojulia/sponsor/9/avatar.svg )] ( https://opencollective.com/biojulia/sponsor/9/website )
84+
85+
86+ ## Questions?
4487
45- If you have a question about contributing or using this package , come
46- on over and chat to us on [ Discord] [ discord-url ] , or you can try the
88+ If you have a question about contributing or using BioJulia software , come
89+ on over and chat to us on [ Discord] ( https:// discord.gg/z73YNFz ) , or you can try the
4790[ Bio category of the Julia discourse site] ( https://discourse.julialang.org/c/domain/bio ) .
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