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Support >65535 CIGAR op-codes in BAM files (#13)
These changes add support for >65535 CIGAR op-codes in CIGAR strings in BAM records. SAM records are not a problem; their plain text formatting permits CIGAR strings of arbitrary length. This change also updates the README, a HUMANS file, and updates the documentation to use the Documenter.jl HTML generation.
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# Changelog | ||
All notable changes to this project will be documented in this file. | ||
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The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) | ||
and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). | ||
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## [Unreleased] | ||
### Added | ||
- Contributing files were added to this project. | ||
- A method called `BAM.ispositivestrand` is added to test for the relevant flag | ||
in BAM records. Thanks @phaverty :smile: | ||
- Support for records with CIGAR strings with >65535 op-codes has been added. | ||
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### Changed | ||
- Documentation has been updated and uses the Documenter.jl native html | ||
generator. | ||
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## [0.2.0] - 2017-08-01 | ||
### Dependencies | ||
- :exclamation: Support for julia v0.5 has been dropped. | ||
- :exclamation: Some dependency lower bound requirements were adjusted for | ||
Automa, BGZFStreams, BioSequences, and IntervalTrees. | ||
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## [0.1.0] - 2017-06-30 | ||
- This initial release extracted the alignment utilities out from Bio.jl into | ||
this dedicated package. | ||
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[Unreleased]: https://github.com/BioJulia/BioAlignments.jl/compare/v0.2.0...HEAD | ||
[0.2.0]: https://github.com/BioJulia/BioAlignments.jl/compare/v0.1.0...v0.2.0 | ||
[0.1.0]: https://github.com/BioJulia/BioAlignments.jl/tree/v0.1.0 |
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# The humans responsible for BioAlignments | ||
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## BioAlignments.jl Maintainers | ||
- Ben J. Ward | ||
- GitHub: [BenJWard](https://github.com/BenJWard) | ||
- Email: [email protected] | ||
- Twitter: @Ward9250 | ||
- Kenta Sato | ||
- GitHub: [bicycle1885](https://github.com/bicycle1885) | ||
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## Thanks | ||
- Peter Haverty | ||
- GitHub [phaverty](https://github.com/phaverty) | ||
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[Full contributors list](https://github.com/BioJulia/BioAlignments.jl/graphs/contributors) | ||
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_Is somebody missing from this file? That won't do! Please file an Issue or PR and let's fix that!_ |
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# BioAlignments.jl | ||
BioAlignments | ||
============= | ||
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**Latest release:** | ||
[![latest release][release-img]][release-url] | ||
[![MIT license][license-img]][license-url] | ||
[![stable documentation][docs-stable-img]][docs-stable-url] | ||
[![latest documentation][docs-latest-img]][docs-latest-url] | ||
![lifecycle][lifecycle-maturing] | ||
[![Chat on Discord][discord-img]][discord-url] | ||
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[![Latest Release][release-img]][release-url] | ||
[![BioAlignments][juliapkg06-img]][juliapkg-url] | ||
[![BioAlignments][juliapkg06-img]][juliapkg-url] | ||
[![License][license-img]][license-url] | ||
[![Docs Stable][docs-stable-img]][docs-stable-url] | ||
![BioJulia maintainer: bicycle1885](https://img.shields.io/badge/BioJulia%20Maintainer-bicycle1885-orange.svg) | ||
![BioJulia maintainer: Ward9250](https://img.shields.io/badge/BioJulia%20Maintainer-Ward9250-orange.svg) | ||
Description | ||
----------- | ||
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**Development status:** | ||
BioAlignments provides alignment algorithms, data structures, and I/O | ||
tools for SAM and BAM file formats. | ||
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[![Build Status][travis-img]][travis-url] | ||
[![Build status][appveyor-img]][appveyor-url] | ||
[![codecov.io][codecov-img]][codecov-url] | ||
[![Docs Latest][docs-latest-img]][docs-latest-url] | ||
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## Description | ||
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BioAlignments.jl provides alignment algorithms, data structures, and I/O tools | ||
for SAM and BAM file formats. | ||
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## Installation | ||
Installation | ||
------------ | ||
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Install BioAlignments from the Julia REPL: | ||
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```julia | ||
julia> Pkg.add("BioAlignments") | ||
using Pkg | ||
add("BioAlignments") | ||
#Pkg.add("BioAlignments") for julia prior to v0.7 | ||
``` | ||
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If you are interested in the cutting edge of the development, please check out | ||
the master branch to try new features before release. | ||
If you are interested in the cutting edge of the development, please | ||
check out the master branch to try new features before release. | ||
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Testing | ||
------- | ||
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BioAlignments is tested against julia `0.6` and current `0.7-dev` on | ||
Linux, OS X, and Windows. | ||
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| **Latest release** | **Latest build status** | | ||
|:------------------:|:-----------------------:| | ||
| [![julia06][juliapkg06-img]][juliapkg-url] [![julia07][juliapkg07-img]][juliapkg-url] | [![travis][travis-img]][travis-url] [![appveyor][appveyor-img]][appveyor-url] [![coverage][codecov-img]][codecov-url] | | ||
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Contributing and Questions | ||
-------------------------- | ||
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## Contributing and Questions | ||
We appreciate contributions from users including reporting bugs, fixing | ||
issues, improving performance and adding new features. | ||
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We appreciate contributions from users including reporting bugs, fixing issues, | ||
improving performance and adding new features. | ||
Please go to the [contributing section of the documentation](biojulia.github.io/BioAlignments.jl/stable/contributing) | ||
for more information. | ||
Take a look at the [CONTRIBUTING](CONTRIBUTING.md) file provided with | ||
this package for detailed contributor and maintainer guidelines. | ||
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If you have a question about | ||
contributing or using this package, you are encouraged to use the | ||
[Bio category of the Julia discourse | ||
site](https://discourse.julialang.org/c/domain/bio). | ||
If you have a question about contributing or using this package, come | ||
on over and chat to us on [Discord][discord-url], or you can try the | ||
[Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio). | ||
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[release-img]: https://img.shields.io/github/release/BioJulia/BioAlignments.jl.svg | ||
[release-url]: https://github.com/BioJulia/BioAlignments.jl/releases/latest | ||
[juliapkg05-img]: http://pkg.julialang.org/badges/BioAlignments_0.5.svg | ||
[juliapkg06-img]: http://pkg.julialang.org/badges/BioAlignments_0.6.svg | ||
[juliapkg-url]: http://pkg.julialang.org/?pkg=BioAlignments | ||
[license-img]: https://img.shields.io/badge/license-MIT-green.svg | ||
[license-url]: https://github.com/BioJulia/BioAlignments.jl/blob/master/LICENSE | ||
[docs-stable-img]: https://img.shields.io/badge/docs-stable-blue.svg | ||
[docs-stable-url]: https://biojulia.github.io/BioAlignments.jl/stable | ||
[docs-latest-img]: https://img.shields.io/badge/docs-latest-blue.svg | ||
[docs-latest-url]: https://biojulia.github.io/BioAlignments.jl/latest/ | ||
[travis-img]: https://travis-ci.org/BioJulia/BioAlignments.jl.svg?branch=master | ||
[travis-url]: https://travis-ci.org/BioJulia/BioAlignments.jl | ||
[appveyor-img]: https://ci.appveyor.com/api/projects/status/klkynmkr1tgd30gq/branch/master?svg=true | ||
[appveyor-url]: https://ci.appveyor.com/project/Ward9250/bioalignments-jl/branch/master | ||
[codecov-img]: http://codecov.io/github/BioJulia/BioAlignments.jl/coverage.svg?branch=master | ||
[codecov-url]: http://codecov.io/github/BioJulia/BioAlignments.jl?branch=master | ||
[release-img]: https://img.shields.io/github/release/BioJulia/BioAlignments.jl.svg?style=flat-square | ||
[release-url]: https://github.com/BioJulia/BioAlignments.jl/releases/latest | ||
[license-img]: https://img.shields.io/badge/license-MIT-green.svg?style=flat-square | ||
[license-url]: https://github.com/BioJulia/BioAlignments.jl/blob/master/LICENSE | ||
[docs-stable-img]: https://img.shields.io/badge/docs-stable-blue.svg?style=flat-square | ||
[docs-stable-url]: https://biojulia.github.io/BioAlignments.jl/stable | ||
[docs-latest-img]: https://img.shields.io/badge/docs-latest-blue.svg?style=flat-square | ||
[docs-latest-url]: https://biojulia.github.io/BioAlignments.jl/latest/ | ||
[lifecycle-experimental]: https://img.shields.io/badge/lifecycle-experimental-orange.svg?style=flat-square | ||
[lifecycle-maturing]: https://img.shields.io/badge/lifecycle-maturing-blue.svg?style=flat-square | ||
[lifecycle-stable]: https://img.shields.io/badge/lifecycle-stable-brightgreen.svg?style=flat-square | ||
[lifecycle-retired]: https://img.shields.io/badge/lifecycle-retired-orange.svg?style=flat-square | ||
[lifecycle-archived]: https://img.shields.io/badge/lifecycle-archived-red.svg?style=flat-square | ||
[lifecycle-dormant]: https://img.shields.io/badge/lifecycle-dormant-blue.svg?style=flat-square | ||
[lifecycle-questioning]: https://img.shields.io/badge/lifecycle-questioning-blue.svg?style=flat-square | ||
[discord-img]: https://img.shields.io/badge/discord-chat-blue.svg?style=flat-square&logo=discord&colorB=%237289DA | ||
[discord-url]: https://discord.gg/z73YNFz | ||
[juliapkg06-img]: http://pkg.julialang.org/badges/BioAlignments_0.6.svg?style=flat-square | ||
[juliapkg07-img]: http://pkg.julialang.org/badges/BioAlignments_0.7.svg?style=flat-square | ||
[juliapkg-url]: http://pkg.julialang.org/?pkg=BioAlignments | ||
[travis-img]: https://img.shields.io/travis/BioJulia/BioAlignments.jl/master.svg?label=Linux+/+macOS | ||
[travis-url]: https://travis-ci.org/BioJulia/BioAlignments.jl | ||
[appveyor-img]: https://ci.appveyor.com/api/projects/status/klkynmkr1tgd30gq/branch/master?svg=true | ||
[appveyor-url]: https://ci.appveyor.com/project/Ward9250/bioalignments-jl/branch/master | ||
[codecov-img]: http://codecov.io/github/BioJulia/BioAlignments.jl/coverage.svg?branch=master | ||
[codecov-url]: http://codecov.io/github/BioJulia/BioAlignments.jl?branch=master |
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julia 0.6 | ||
Automa 0.3 | ||
BGZFStreams 0.1 | ||
BioCore 1.0 | ||
BioSequences 0.5 | ||
BioSymbols 1.0 | ||
BufferedStreams 0.3 | ||
GenomicFeatures 0.1 | ||
IntervalTrees 0.2 | ||
Automa 0.6.1 | ||
BGZFStreams 0.1.4 | ||
BioCore 1.4 | ||
BioSequences 0.8.3 | ||
BioSymbols 2.0 | ||
BufferedStreams 0.4 | ||
GenomicFeatures 0.2.1 | ||
IntervalTrees 0.4.1 |
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using Documenter, BioAlignments | ||
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makedocs( | ||
modules=[BioAlignments]) | ||
format = :html, | ||
sitename = "BioAlignments.jl", | ||
pages = [ | ||
"Home" => "index.md", | ||
"Alignment representation" => "alignments.md", | ||
"Pairwise alignment" => "pairalign.md", | ||
"IO" => [ | ||
"SAM and BAM" => "hts-files.md" | ||
], | ||
"References" => "references.md" | ||
], | ||
authors = "Kenta Sato, Ben J. Ward, The BioJulia Organisation and other contributors." | ||
) | ||
deploydocs( | ||
deps=Deps.pip("mkdocs", "pygments", "mkdocs-material"), | ||
repo="github.com/BioJulia/BioAlignments.jl.git", | ||
julia="0.6", | ||
osname="linux") | ||
repo = "github.com/BioJulia/BioAlignments.jl.git", | ||
julia = "0.6", | ||
osname = "linux", | ||
target = "build", | ||
deps = nothing, | ||
make = nothing | ||
) |
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