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Documentation
- API autodocs. - Inline links for documenter. - Logo. - Badges.
This commit is contained in:
Ciarán O'Mara
parent
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commit
1bcd7c344c
7 changed files with 260 additions and 28 deletions
77
README.md
77
README.md
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@ -1,3 +1,76 @@
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# XAM.jl
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# <img src="./docs/src/assets/logo.svg" width="30%" align="right" /> XAM.jl
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In development: minimal working separation of SAM and BAM from BioAlignments.
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||||
[](https://www.repostatus.org/#wip)
|
||||
[](https://github.com/BioJulia/XAM.jl/releases/latest)
|
||||
[](https://github.com/BioJulia/XAM.jl/blob/master/LICENSE)
|
||||
[](https://biojulia.github.io/XAM.jl/stable)
|
||||
[](https://biojulia.github.io/XAM.jl/dev/)
|
||||
[](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:
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```julia
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registry add https://github.com/BioJulia/BioJuliaRegistry.git
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```
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||||
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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:
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```julia
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add XAM
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```
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||||
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.
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||||
|
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## Testing
|
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XAM is tested against Julia `1.X` on Linux, OS X, and Windows.
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||||
|
||||
**Latest build status:**
|
||||
|
||||
[](https://github.com/BioJulia/XAM.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster)
|
||||
[](https://github.com/BioJulia/XAM.jl/actions?query=workflow%3ADocumentation+branch%3Amaster)
|
||||
[](https://codecov.io/gh/BioJulia/XAM.jl)
|
||||
|
||||
## Contributing
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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).
|
||||
|
||||
[](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/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/1/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/2/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/3/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/4/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/5/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/6/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/7/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/8/website)
|
||||
[](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).
|
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|
|
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6
docs/Project.toml
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6
docs/Project.toml
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[deps]
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Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
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Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
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[compat]
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Documenter = "0.24"
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21
docs/make.jl
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21
docs/make.jl
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@ -0,0 +1,21 @@
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using Pkg
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using Documenter, XAM
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makedocs(
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format = Documenter.HTML(
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edit_link = "develop"
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),
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modules = [XAM, XAM.SAM, XAM.BAM],
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sitename = "XAM.jl",
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pages = [
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"Home" => "index.md",
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"SAM and BAM" => "man/hts-files.md",
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"API Reference" => "man/api.md"
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],
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authors = replace(join(Pkg.TOML.parsefile("Project.toml")["authors"], ", "), r" <.*?>" => "" ) * ", The BioJulia Organisation, and other contributors."
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)
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deploydocs(
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repo = "github.com/BioJulia/XAM.jl.git",
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devbranch = "develop",
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push_preview = true
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)
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docs/src/assets/logo.svg
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docs/src/assets/logo.svg
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@ -0,0 +1,26 @@
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 136.48101 51.472999">
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<g id="bubble-helix">
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<circle cx="5.9792" cy="20.3" r="5.9792" fill="#945bb0"/>
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<circle cx="21.317" cy="39.5" r="4.9393" fill="#4266d5"/>
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<circle cx="16.378" cy="11.7" r="4.9393" fill="#c93d39"/>
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<circle cx="35.095" cy="35.9" r="5.9792" fill="#945bb0"/>
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<circle cx="47.184" cy="23.8" r="7.409" fill="#4266d5"/>
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<circle cx="28.986" cy="9.7" r="4.5494" fill="#3b972e"/>
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<circle cx="89.428" cy="46.5" r="4.9393" fill="#c93d39"/>
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<circle cx="71.62" cy="5.6" r="5.5892" fill="#945bb0"/>
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<circle cx="121.01" cy="15.5" r="5.5892" fill="#c93d39"/>
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<circle cx="59.662" cy="30.3" r="2.4697" fill="#4266d5"/>
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<circle cx="103.6" cy="19.9" r="3.2496" fill="#c93d39"/>
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<circle cx="123.61" cy="36.5" r="2.7296" fill="#4266d5"/>
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<circle cx="127.64" cy="5.2" r="3.8995" fill="#3b972e"/>
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<circle cx="132.58" cy="39.2" r="3.8995" fill="#945bb0"/>
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<circle cx="67.591" cy="37.4" r="3.3795" fill="#3b972e"/>
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<circle cx="95.017" cy="13.9" r="4.2894" fill="#4266d5"/>
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<circle cx="77.729" cy="42.9" r="3.8995" fill="#945bb0"/>
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<circle cx="102.56" cy="42.0" r="5.8492" fill="#4266d5"/>
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<circle cx="113.6" cy="28.8" r="6.7591" fill="#3b972e"/>
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<circle cx="57.582" cy="11.0" r="6.3691" fill="#c93d39"/>
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<circle cx="38.735" cy="14.8" r="3.3795" fill="#c93d39"/>
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<circle cx="84.618" cy="7.9" r="5.3293" fill="#3b972e"/>
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</g>
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</svg>
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|
After Width: | Height: | Size: 1.4 KiB |
77
docs/src/index.md
Normal file
77
docs/src/index.md
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@ -0,0 +1,77 @@
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# XAM.jl
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||||
[](https://www.repostatus.org/#wip)
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[](https://github.com/BioJulia/XAM.jl/releases/latest)
|
||||
[](https://github.com/BioJulia/XAM.jl/blob/master/LICENSE)
|
||||
[](https://biojulia.github.io/XAM.jl/stable)
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||||
[](https://biojulia.github.io/XAM.jl/dev/)
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||||
[](https://gitter.im/BioJulia/XAM.jl)
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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
|
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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:
|
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```julia
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registry add https://github.com/BioJulia/BioJuliaRegistry.git
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```
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|
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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
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add XAM
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```
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|
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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.
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||||
|
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## Testing
|
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XAM is tested against Julia `1.X` on Linux, OS X, and Windows.
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||||
|
||||
**Latest build status:**
|
||||
|
||||
[](https://github.com/BioJulia/XAM.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster)
|
||||
[](https://github.com/BioJulia/XAM.jl/actions?query=workflow%3ADocumentation+branch%3Amaster)
|
||||
[](https://codecov.io/gh/BioJulia/XAM.jl)
|
||||
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## Contributing
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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).
|
||||
|
||||
[](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/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/1/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/2/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/3/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/4/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/5/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/6/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/7/website)
|
||||
[](https://opencollective.com/biojulia/sponsor/8/website)
|
||||
[](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).
|
||||
38
docs/src/man/api.md
Normal file
38
docs/src/man/api.md
Normal file
|
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@ -0,0 +1,38 @@
|
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```@meta
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CurrentModule = XAM
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DocTestSetup = quote
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using XAM
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end
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```
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|
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# API Reference
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## SAM API
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### Public
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```@autodocs
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Modules = [XAM.SAM]
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private = false
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```
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### Internal
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```@autodocs
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Modules = [XAM.SAM]
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public = false
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```
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## BAM API
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### Public
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```@autodocs
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Modules = [XAM.BAM]
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private = false
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```
|
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|
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### Internal
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```@autodocs
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Modules = [XAM.BAM]
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public = false
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```
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|
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@ -1,15 +1,10 @@
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# SAM and BAM
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|
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## Introduction
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High-throughput sequencing (HTS) technologies generate a large amount of data in the form of a large number of nucleotide sequencing reads.
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One of the most common tasks in bioinformatics is to align these reads against known reference genomes, chromosomes, or contigs.
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BioAlignments provides several data formats commonly used for this kind of task.
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The `XAM` package offers high-performance tools for SAM and BAM file formats, which are the most popular file formats.
|
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|
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BioAlignments offers high-performance tools for SAM and BAM file formats, which are the most popular file formats.
|
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|
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If you have questions about the SAM and BAM formats or any of the terminology used when discussing these formats, see the published [specification][samtools-spec], which is maintained by the [samtools group][samtools].
|
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If you have questions about the SAM and BAM formats or any of the terminology used when discussing these formats, see the published [specification](https://samtools.github.io/hts-specs/SAMv1.pdf), which is maintained by the [samtools group](https://samtools.github.io/).
|
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A very very simple SAM file looks like the following:
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|
|
@ -28,7 +23,7 @@ Where the first two lines are part of the "header", and the following lines are
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Each record describes how a read aligns to some reference sequence.
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Sometimes one record describes one read, but there are other cases like chimeric reads and split alignments, where multiple records apply to one read.
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In the example above, `r003` is a chimeric read, and `r004` is a split alignment, and `r001` are mate pair reads.
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Again, we refer you to the official [specification][samtools-spec] for more details.
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Again, we refer you to the official [specification](https://samtools.github.io/hts-specs/SAMv1.pdf) for more details.
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A BAM file stores this same information but in a binary and compressible format that does not make for pretty printing here!
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|
@ -37,7 +32,7 @@ A BAM file stores this same information but in a binary and compressible format
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A typical script iterating over all records in a file looks like below:
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```julia
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using BioAlignments
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using XAM
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# Open a BAM file.
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reader = open(BAM.Reader, "data.bam")
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@ -72,7 +67,7 @@ end
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Both `SAM.Reader` and `BAM.Reader` implement the `header` function, which returns a `SAM.Header` object.
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To extract certain information out of the headers, you can use the `find` method on the header to extract information according to SAM/BAM tag.
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Again we refer you to the [specification][samtools-spec] for full details of all the different tags that can occur in headers, and what they mean.
|
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Again we refer you to the [specification](https://samtools.github.io/hts-specs/SAMv1.pdf) for full details of all the different tags that can occur in headers, and what they mean.
|
||||
|
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Below is an example of extracting all the info about the reference sequences from the BAM header.
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In SAM/BAM, any description of a reference sequence is stored in the header, under a tag denoted `SQ` (think `reference SeQuence`!).
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|
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@ -110,7 +105,8 @@ In the above we can see there were 7 sequences in the reference: 5 chromosomes,
|
|||
|
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## SAM and BAM Records
|
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|
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BioAlignments supports the following accessors for `SAM.Record` types.
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### SAM.Record
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The `XAM` package supports the following accessors for `SAM.Record` types.
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|
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```@docs
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XAM.SAM.flag
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|
|
@ -134,7 +130,8 @@ XAM.SAM.quality
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|||
XAM.SAM.auxdata
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```
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BioAlignments supports the following accessors for `BAM.Record` types.
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### BAM.Record
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The `XAM` package supports the following accessors for `BAM.Record` types.
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|
||||
```@docs
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XAM.BAM.flag
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|
|
@ -178,7 +175,7 @@ Tagged auxiliary data follows a format of `TAG:TYPE:VALUE`.
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|||
| 'H' | Byte array in Hex format |
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| 'B' | Integer of numeric array |
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|
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For more information about these tags and their types we refer you to the [SAM/BAM specification][samtools-spec] and the additional [optional fields specification][samtags] document.
|
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For more information about these tags and their types we refer you to the [SAM/BAM specification](https://samtools.github.io/hts-specs/SAMv1.pdf) and the additional [optional fields specification](https://samtools.github.io/hts-specs/SAMtags.pdf) document.
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There are some tags that are reserved, predefined standard tags, for specific uses.
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|
|
@ -200,8 +197,8 @@ end
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|||
|
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## Getting records in a range
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BioAlignments supports the BAI index to fetch records in a specific range from a BAM file.
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[Samtools][samtools] provides `index` subcommand to create an index file (.bai) from a sorted BAM file.
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The `XAM` package supports the BAI index to fetch records in a specific range from a BAM file.
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[Samtools](https://samtools.github.io/) provides `index` subcommand to create an index file (.bai) from a sorted BAM file.
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```console
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$ samtools index -b SRR1238088.sort.bam
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@ -209,7 +206,7 @@ $ ls SRR1238088.sort.bam*
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SRR1238088.sort.bam SRR1238088.sort.bam.bai
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```
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`eachoverlap(reader, chrom, range)` returns an iterator of BAM records overlapping the query interval:
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The method `eachoverlap(reader, chrom, range)` returns an iterator of BAM records overlapping the query interval:
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```julia
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reader = open(BAM.Reader, "SRR1238088.sort.bam", index="SRR1238088.sort.bam.bai")
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|
|
@ -222,14 +219,14 @@ close(reader)
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|
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## Getting records overlapping genomic features
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||||
|
||||
`eachoverlap` also accepts the `Interval` type defined in [GenomicFeatures.jl][genomicfeatures].
|
||||
The `eachoverlap` method also accepts the `Interval` type defined in [GenomicFeatures.jl](https://github.com/BioJulia/GenomicFeatures.jl).
|
||||
|
||||
This allows you to do things like first read in the genomic features from a GFF3 file, and then for each feature, iterate over all the BAM records that overlap with that feature.
|
||||
|
||||
```julia
|
||||
# Load GFF3 module.
|
||||
using GenomicFeatures
|
||||
using BioAlignments
|
||||
using GFF3
|
||||
using XAM
|
||||
|
||||
# Load genomic features from a GFF3 file.
|
||||
features = open(collect, GFF3.Reader, "TAIR10_GFF3_genes.gff")
|
||||
|
|
@ -289,7 +286,7 @@ SAM.Writer(IOStream(<file my-data.sam>))
|
|||
|
||||
```
|
||||
|
||||
To make a BAM Writer is slightly different, as you need to use a specific stream type from the [BGZFStreams][bgzfstreams] package:
|
||||
To make a BAM Writer is slightly different, as you need to use a specific stream type from the (https://github.com/BioJulia/BGZFStreams.jl)[https://github.com/BioJulia/BGZFStreams.jl] package:
|
||||
|
||||
```julia
|
||||
julia> using BGZFStreams
|
||||
|
|
@ -305,9 +302,3 @@ Once you have a BAM or SAM writer, you can use the `write` method to write `BAM.
|
|||
julia> write(bamw, rec) # Here rec is a `BAM.Record`
|
||||
330780
|
||||
```
|
||||
|
||||
[samtools]: https://samtools.github.io/
|
||||
[samtools-spec]: https://samtools.github.io/hts-specs/SAMv1.pdf
|
||||
[samtags]: https://samtools.github.io/hts-specs/SAMtags.pdf
|
||||
[bgzfstreams]: https://github.com/BioJulia/BGZFStreams.jl
|
||||
[genomicfeatures]: https://github.com/BioJulia/GenomicFeatures.jl
|
||||
|
|
|
|||
Loading…
Reference in a new issue