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.

Author: Ben J. Ward

.travis.yml

@@ -5,27 +5,12 @@ os:
   - osx
 julia:
   - 0.6
-  # - nightly
+  - nightly
 matrix:
   allow_failures:
-    # - julia: 0.6
-    # - julia: nightly
+      - julia: nightly
 notifications:
   email: false
-git:
-  depth: 99999999
-
-## uncomment and modify the following lines to manually install system packages
-#addons:
-#  apt: # apt-get for linux
-#    packages:
-#    - gfortran
-#before_script: # homebrew for mac
-#  - if [ $TRAVIS_OS_NAME = osx ]; then brew install gcc; fi
-
-## uncomment the following lines to override the default test script
-#script:
-#  - julia -e 'Pkg.clone(pwd()); Pkg.build("BioAlignments"); Pkg.test("BioAlignments"; coverage=true)'
 after_success:
   # push coverage results to Codecov
   - julia -e 'cd(Pkg.dir("BioAlignments")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'

CHANGELOG.md

@@ -0,0 +1,30 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+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).
+
+## [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.
+
+### Changed
+- Documentation has been updated and uses the Documenter.jl native html
+  generator.
+
+## [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.
+
+## [0.1.0] - 2017-06-30
+- This initial release extracted the alignment utilities out from Bio.jl into
+  this dedicated package.
+
+[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

HUMANS.md

@@ -0,0 +1,17 @@
+# The humans responsible for BioAlignments
+
+## BioAlignments.jl Maintainers
+- Ben J. Ward
+  - GitHub: [BenJWard](https://github.com/BenJWard)
+  - Email: ben.ward@earlham.ac.uk
+  - Twitter: @Ward9250
+- Kenta Sato
+  - GitHub: [bicycle1885](https://github.com/bicycle1885)
+
+## Thanks
+- Peter Haverty
+  - GitHub [phaverty](https://github.com/phaverty)
+
+[Full contributors list](https://github.com/BioJulia/BioAlignments.jl/graphs/contributors)
+
+_Is somebody missing from this file? That won't do! Please file an Issue or PR and let's fix that!_

LICENSE.md

@@ -1,4 +1,4 @@
-The BioSequences.jl package is licensed under the MIT "Expat" License:
+The BioAlignments.jl package is licensed under the MIT "Expat" License:
 
 > Copyright (c) 2014: BioJulia.
 >

README.md

@@ -1,64 +1,47 @@
-# BioAlignments.jl
+# BioAlignments
 
-**Latest release:**
-
-[![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)
-
-**Development status:**
-
-[![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]
+[![latest release](https://img.shields.io/github/release/BioJulia/BioAlignments.jl.svg?style=flat-square)](https://github.com/BioJulia/BioAlignments.jl/releases/latest)
+[![MIT license](https://img.shields.io/badge/license-MIT-green.svg?style=flat-square)](https://github.com/BioJulia/BioAlignments.jl/blob/master/LICENSE)
+[![stable documentation](https://img.shields.io/badge/docs-stable-blue.svg?style=flat-square)](https://biojulia.github.io/BioAlignments.jl/stable)
+[![latest documentation](https://img.shields.io/badge/docs-latest-blue.svg?style=flat-square)](https://biojulia.github.io/BioAlignments.jl/latest/)
+![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg?style=flat-square)
+[![Chat on Discord](https://img.shields.io/badge/discord-chat-blue.svg?style=flat-square&logo=discord&colorB=%237289DA)](https://discord.gg/z73YNFz)
 
 ## Description
 
-BioAlignments.jl provides alignment algorithms, data structures, and I/O tools
-for SAM and BAM file formats.
+BioAlignments provides alignment algorithms, data structures, and I/O
+tools for SAM and BAM file formats.
 
 ## Installation
 
 Install BioAlignments from the Julia REPL:
 
 ```julia
-julia> Pkg.add("BioAlignments")
+using Pkg
+add("BioAlignments")
+#Pkg.add("BioAlignments") for julia prior to v0.7
 ```
 
-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.
+
+## Testing
+
+BioAlignments is tested against julia `0.6` and current `0.7-dev` on
+Linux, OS X, and Windows.
+
+| **Latest release** | **Latest build status** |
+|:------------------:|:-----------------------:|
+| [![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) |
 
 ## Contributing and Questions
 
-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.
+We appreciate contributions from users including reporting bugs, fixing
+issues, improving performance and adding new features.
 
-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).
+Take a look at the [CONTRIBUTING](CONTRIBUTING.md) file provided with
+this package for detailed contributor and maintainer guidelines.
 
-[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
+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).

REQUIRE

@@ -1,9 +1,9 @@
 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

docs/make.jl

@@ -1,9 +1,24 @@
 using Documenter, BioAlignments
 
 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"
+        ],
+        "API Reference" => "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
+)