README.rdoc in scaffolder-0.2.6 vs README.rdoc in scaffolder-0.4.0

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@@ -1,25 +1,37 @@ -= scaffolder +== Synopsis -Description goes here. +A simple genome scaffolder API for merging sequence contigs to build a continuous +draft sequence. The draft sequence is constructed through specifying the order of +contigs in in human-readable YAML files. Since the draft genome is specified by the +scaffold YAML it is easy to remove or manipulate already sequences. In addition as +the scaffold file is easy to edit and is ideal for version control and +repeatability. -== Note on Patches/Pull Requests - -* Fork the project. -* Make your feature addition or bug fix. -* Add tests for it. This is important so I don't break it in a - future version unintentionally. -* Commit, do not mess with rakefile, version, or history. - (if you want to have your own version, that is fine but bump version in a commit by itself I can ignore when I pull) -* Send me a pull request. Bonus points for topic branches. +== Feature List -== Copyright +* Construct a draft sequence scaffold using human-readable and versionable + plain text files. +* A simple and extensible Ruby API to traverse the scaffold. -Copyright (c) 2010 Michael Barton. See LICENSE for details. +== Installing -== Notes +Ruby and RubyGems are required to use scaffolder. Scaffolder is installed on +the command line using: -Inserts processed are processed in reverse order according to end position. Last insert added up until first insert. Done to preserve insert coordinates. + $ gem install scaffolder -Overlapping inserts may cause unexpected behaviour +== Documentation -Sequence reversed after inserts have been added. +See the Scaffolder class for getting started with Scaffolder. + +== Contact + +Scaffolder was developed by Michael Barton (www.michaelbarton.me.uk). Pull +requests, patches and bug reports are welcome. The source code is available on +github[http://github.com/michaelbarton/scaffolder]. Bug reports and feature +requests may also be made there. + +== Copyright + +Scaffolder © 2010 by Michael Barton. Scaffolder is licensed under the MIT +license. Please see the LICENSE document for more information.