bio-gngm 0.1.0

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem "bio", ">= 1.4.2"
+gem "bio-samtools", ">=0.5.0"
+gem "rinruby", ">=2.0.2"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler"
+  gem "rcov", ">= 0"
+  gem "bio", ">= 1.4.2"
+  gem "bio-samtools", ">=0.5.0"
+  gem "rinruby", ">=2.0.2"
+  gem 'rdoc'
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    bio (1.4.2)
+    bio-samtools (0.5.0)
+      bio (>= 1.4.2)
+      ffi
+    ffi (1.0.11)
+    git (1.2.5)
+    jeweler (1.6.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+    json (1.6.3)
+    rake (0.9.2.2)
+    rcov (0.9.11)
+    rdoc (3.11)
+      json (~> 1.4)
+    rinruby (2.0.2)
+    shoulda (2.11.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bio (>= 1.4.2)
+  bio-samtools (>= 0.5.0)
+  bundler (~> 1.0.0)
+  jeweler
+  rcov
+  rdoc
+  rinruby (>= 2.0.2)
+  shoulda

data/LICENSE.txt

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+Copyright (c) 2011 Dan MacLean
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= bio-gngm
+
+Ruby Gem for performing identification of causative mutations in a model genome using the NGM method.
+
+A Bio::Util::Gngm object represents a single region on a reference genome that is to be examined using the NGM technique described in Austin et al (2011) http://bar.utoronto.ca/ngm/description.html and http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2011.04619.x/abstract;jsessionid=F73E2DA628523B26205297CEE95526DA.d02t04
+Austin _et_ _al_ (2011) *Next-generation* *mapping* *of* *Arabidopsis* *genes* _Plant_ _Journal_ *67*(4):7125-725 . 
+
+Bio::Util::Gngm provides methods for finding SNPs, small INDELS and larger INDELS, creating histograms of polymorphism frequency, 
+creating and clustering density curves, creating signal plots and finding peaks. The ratio of reference-agreeing and reference-differing reads can be specified. 
+
+== Background
+The basic concept of the technique is that density curves of polymorphism frequency across the region of interest are plotted and analysed. Each curve is called a thread, as it represents a polymorphism that
+was called with a statistic within a certain user-specified range, eg if a SNP was called with 50% non-reference bases from sequence reads (say all A), and 50% reference reads (all T) then a discordant
+chastity statistic (ChD) of 0.5 would be calculated and assigned to that SNP. Depending on the width and slide of the windows the user had specified, the frequency of SNPs with ChD in the specified range
+would be drawn in the same density curve. 
+
+Finding regions enriched in a target ChD and depleted in others can point to causative mutations.
+
+== Contributing to bio-gngm
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2011 Dan MacLean. See LICENSE.txt for
+further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-gngm"
+  gem.homepage = "http://github.com/danmaclean/bioruby-gngm"
+  gem.license = "MIT"
+  gem.summary = %Q{Next-Generation Mapping of Mutations}
+  gem.description = %Q{Identify causative mutations in a model genome from NGS reads using the NGM method.}
+  gem.email = "maclean.daniel@gmail.com"
+  gem.authors = ["Dan MacLean"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+  test.rcov_opts << '--exclude "gems/*"'
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-gngm #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/bio-gngm.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "bio-gngm"
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Dan MacLean"]
+  s.date = "2012-03-19"
+  s.description = "Identify causative mutations in a model genome from NGS reads using the NGM method."
+  s.email = "maclean.daniel@gmail.com"
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bio-gngm.gemspec",
+    "doc/Bio.html",
+    "doc/Bio/DB.html",
+    "doc/Bio/DB/Pileup.html",
+    "doc/Bio/DB/Vcf.html",
+    "doc/Bio/Util.html",
+    "doc/Bio/Util/Gngm.html",
+    "doc/LICENSE_txt.html",
+    "doc/_index.html",
+    "doc/class_list.html",
+    "doc/created.rid",
+    "doc/css/common.css",
+    "doc/css/full_list.css",
+    "doc/css/style.css",
+    "doc/doc/created.rid",
+    "doc/file_list.html",
+    "doc/frames.html",
+    "doc/images/add.png",
+    "doc/images/bands.png",
+    "doc/images/brick.png",
+    "doc/images/brick_link.png",
+    "doc/images/bug.png",
+    "doc/images/bullet_black.png",
+    "doc/images/bullet_toggle_minus.png",
+    "doc/images/bullet_toggle_plus.png",
+    "doc/images/date.png",
+    "doc/images/delete.png",
+    "doc/images/find.png",
+    "doc/images/loadingAnimation.gif",
+    "doc/images/macFFBgHack.png",
+    "doc/images/package.png",
+    "doc/images/page_green.png",
+    "doc/images/page_white_text.png",
+    "doc/images/page_white_width.png",
+    "doc/images/plugin.png",
+    "doc/images/ruby.png",
+    "doc/images/signal.png",
+    "doc/images/tag_blue.png",
+    "doc/images/tag_green.png",
+    "doc/images/threads.png",
+    "doc/images/transparent.png",
+    "doc/images/wrench.png",
+    "doc/images/wrench_orange.png",
+    "doc/images/zoom.png",
+    "doc/index.html",
+    "doc/js/app.js",
+    "doc/js/darkfish.js",
+    "doc/js/full_list.js",
+    "doc/js/jquery.js",
+    "doc/js/navigation.js",
+    "doc/js/search.js",
+    "doc/js/search_index.js",
+    "doc/js/searcher.js",
+    "doc/lib/bio-gngm_rb.html",
+    "doc/lib/bio/util/bio-gngm_rb.html",
+    "doc/method_list.html",
+    "doc/rdoc.css",
+    "doc/table_of_contents.html",
+    "examples/.DS_Store",
+    "examples/make_histograms.rb",
+    "examples/make_threads.rb",
+    "examples/make_threads_isize.rb",
+    "examples/use_indels.rb",
+    "lib/bio-gngm.rb",
+    "lib/bio/util/bio-gngm.rb",
+    "scripts/get_subseq.rb",
+    "scripts/make_histograms_laerfyve.rb",
+    "scripts/make_histograms_laerfyve_stitched.rb",
+    "scripts/make_threads_isize_laerfyfe.rb",
+    "scripts/make_threads_unmapped_laerfyfe.rb",
+    "scripts/make_threads_unmapped_laerfyfe_pseudo.rb",
+    "scripts/make_threads_unmapped_simulation.rb",
+    "scripts/make_threads_unmapped_simulation_immediate_region.rb",
+    "scripts/optimise_freq_window_size.rb",
+    "stitched_contigs.zip",
+    "test/data/ids2.txt",
+    "test/data/sorted.bam",
+    "test/data/test",
+    "test/data/test.bam",
+    "test/data/test.fa",
+    "test/data/test.fai",
+    "test/data/test.sai",
+    "test/data/test.tam",
+    "test/data/test_chr.fasta",
+    "test/data/test_chr.fasta.amb",
+    "test/data/test_chr.fasta.ann",
+    "test/data/test_chr.fasta.bwt",
+    "test/data/test_chr.fasta.fai",
+    "test/data/test_chr.fasta.pac",
+    "test/data/test_chr.fasta.rbwt",
+    "test/data/test_chr.fasta.rpac",
+    "test/data/test_chr.fasta.rsa",
+    "test/data/test_chr.fasta.sa",
+    "test/data/testu.bam",
+    "test/data/testu.bam.bai",
+    "test/helper.rb",
+    "test/test_bio-gngm.rb"
+  ]
+  s.homepage = "http://github.com/danmaclean/bioruby-gngm"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.10"
+  s.summary = "Next-Generation Mapping of Mutations"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_runtime_dependency(%q<bio-samtools>, [">= 0.5.0"])
+      s.add_runtime_dependency(%q<rinruby>, [">= 2.0.2"])
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, [">= 0"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_development_dependency(%q<bio-samtools>, [">= 0.5.0"])
+      s.add_development_dependency(%q<rinruby>, [">= 2.0.2"])
+      s.add_development_dependency(%q<rdoc>, [">= 0"])
+    else
+      s.add_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_dependency(%q<bio-samtools>, [">= 0.5.0"])
+      s.add_dependency(%q<rinruby>, [">= 2.0.2"])
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, [">= 0"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_dependency(%q<bio-samtools>, [">= 0.5.0"])
+      s.add_dependency(%q<rinruby>, [">= 2.0.2"])
+      s.add_dependency(%q<rdoc>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<bio>, [">= 1.4.2"])
+    s.add_dependency(%q<bio-samtools>, [">= 0.5.0"])
+    s.add_dependency(%q<rinruby>, [">= 2.0.2"])
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, [">= 0"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.2"])
+    s.add_dependency(%q<bio-samtools>, [">= 0.5.0"])
+    s.add_dependency(%q<rinruby>, [">= 2.0.2"])
+    s.add_dependency(%q<rdoc>, [">= 0"])
+  end
+end
+

data/doc/Bio.html

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+<!DOCTYPE html>
+
+<html>
+<head>
+<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
+
+<title>Module: Bio</title>
+
+<link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
+
+<script type="text/javascript">
+  var rdoc_rel_prefix = "./";
+</script>
+
+<script type="text/javascript" charset="utf-8" src="./js/jquery.js"></script>
+<script type="text/javascript" charset="utf-8" src="./js/navigation.js"></script>
+<script type="text/javascript" charset="utf-8" src="./js/search_index.js"></script>
+<script type="text/javascript" charset="utf-8" src="./js/search.js"></script>
+<script type="text/javascript" charset="utf-8" src="./js/searcher.js"></script>
+<script type="text/javascript" charset="utf-8" src="./js/darkfish.js"></script>
+
+
+<body id="top" class="module">
+<nav id="metadata">
+  <nav id="home-section" class="section">
+  <h3 class="section-header">
+    <a href="./index.html">Home</a>
+    <a href="./table_of_contents.html#classes">Classes</a>
+    <a href="./table_of_contents.html#methods">Methods</a>
+  </h3>
+</nav>
+
+
+  <nav id="search-section" class="section project-section" class="initially-hidden">
+  <form action="#" method="get" accept-charset="utf-8">
+    <h3 class="section-header">
+      <input type="text" name="search" placeholder="Search" id="search-field"
+             title="Type to search, Up and Down to navigate, Enter to load">
+    </h3>
+  </form>
+
+  <ul id="search-results" class="initially-hidden"></ul>
+</nav>
+
+
+  <div id="file-metadata">
+    <nav id="file-list-section" class="section">
+  <h3 class="section-header">Defined In</h3>
+  <ul>
+    <li>lib/bio/util/bio-gngm.rb
+  </ul>
+</nav>
+
+    
+  </div>
+
+  <div id="class-metadata">
+    
+    
+    
+    
+  </div>
+
+  <div id="project-metadata">
+    <nav id="fileindex-section" class="section project-section">
+  <h3 class="section-header">Pages</h3>
+
+  <ul>
+  
+    <li class="file"><a href="./LICENSE_txt.html">LICENSE</a>
+  
+  </ul>
+</nav>
+
+    <nav id="classindex-section" class="section project-section">
+  <h3 class="section-header">Class and Module Index</h3>
+
+  <ul class="link-list">
+  
+    <li><a href="./Bio.html">Bio</a>
+  
+    <li><a href="./Bio/DB.html">Bio::DB</a>
+  
+    <li><a href="./Bio/DB/Pileup.html">Bio::DB::Pileup</a>
+  
+    <li><a href="./Bio/DB/Vcf.html">Bio::DB::Vcf</a>
+  
+    <li><a href="./Bio/Util.html">Bio::Util</a>
+  
+    <li><a href="./Bio/Util/Gngm.html">Bio::Util::Gngm</a>
+  
+  </ul>
+</nav>
+
+  </div>
+</nav>
+
+<div id="documentation">
+  <h1 class="module">module Bio</h1>
+
+  <div id="description" class="description">
+    
+  </div><!-- description -->
+
+  
+  
+  
+  <section id="5Buntitled-5D" class="documentation-section">
+    
+
+    
+
+    
+
+    
+
+    <!-- Methods -->
+    
+  </section><!-- 5Buntitled-5D -->
+
+</div><!-- documentation -->
+
+
+<footer id="validator-badges">
+  <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
+  <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
+  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
+</footer>
+