bio-freebayes 0.1.5

checksums.yaml

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+SHA1:
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+  data.tar.gz: 608d8848276886fad612e67f6ce3c31238a7b61b
+SHA512:
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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/

data/.rspec

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+--format documentation
+--color

data/.travis.yml

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+language: ruby
+rvm:
+  - 2.0.0

data/CODE_OF_CONDUCT.md

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+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the [Contributor Covenant](http:contributor-covenant.org), version 1.0.0, available at [http://contributor-covenant.org/version/1/0/0/](http://contributor-covenant.org/version/1/0/0/)

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in bio-freebayes.gemspec
+gemspec

data/README.md

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+# Bio::Freebayes
+
+Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/bio/freebayes`. To experiment with that code, run `bin/console` for an interactive prompt.
+
+TODO: Delete this and the text above, and describe your gem
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'bio-freebayes'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install bio-freebayes
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release` to create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+1. Fork it ( https://github.com/[my-github-username]/bio-freebayes/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "bio/freebayes"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/setup

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+#!/bin/bash
+set -euo pipefail
+IFS=$'\n\t'
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/bio-freebayes.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'bio/freebayes/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "bio-freebayes"
+  spec.version       = Bio::Freebayes::VERSION
+  spec.authors       = ["Natapol Pornputtapong"]
+  spec.email         = ["natapol.por@gmail.com"]
+
+  spec.summary       = %q{The API for Freebayes version #{Bio::Freebayes::EXTVERSION}}
+  spec.description   = %q{The API for Freebayes version #{Bio::Freebayes::EXTVERSION}}
+  spec.homepage      = "http://rubygems.org/gems/bio-freebayes"
+
+  # Prevent pushing this gem to RubyGems.org by setting 'allowed_push_host', or
+  # delete this section to allow pushing this gem to any host.
+  if spec.respond_to?(:metadata)
+    spec.metadata['allowed_push_host'] = "TODO: Set to 'http://mygemserver.com'"
+  else
+    raise "RubyGems 2.0 or newer is required to protect against public gem pushes."
+  end
+
+  spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+  spec.extensions = ["ext/mkrf_conf.rb"]
+  
+  spec.add_runtime_dependency "bio-vcf", "~> 0.8"
+  
+  spec.add_development_dependency "bundler", "~> 1.9"
+  spec.add_development_dependency "rake", "~> 10.0"
+end

data/ext/mkrf_conf.rb

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+# coding: utf-8
+
+path = File.expand_path(File.dirname(__FILE__))
+
+require '../lib/bio/freebayes/version'
+version = Bio::Freebayes::EXTVERSION
+
+File.open(File.join(path,"Rakefile"),"w") do |rakefile|
+rakefile.write <<-RAKE
+require 'rbconfig'
+require 'open-uri'
+require 'fileutils'
+include FileUtils::Verbose
+require 'rake/clean'
+require 'mkmf'
+
+task :freebayes do
+	
+	missing = []
+	['git', 'cmake'].each do |exe|
+		 missing.push(exe) if !find_executable(exe)
+	end
+	
+	raise "Missing \#\{missing.join(', ')\}"  if !missing.empty?
+	
+	sh "git clone --recursive git://github.com/ekg/freebayes.git"
+	mkdir "../lib/bio/freebayes/external"
+	
+	cd "freebayes" do
+		sh "git checkout v#{version} && git submodule update --recursive"
+		sh "make"
+		mv "bin/freebayes", "../../lib/bio/freebayes/external"
+		mv "bin/bamleftalign", "../../lib/bio/freebayes/external"
+	end
+	
+	rm_rf "freebayes"
+	
+end
+
+task :default => [:freebayes]
+RAKE
+
+end

data/lib/bio/freebayes.rb

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+require "bio/freebayes/version"
+require 'open3'
+
+module Bio
+	class Freebayes
+		
+		# instantiate Freebayes command tools
+		def initialize(path = nil)
+			@filter = nil
+			@eval = nil
+			@path = path || File.join(File.expand_path(File.dirname(__FILE__)), 'freebayes', 'external', 'freebayes')
+		end
+		
+		# run freebayes tools for command and all options please go to 
+		# https://github.com/ekg/freebayes
+		#
+		# @param [String] fasta_reference path of the reference fasta file
+		# @param [String] bam path of the alignment file in bam format
+		# @param [Array] options of freebayes command
+		# @return [String] A VCF string
+		def run(fasta_reference, bam, *options)
+			result = `#{@path} #{options.flatten.join(' ')} --fasta-reference #{fasta_reference} #{bam}`
+			if @filter != nil || @eval != nil || @filter != '' || @eval != ''
+				Open3.popen2("bio-vcf #{@filter != nil && !@filter.empty? ? "--filter '#{@filter}' " : ''}#{@eval != nil && !@eval.empty? ? "--eval '#{@eval}' " : ''}") {|stdin, stdout, wthr|
+					stdin.print result
+					stdin.close
+					return stdout.gets
+				}
+			else 
+				return result
+			end
+		end
+		
+		# set bio-vcf Filter
+		# for details please go to https://github.com/pjotrp/bioruby-vcf
+		# the chaning have to end with run
+		# 
+		# @param [String] filter a VCF filter for bio-vcf
+		# @return [Freebayes] return freebayes object for chaining
+		def vcffilter(filter)
+			@filter = filter
+			return self
+		end
+		
+		# set command for the eval option of bio-vcf 
+		# more details please go to https://github.com/pjotrp/bioruby-vcf
+		# the chaning have to end with run
+		# 
+		# @param [String] eval a VCF filter for bio-vcf
+		# @return [Freebayes] return freebayes object for chaining
+		def vcfeval(eval)
+			@eval = eval
+			return self
+		end
+		
+		# run help
+		# https://github.com/ekg/freebayes
+		#
+		def help
+			`#{@path} -h`
+		end
+	end
+	
+end

data/lib/bio/freebayes/version.rb

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+module Bio
+	class Freebayes
+		VERSION = "0.1.5"
+		EXTVERSION = "0.9.20"
+	end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: bio-freebayes
+version: !ruby/object:Gem::Version
+  version: 0.1.5
+platform: ruby
+authors:
+- Natapol Pornputtapong
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2015-05-21 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio-vcf
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.9'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.9'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+description: 'The API for Freebayes version #{Bio::Freebayes::EXTVERSION}'
+email:
+- natapol.por@gmail.com
+executables: []
+extensions:
+- ext/mkrf_conf.rb
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- bio-freebayes.gemspec
+- ext/mkrf_conf.rb
+- lib/bio/freebayes.rb
+- lib/bio/freebayes/version.rb
+homepage: http://rubygems.org/gems/bio-freebayes
+licenses: []
+metadata:
+  allowed_push_host: 'TODO: Set to ''http://mygemserver.com'''
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.0.14
+signing_key: 
+specification_version: 4
+summary: 'The API for Freebayes version #{Bio::Freebayes::EXTVERSION}'
+test_files: []
+has_rdoc: