shaq_lib 0.0.1

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 4e78132d369c3339be61e910d2aed506a5723f99
+  data.tar.gz: 4956ff48790446388a0d871343228661bbbe6ec1
+SHA512:
+  metadata.gz: 84f0148731c233e5a98d8df330b655875a34e96d3b5878f9b7a9f5e135fe40b56d9573e9d16ec6d1e24f103ee3f4d9ff1c9ca295d90d92dd1e3aaa0f8fda8170
+  data.tar.gz: 20643dc104db18781e8e9c49f77baf1a69b72d7dd5d090adf96719bc87c8fdc670129b7729dce3f46934c3f092a2984a665b26c603c2e96d53db2612cabb76ea

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/.ruby-gemset

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+shaq_lib

data/.ruby-version

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+ruby-2.3.0

data/.travis.yml

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+language: ruby
+rvm:
+  - 2.3.0
+before_install: gem install bundler -v 1.11.2

data/CODE_OF_CONDUCT.md

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+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, and in the interest of
+fostering an open and welcoming community, 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, ethnicity, age, religion, or nationality.
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery
+* Personal attacks
+* Trolling or insulting/derogatory comments
+* Public or private harassment
+* Publishing other's private information, such as physical or electronic
+  addresses, without explicit permission
+* Other unethical or 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, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+By adopting this Code of Conduct, project maintainers commit themselves to
+fairly and consistently applying these principles to every aspect of managing
+this project. Project maintainers who do not follow or enforce the Code of
+Conduct may be permanently removed from the project team.
+
+This code of conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting a project maintainer at moorer@udel.edu. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. Maintainers are
+obligated to maintain confidentiality with regard to the reporter of an
+incident.
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 1.3.0, available at
+[http://contributor-covenant.org/version/1/3/0/][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/3/0/

data/Gemfile

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

data/README.md

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+# ShaqLib #
+
+Library code for the [Shaq](https://github.com/mooreryan/shaq)
+assembler.
+
+## Installation ##
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'shaq_lib'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install shaq_lib
+
+
+## Development ##
+
+After checking out the repo, run `bin/setup` to install
+dependencies. Then, run `rake spec` to run the tests. You can also 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`, which will
+create a git tag for the version, push git commits and tags, and push
+the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing ##
+
+Bug reports and pull requests are welcome on GitHub at
+https://github.com/[mooreryan]/shaq_lib. This project is intended to be
+a safe, welcoming space for collaboration, and contributors are
+expected to adhere to the
+[Contributor Covenant](http://contributor-covenant.org) code of
+conduct.

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+require "rake/extensiontask"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec
+
+Rake::ExtensionTask.new do |ext|
+  ext.name    = "shaq_lib"
+  ext.ext_dir = "ext/shaq_lib"
+  ext.lib_dir = "lib/shaq_lib"
+end
+
+Rake::Task[:spec].prerequisites << :compile

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "shaq_lib"
+
+# 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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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/ext/shaq_lib/extconf.rb

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+require "mkmf"
+
+create_makefile "shaq_lib/shaq_lib"

data/ext/shaq_lib/shaq_lib.c

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+#include <ruby.h>
+
+static VALUE kmers(VALUE klass, VALUE str, VALUE ksize)
+{
+  long i = 0;
+  long j = 0;
+  long k = NUM2LONG(ksize);
+  long num_kmers = RSTRING_LEN(str) - k + 1;
+
+  char *c_str = RSTRING_PTR(str);
+
+  for (i = 0; i < num_kmers; ++i) {
+    char substr[k+1];
+
+    for (j = 0; j < k; ++j) {
+      substr[j] = c_str[i+j];
+    }
+    substr[j] = '\0';
+
+    /* for this, put the length without the null char */
+    rb_yield(rb_str_new(substr, k));
+  }
+
+  return str;
+}
+
+void Init_shaq_lib(void)
+{
+  VALUE ModuleShaqLib = rb_define_module("ShaqLib");
+  rb_define_singleton_method(ModuleShaqLib, "kmers", kmers, 2);
+}

data/lib/shaq_lib/version.rb

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+module ShaqLib
+  VERSION = "0.0.1"
+end

data/lib/shaq_lib.rb

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+require "shaq_lib/shaq_lib"
+require "shaq_lib/version"
+
+module ShaqLib
+end

data/shaq_lib.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'shaq_lib/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "shaq_lib"
+  spec.version       = ShaqLib::VERSION
+  spec.authors       = ["Ryan Moore"]
+  spec.email         = ["moorer@udel.edu"]
+  spec.license       = "GPLv3"
+
+  spec.summary       = %q{Library code for Shaq assembler}
+  spec.description   = %q{Library code for Shaq assembler}
+  spec.homepage      = "https://github.com/mooreryan/shaq_lib"
+
+  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", "ext"]
+
+  spec.platform      = Gem::Platform::RUBY
+  spec.extensions    = ["ext/shaq_lib/extconf.rb"]
+
+  spec.add_development_dependency "bundler", "~> 1.11"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+  spec.add_development_dependency "rake-compiler", "~> 0.9.7"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: shaq_lib
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Ryan Moore
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2016-04-23 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.11'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.11'
+- !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'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: rake-compiler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.9.7
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.9.7
+description: Library code for Shaq assembler
+email:
+- moorer@udel.edu
+executables: []
+extensions:
+- ext/shaq_lib/extconf.rb
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".ruby-gemset"
+- ".ruby-version"
+- ".travis.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- ext/shaq_lib/extconf.rb
+- ext/shaq_lib/shaq_lib.c
+- lib/shaq_lib.bundle
+- lib/shaq_lib.rb
+- lib/shaq_lib/shaq_lib.bundle
+- lib/shaq_lib/version.rb
+- shaq_lib.gemspec
+homepage: https://github.com/mooreryan/shaq_lib
+licenses:
+- GPLv3
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+- ext
+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: 2.5.1
+signing_key: 
+specification_version: 4
+summary: Library code for Shaq assembler
+test_files: []