bio-sambamba 0.0.1

data/.document

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

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+
+gem "bio", "~> 1.4.2"
+gem "oj", "~> 1.2.9"
+
+group :development do
+  gem "bundler", "~> 1.1.4"
+  gem "jeweler", "~> 1.8.3"
+  gem "rspec", "~> 2.7.0"
+  gem "cucumber", "~> 1.2.0"
+end

data/LICENSE.txt

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+Copyright (c) 2012 Artem Tarasov
+
+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.md

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+# bio-sambamba
+
+[![Build Status](https://secure.travis-ci.org/lomereiter/bioruby-sambamba.png)](http://travis-ci.org/lomereiter/bioruby-sambamba)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+    rake build
+    rake install
+```
+
+In order to use the gem, you also need <code>sambamba</code> tool installed.
+For that, do the following:
+
+* install [DMD compiler](http://dlang.org/download.html)
+* install [Ragel](http://www.complang.org/ragel/) finite state machine compiler
+* clone sambamba repository and compile the tool
+
+```sh
+    git clone https://github.com/lomereiter/sambamba.git
+    cd sambamba/CLItools/
+    make
+```
+
+* place the executable file <code>build/sambamba</code> to somewhere in your $PATH,
+  for example:
+
+```sh
+    cp build/sambamba /usr/local/bin
+```
+
+## Usage
+
+```ruby
+    require 'bio-sambamba'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/lomereiter/bioruby-sambamba
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at [#bio-sambamba](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) 2012 Artem Tarasov. 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-sambamba"
+  gem.homepage = "http://github.com/lomereiter/bioruby-sambamba"
+  gem.license = "MIT"
+  gem.summary = %Q{Ruby wrapper for Sambamba tool}
+  gem.description = %Q{New Sambamba library comes with a command-line tool for working with SAM/BAM files. This gem brings some of its functionality to Ruby.}
+  gem.email = "lomereiter@gmail.com"
+  gem.authors = ["Artem Tarasov"]
+  # dependencies defined in Gemfile
+
+  gem.files.include "lib/bio-sambamba/*.rb"
+  gem.files.include "lib/bio-sambamba.rb"
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'cucumber/rake/task'
+Cucumber::Rake::Task.new do |features|
+end
+
+task :test => :cucumber
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-sambamba #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/features/iterate-alignments.feature

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+Feature: iterating alignment records
+
+    In order to have access to all information contained in a BAM file,
+    As a bioinformatician,
+    I want to be able to iterate alignment records from Ruby
+    And have access to all their fields and tags.
+
+    Scenario: accessing alignment records
+        Given I opened a valid BAM file
+        When I use its 'alignments' method
+        Then I should be able to iterate the returned object with 'each'
+        And the objects which I iterate over should represent the alignments
+        And I should be able to access all fields mentioned in SAM/BAM format specification
+
+    Scenario: access existing alignment tag
+        Given I have an alignment
+          And it contains some tags
+         When I access it like a hash
+          And I use 2-character string as a key
+          And the alignment has such tag
+         Then I should be able to see corresponding value
+          And it should be a simple Ruby object (Array, Numeric, or String)
+
+    Scenario: invalid tag key (not of length 2)
+        Given I have an alignment
+         When I access it like a hash
+          But I use string of length different than two, as a key,
+         Then exception should be thrown.
+
+    Scenario: accessing non-existing alignment tag
+        Given I have an alignment
+          And it contains some tags
+         When I access it like a hash
+          But it doesn't contain the requested tag
+          Then nil should be returned.
+
+    Scenario: fetching all tags as a hash
+        Given I have an alignment
+         When I use its 'tags' method
+         Then I should be able to work with the returned object just like with Hash

data/features/random-access.feature

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+Feature: random access to BAM file
+    In order to retrieve information about specific regions,
+    I want to be able to quickly fetch alignments overlapping a region.
+
+    Scenario: fetching alignments
+        Given I have a BAM file
+          And it's sorted by coordinate
+          And I have its index as well
+         When I specify reference sequence and region (1-based beginning and end positions)
+         Then I should be able to immediately have access to alignments overlapping it

data/features/sam-header.feature

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+Feature: access to information from SAM header
+
+    In order to work with BAM file,
+    I want to see what its header contains.
+
+    Background:
+        Given I opened a valid BAM file
+          And it contains SAM header
+
+    Scenario: getting raw text
+         When I call 'header' method
+         Then I should see text of SAM header
+
+    Scenario: accessing version and sorting order
+         When SAM header contains @HD line
+         Then I should be able to see format version
+          And I should be able to see sorting order
+
+    Scenario: getting information about reference sequences
+         When SAM header contains @SQ lines
+         Then I should be able to iterate them
+          And I should be able to see sequence names
+          And I should be able to see their lengths

data/features/step_definitions/iterate-alignments_steps.rb

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+Before do
+  @bam = Bio::Bam::File.new 'test/data/ex1_header.bam'
+end
+
+When /^I use its 'alignments' method$/ do
+  @bam.should respond_to(:alignments)
+end
+
+Then /^I should be able to iterate the returned object with 'each'$/ do
+  @bam.alignments.should respond_to(:each)
+end
+
+Then /^the objects which I iterate over should represent the alignments$/ do
+  @bam.alignments.take(100).each do |read|
+    read.should be_instance_of(Bio::Bam::Alignment)
+  end
+end
+
+Then /^I should be able to access all fields mentioned in SAM\/BAM format specification$/ do
+  @read = @bam.alignments.first
+  @read.read_name.should == 'EAS56_57:6:190:289:82'
+  @read.sequence.should == 'CTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA'
+  @read.position.should == 100
+  @read.flag.should == 69
+  @read.mapping_quality.should == 0
+  @read.cigar_string.should == '*'
+  @read.reference.should == 'chr1'
+  @read.quality.should == [27, 27, 27, 22, 27, 27, 27, 26, 27, 27, 27, 27, 27, 27, 27, 27, 23, 26, 26, 27, 22, 26, 19, 27, 26, 27, 26, 26, 26, 26, 26, 24, 19, 27, 26]
+end
+
+Given /^I have an alignment$/ do
+  @read = @bam.alignments.first
+end
+
+Given /^it contains some tags$/ do
+end
+
+When /^I access it like a hash$/ do
+  @read.should respond_to(:[])
+end
+
+When /^I use 2-character string as a key$/ do
+  @key = 'MF'
+end
+
+When /^the alignment has such tag$/ do
+  @read[@key].should_not be_nil
+end
+
+Then /^I should be able to see corresponding value$/ do
+  @read[@key].should be == 192
+end
+
+Then /^it should be a simple Ruby object \(Array, Numeric, or String\)$/ do
+  @read[@key].should be_kind_of Numeric
+end
+
+When /^I use string of length different than two, as a key,$/ do
+  @key = 'key'
+end
+
+Then /^exception should be thrown\.$/ do
+  expect{@read[@key]}.to raise_error(RuntimeError)
+end
+
+When /^it doesn't contain the requested tag$/ do
+  @key = 'hq'
+end
+
+Then /^nil should be returned\.$/ do
+  @read[@key].should be_nil
+end
+
+When /^I use its 'tags' method$/ do
+  @tags = @read.tags
+end
+
+Then /^I should be able to work with the returned object just like with Hash$/ do
+  @tags.should be_kind_of Hash
+  @tags['MF'].should be == 192
+  @tags.keys.should be == ['MF']
+  @tags.values.should be == [192]
+end

data/features/step_definitions/random-access_steps.rb

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+Before do
+    @bam = Bio::Bam::File.new './test/data/ex1_header.bam'
+end
+
+Given /^it's sorted by coordinate$/ do
+    @bam.header.sorting_order.should == 'coordinate'
+end
+
+Given /^I have its index as well$/ do
+    @bam.should have_index
+end
+
+When /^I specify reference sequence and region \(1-based beginning and end positions\)$/ do
+    @region = (1400 ... 1500)
+    @chr = "chr2"
+end
+
+Then /^I should be able to immediately have access to alignments overlapping it$/ do
+    @alignments = @bam.fetch @chr, @region
+    @alignments.should respond_to(:each).with(0).arguments
+    @alignments.to_a.length.should == 77
+end

data/features/step_definitions/sam-header_steps.rb

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+Given /^I opened a valid BAM file$/ do
+  filename = './test/data/ex1_header.bam'
+  File.exists?(filename).should be_true
+  @bamfile = Bio::Bam::File.new filename
+end
+
+Given /^it contains SAM header$/ do
+  @bamfile.header.raw_contents.length.should be > 0
+end
+
+When /^I call 'header' method$/ do
+  @header = @bamfile.header
+end
+
+Then /^I should see text of SAM header$/ do
+  @header.raw_contents.should be_kind_of String
+end
+
+Given /^SAM header contains @HD line$/ do
+  @header = @bamfile.header
+  @header.raw_contents.should =~ /^@HD/
+end
+
+Then /^I should be able to see format version$/ do
+  @version = @header.version
+  @version.should be_kind_of String
+  @version.length.should be > 0
+end
+
+Then /^I should be able to see sorting order$/ do
+  @sorting_order = @header.sorting_order
+  @sorting_order.should be_kind_of String
+  @sorting_order.length.should be > 0
+end
+
+Given /^SAM header contains @SQ lines$/ do
+  @header = @bamfile.header
+  @header.sq_lines.length.should be > 0
+end
+
+Then /^I should be able to iterate them$/ do
+  @sq_lines = @header.sq_lines
+  @sq_lines.should be_kind_of Array
+end
+
+Then /^I should be able to see sequence names$/ do
+  @line = @sq_lines.first
+  @line.should respond_to(:sequence_name).with(0).arguments
+  @line.sequence_name.should be_kind_of String
+  @line.sequence_name.length.should be > 0
+end
+
+Then /^I should be able to see their lengths$/ do
+  @line.should respond_to(:sequence_length).with(0).arguments
+  @line.sequence_length.should be_kind_of Numeric
+end

data/features/step_definitions/validation-steps.rb

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+Before do
+  # this file is known to contain some invalid records
+  @tagsbam = Bio::Bam::File.new './test/data/tags.bam'
+end
+
+Given /^I have an alignment from a BAM file$/ do
+  @alignment = @tagsbam.alignments.to_a[32]
+end
+
+When /^I call 'valid\?' method$/ do
+  pending
+#  @is_valid = @alignment.valid?
+end
+
+Then /^it should return whether it is valid or not$/ do
+  @is_valid.should be_true
+end
+
+Given /^I have a BAM file$/ do
+end
+
+When /^I want to iterate over its records$/ do
+  @records = @tagsbam.alignments
+end
+
+Then /^I should have an option to skip invalid ones$/ do
+  @records.should respond_to(:each_valid).with(0).arguments
+end
+
+Then /^all the reads in this case should be valid$/ do
+  count = 0
+  @records.each_valid {|read| count += 1 }
+  count.should == 411
+end