bio-samtools 0.2.0

data/test/samples/small/test_chr.fasta.amb

@@ -0,0 +1,2 @@
+69930 1 1
+41554 50 N

data/test/samples/small/test_chr.fasta.ann

@@ -0,0 +1,3 @@
+69930 1 11
+0 chr_1 (null)
+0 69930 1

data/test/samples/small/test_chr.fasta.fai

@@ -0,0 +1 @@
+chr_1	69930	7	70	71

data/test/test_bio-samtools.rb

@@ -0,0 +1,7 @@
+require 'helper'
+
+class TestBioSamtools < Test::Unit::TestCase
+  should "probably rename this file and start testing for real" do
+    flunk "hey buddy, you should probably rename this file and start testing for real"
+  end
+end

metadata

@@ -0,0 +1,185 @@
+--- !ruby/object:Gem::Specification 
+name: bio-samtools
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.2.0
+platform: ruby
+authors: 
+- Ricardo Ramirez-Gonzalez
+- Dan MacLean
+- Raoul J.P. Bonnal
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-05-23 00:00:00 +02:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: ffi
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :runtime
+  prerelease: false
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: shoulda
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: bundler
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
+  name: rcov
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id005
+- !ruby/object:Gem::Dependency 
+  name: bio
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.4.1
+  type: :development
+  prerelease: false
+  version_requirements: *id006
+- !ruby/object:Gem::Dependency 
+  name: ffi
+  requirement: &id007 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id007
+description: |-
+  Binder of samtools for ruby, on the top of FFI. 
+  
+    This project was born from the need to add support of BAM files to 
+    the gee_fu genome browser (http://github.com/danmaclean/gee_fu).
+email: ilpuccio.febo@gmail.com
+executables: []
+
+extensions: 
+- ext/mkrf_conf.rb
+extra_rdoc_files: 
+- LICENSE.txt
+- README.rdoc
+files: 
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bio-samtools.gemspec
+- ext/mkrf_conf.rb
+- lib/bio-samtools.rb
+- lib/bio/.DS_Store
+- lib/bio/db/sam.rb
+- lib/bio/db/sam/bam.rb
+- lib/bio/db/sam/external/COPYING
+- lib/bio/db/sam/external/VERSION
+- lib/bio/db/sam/faidx.rb
+- lib/bio/db/sam/library.rb
+- lib/bio/db/sam/sam.rb
+- test/basictest.rb
+- test/coverage.rb
+- test/coverage_plot.rb
+- test/feature.rb
+- test/helper.rb
+- test/samples/small/ids2.txt
+- test/samples/small/sorted.bam
+- test/samples/small/test
+- test/samples/small/test.bam
+- test/samples/small/test.fa
+- test/samples/small/test.fai
+- test/samples/small/test.sai
+- test/samples/small/test.tam
+- test/samples/small/test_chr.fasta
+- test/samples/small/test_chr.fasta.amb
+- test/samples/small/test_chr.fasta.ann
+- test/samples/small/test_chr.fasta.bwt
+- test/samples/small/test_chr.fasta.fai
+- test/samples/small/test_chr.fasta.pac
+- test/samples/small/test_chr.fasta.rbwt
+- test/samples/small/test_chr.fasta.rpac
+- test/samples/small/test_chr.fasta.rsa
+- test/samples/small/test_chr.fasta.sa
+- test/samples/small/testu.bam
+- test/samples/small/testu.bam.bai
+- test/test_bio-samtools.rb
+has_rdoc: true
+homepage: http://github.com/helios/bioruby-samtools
+licenses: 
+- MIT
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: -2254602407450598476
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.5.0
+signing_key: 
+specification_version: 3
+summary: Binder of samtools for ruby, on the top of FFI.
+test_files: []
+