bio-samtools 0.2.4 → 0.2.5

data/Gemfile

@@ -3,7 +3,7 @@ source "http://rubygems.org"
 # Example:
 #   gem "activesupport", ">= 2.3.5"
 gem "ffi"
-gem "bio", ">= 1.4.1"
+gem "bio", ">= 1.4.2"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
@@ -12,6 +12,6 @@ group :development do
   gem "bundler", "~> 1.0.0"
   gem "jeweler"
   gem "rcov", ">= 0"
-  gem "bio", ">= 1.4.1"
+  gem "bio", ">= 1.4.2"
   gem "ffi"
 end

data/Gemfile.lock

@@ -1,22 +1,25 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    bio (1.4.1)
+    bio (1.4.2)
     ffi (1.0.9)
+    ffi (1.0.9-java)
     git (1.2.5)
     jeweler (1.6.0)
       bundler (~> 1.0.0)
       git (>= 1.2.5)
       rake
-    rake (0.9.0)
+    rake (0.9.2)
     rcov (0.9.9)
+    rcov (0.9.9-java)
     shoulda (2.11.3)
 
 PLATFORMS
+  java
   ruby
 
 DEPENDENCIES
-  bio (>= 1.4.1)
+  bio (>= 1.4.2)
   bundler (~> 1.0.0)
   ffi
   jeweler

data/VERSION

@@ -1 +1 @@
-0.2.4
+0.2.5

data/bio-samtools.gemspec

@@ -5,17 +5,17 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-samtools}
-  s.version = "0.2.4"
+  s.version = "0.2.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Ricardo Ramirez-Gonzalez", "Dan MacLean", "Raoul J.P. Bonnal"]
-  s.date = %q{2011-06-01}
+  s.authors = [%q{Ricardo Ramirez-Gonzalez}, %q{Dan MacLean}, %q{Raoul J.P. Bonnal}]
+  s.date = %q{2011-10-26}
   s.description = %q{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).}
   s.email = %q{ilpuccio.febo@gmail.com}
-  s.extensions = ["ext/mkrf_conf.rb"]
+  s.extensions = [%q{ext/mkrf_conf.rb}]
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.rdoc"
@@ -67,9 +67,9 @@ Gem::Specification.new do |s|
     "test/test_bio-samtools.rb"
   ]
   s.homepage = %q{http://github.com/helios/bioruby-samtools}
-  s.licenses = ["MIT"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.5.0}
+  s.licenses = [%q{MIT}]
+  s.require_paths = [%q{lib}]
+  s.rubygems_version = %q{1.8.6}
   s.summary = %q{Binder of samtools for ruby, on the top of FFI.}
 
   if s.respond_to? :specification_version then
@@ -77,31 +77,31 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<ffi>, [">= 0"])
-      s.add_runtime_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_runtime_dependency(%q<bio>, [">= 1.4.2"])
       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>, [">= 1.4.1"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.2"])
       s.add_development_dependency(%q<ffi>, [">= 0"])
     else
       s.add_dependency(%q<ffi>, [">= 0"])
-      s.add_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_dependency(%q<bio>, [">= 1.4.2"])
       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>, [">= 1.4.1"])
+      s.add_dependency(%q<bio>, [">= 1.4.2"])
       s.add_dependency(%q<ffi>, [">= 0"])
     end
   else
     s.add_dependency(%q<ffi>, [">= 0"])
-    s.add_dependency(%q<bio>, [">= 1.4.1"])
+    s.add_dependency(%q<bio>, [">= 1.4.2"])
     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>, [">= 1.4.1"])
+    s.add_dependency(%q<bio>, [">= 1.4.2"])
     s.add_dependency(%q<ffi>, [">= 0"])
   end
 end

data/lib/bio/db/sam/library.rb

@@ -13,7 +13,14 @@ module Bio
           when /darwin/
             '1.dylib'
           when /windows/
-            'dll'  
+            'dll'
+          else
+            case RUBY_DESCRIPTION
+            when /darwin.*java/
+              '1.dylib'
+            when /linux.*java/
+            'so.1'
+            end
           end
 
           File.join(File.expand_path(File.dirname(__FILE__)),'external',"libbam.#{lib_os}")

metadata

@@ -1,122 +1,117 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: bio-samtools
-version: !ruby/object:Gem::Version 
+version: !ruby/object:Gem::Version
+  version: 0.2.5
   prerelease: 
-  version: 0.2.4
 platform: ruby
-authors: 
+authors:
 - Ricardo Ramirez-Gonzalez
 - Dan MacLean
 - Raoul J.P. Bonnal
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2011-06-01 00:00:00 +02:00
-default_executable: 
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2011-10-26 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: ffi
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: &2152414440 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
+  version_requirements: *2152414440
+- !ruby/object:Gem::Dependency
   name: bio
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  requirement: &2152413500 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: 1.4.1
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
+  version_requirements: *2152413500
+- !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  requirement: &2152412540 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
   prerelease: false
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
+  version_requirements: *2152412540
+- !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  requirement: &2152411700 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
+      - !ruby/object:Gem::Version
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
+  version_requirements: *2152411700
+- !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  requirement: &2152410900 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
   prerelease: false
-  version_requirements: *id005
-- !ruby/object:Gem::Dependency 
+  version_requirements: *2152410900
+- !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  requirement: &2152410220 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
   prerelease: false
-  version_requirements: *id006
-- !ruby/object:Gem::Dependency 
+  version_requirements: *2152410220
+- !ruby/object:Gem::Dependency
   name: bio
-  requirement: &id007 !ruby/object:Gem::Requirement 
+  requirement: &2152409600 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: 1.4.1
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *id007
-- !ruby/object:Gem::Dependency 
+  version_requirements: *2152409600
+- !ruby/object:Gem::Dependency
   name: ffi
-  requirement: &id008 !ruby/object:Gem::Requirement 
+  requirement: &2152408900 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
   prerelease: false
-  version_requirements: *id008
-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).
+  version_requirements: *2152408900
+description: ! "Binder of samtools for ruby, on the top of FFI. \n\n  This project
+  was born from the need to add support of BAM files to \n  the gee_fu genome browser
+  (http://github.com/danmaclean/gee_fu)."
 email: ilpuccio.febo@gmail.com
 executables: []
-
-extensions: 
+extensions:
 - ext/mkrf_conf.rb
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
-files: 
+files:
 - .document
 - Gemfile
 - Gemfile.lock
@@ -161,36 +156,32 @@ files:
 - 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: 
+licenses:
 - MIT
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 4574073522320784931
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: -1844225119409437910
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.5.0
+rubygems_version: 1.8.6
 signing_key: 
 specification_version: 3
 summary: Binder of samtools for ruby, on the top of FFI.
 test_files: []
-