snp-search 2.0.0 → 2.2.0

data/Gemfile

@@ -5,9 +5,10 @@ source "http://rubygems.org"
 
  gem "activerecord", "~> 3.1.3"
  gem "bio", "~> 1.4.2"
- gem "slop", "~> 2.4.0"
+ gem "slop", "~> 3.3.1"
  gem 'sqlite3', "~> 1.3.4"
  gem 'activerecord-import', "~> 0.2.8"
+ gem "diff-lcs", "~> 1.1.3"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.

data/Gemfile.lock

@@ -36,7 +36,7 @@ GEM
     rspec-expectations (2.3.0)
       diff-lcs (~> 1.1.2)
     rspec-mocks (2.3.0)
-    slop (2.4.0)
+    slop (3.3.1)
     sqlite3 (1.3.4)
     tzinfo (0.3.31)
 
@@ -48,8 +48,9 @@ DEPENDENCIES
   activerecord-import (~> 0.2.8)
   bio (~> 1.4.2)
   bundler (~> 1.0.0)
+  diff-lcs (~> 1.1.3)
   jeweler (~> 1.6.4)
   rcov
   rspec (~> 2.3.0)
-  slop (~> 2.4.0)
+  slop (~> 3.3.1)
   sqlite3 (~> 1.3.4)

data/VERSION

@@ -1 +1 @@
-2.0.0
+2.2.0

data/bin/snp-search

@@ -3,8 +3,6 @@ require 'snp_db_connection'
 require 'snp_db_models'
 require 'snp_db_schema'
 require 'activerecord-import'
-gem "slop", "~> 3.3.1"
-# gem "slop", "~> 2.4.0"
 require 'slop'
 
 opts = Slop.parse do
@@ -328,4 +326,4 @@ elsif opts[:output]
 
 else
   puts opts.help
-end
+end

data/snp-search.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "snp-search"
-  s.version = "2.0.0"
+  s.version = "2.2.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Ali Al-Shahib", "Anthony Underwood"]
@@ -48,9 +48,10 @@ Gem::Specification.new do |s|
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<activerecord>, ["~> 3.1.3"])
       s.add_runtime_dependency(%q<bio>, ["~> 1.4.2"])
-      s.add_runtime_dependency(%q<slop>, ["~> 2.4.0"])
+      s.add_runtime_dependency(%q<slop>, ["~> 3.3.1"])
       s.add_runtime_dependency(%q<sqlite3>, ["~> 1.3.4"])
       s.add_runtime_dependency(%q<activerecord-import>, ["~> 0.2.8"])
+      s.add_runtime_dependency(%q<diff-lcs>, ["~> 1.1.3"])
       s.add_development_dependency(%q<rspec>, ["~> 2.3.0"])
       s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
       s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
@@ -58,9 +59,10 @@ Gem::Specification.new do |s|
     else
       s.add_dependency(%q<activerecord>, ["~> 3.1.3"])
       s.add_dependency(%q<bio>, ["~> 1.4.2"])
-      s.add_dependency(%q<slop>, ["~> 2.4.0"])
+      s.add_dependency(%q<slop>, ["~> 3.3.1"])
       s.add_dependency(%q<sqlite3>, ["~> 1.3.4"])
       s.add_dependency(%q<activerecord-import>, ["~> 0.2.8"])
+      s.add_dependency(%q<diff-lcs>, ["~> 1.1.3"])
       s.add_dependency(%q<rspec>, ["~> 2.3.0"])
       s.add_dependency(%q<bundler>, ["~> 1.0.0"])
       s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
@@ -69,9 +71,10 @@ Gem::Specification.new do |s|
   else
     s.add_dependency(%q<activerecord>, ["~> 3.1.3"])
     s.add_dependency(%q<bio>, ["~> 1.4.2"])
-    s.add_dependency(%q<slop>, ["~> 2.4.0"])
+    s.add_dependency(%q<slop>, ["~> 3.3.1"])
     s.add_dependency(%q<sqlite3>, ["~> 1.3.4"])
     s.add_dependency(%q<activerecord-import>, ["~> 0.2.8"])
+    s.add_dependency(%q<diff-lcs>, ["~> 1.1.3"])
     s.add_dependency(%q<rspec>, ["~> 2.3.0"])
     s.add_dependency(%q<bundler>, ["~> 1.0.0"])
     s.add_dependency(%q<jeweler>, ["~> 1.6.4"])

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: snp-search
 version: !ruby/object:Gem::Version
-  version: 2.0.0
+  version: 2.2.0
   prerelease: 
 platform: ruby
 authors:
@@ -14,7 +14,7 @@ date: 2012-08-02 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2165264520 !ruby/object:Gem::Requirement
+  requirement: &2160033340 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,10 @@ dependencies:
         version: 3.1.3
   type: :runtime
   prerelease: false
-  version_requirements: *2165264520
+  version_requirements: *2160033340
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2165263760 !ruby/object:Gem::Requirement
+  requirement: &2160032640 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -33,21 +33,21 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2165263760
+  version_requirements: *2160032640
 - !ruby/object:Gem::Dependency
   name: slop
-  requirement: &2165262760 !ruby/object:Gem::Requirement
+  requirement: &2160031800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 2.4.0
+        version: 3.3.1
   type: :runtime
   prerelease: false
-  version_requirements: *2165262760
+  version_requirements: *2160031800
 - !ruby/object:Gem::Dependency
   name: sqlite3
-  requirement: &2165261900 !ruby/object:Gem::Requirement
+  requirement: &2160021660 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +55,10 @@ dependencies:
         version: 1.3.4
   type: :runtime
   prerelease: false
-  version_requirements: *2165261900
+  version_requirements: *2160021660
 - !ruby/object:Gem::Dependency
   name: activerecord-import
-  requirement: &2165260720 !ruby/object:Gem::Requirement
+  requirement: &2160021080 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,21 @@ dependencies:
         version: 0.2.8
   type: :runtime
   prerelease: false
-  version_requirements: *2165260720
+  version_requirements: *2160021080
+- !ruby/object:Gem::Dependency
+  name: diff-lcs
+  requirement: &2160020440 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.3
+  type: :runtime
+  prerelease: false
+  version_requirements: *2160020440
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2165259280 !ruby/object:Gem::Requirement
+  requirement: &2160019880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +88,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *2165259280
+  version_requirements: *2160019880
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2165258160 !ruby/object:Gem::Requirement
+  requirement: &2160019340 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -88,10 +99,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2165258160
+  version_requirements: *2160019340
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2165257000 !ruby/object:Gem::Requirement
+  requirement: &2160018780 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -99,10 +110,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2165257000
+  version_requirements: *2160018780
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2165255880 !ruby/object:Gem::Requirement
+  requirement: &2160018240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -110,7 +121,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2165255880
+  version_requirements: *2160018240
 description: Use the snp-search tool to create, import, manipulate and query your
   SNP database
 email: ali.al-shahib@hpa.org.uk
@@ -153,7 +164,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1607617824420065040
+      hash: -2122266153834504004
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: