snp-search 2.2.0 → 2.3.0

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Files changed (21) hide show
  1. data/Gemfile +1 -2
  2. data/Gemfile.lock +2 -3
  3. data/README +0 -105
  4. data/README.rdoc +35 -29
  5. data/Rakefile +2 -2
  6. data/VERSION +1 -1
  7. data/bin/snp-search +174 -261
  8. data/lib/create_methods.rb +196 -0
  9. data/lib/filter_ignore_snps_methods.rb +130 -0
  10. data/lib/information_methods.rb +117 -0
  11. data/lib/output_information_methods.rb +131 -0
  12. data/lib/snp-search.rb +18 -280
  13. data/lib/snp_db_connection.rb +1 -2
  14. data/lib/snp_db_models.rb +3 -3
  15. data/lib/snp_db_schema.rb +119 -80
  16. data/pkg/snp-search-1.1.0.gem +0 -0
  17. data/pkg/snp-search-1.2.0.gem +0 -0
  18. data/pkg/snp-search-2.3.0.gem +0 -0
  19. data/snp-search.gemspec +15 -12
  20. metadata +73 -33
  21. data/.rspec +0 -1
data/pkg/snp-search-1.1.0.gem ADDED
Binary file
data/pkg/snp-search-1.2.0.gem ADDED
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data/pkg/snp-search-2.3.0.gem ADDED
Binary file
data/snp-search.gemspec CHANGED
@@ -5,13 +5,13 @@
5
5
 
6
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  Gem::Specification.new do |s|
7
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  s.name = "snp-search"
8
- s.version = "2.2.0"
8
+ s.version = "2.3.0"
9
9
 
10
10
  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
11
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  s.authors = ["Ali Al-Shahib", "Anthony Underwood"]
12
- s.date = "2012-08-02"
12
+ s.date = "2013-04-19"
13
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  s.description = "Use the snp-search tool to create, import, manipulate and query your SNP database"
14
- s.email = "ali.al-shahib@hpa.org.uk"
14
+ s.email = "ali.al-shahib@phe.gov.uk"
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  s.executables = ["snp-search"]
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  s.extra_rdoc_files = [
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  "LICENSE.txt",
@@ -19,7 +19,6 @@ Gem::Specification.new do |s|
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  "README.rdoc"
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  ]
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  s.files = [
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- ".rspec",
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  "Gemfile",
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  "Gemfile.lock",
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  "LICENSE.txt",
@@ -28,18 +27,25 @@ Gem::Specification.new do |s|
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  "Rakefile",
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  "VERSION",
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  "bin/snp-search",
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+ "lib/create_methods.rb",
31
+ "lib/filter_ignore_snps_methods.rb",
32
+ "lib/information_methods.rb",
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+ "lib/output_information_methods.rb",
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  "lib/snp-search.rb",
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  "lib/snp_db_connection.rb",
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  "lib/snp_db_models.rb",
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  "lib/snp_db_schema.rb",
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+ "pkg/snp-search-1.1.0.gem",
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+ "pkg/snp-search-1.2.0.gem",
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+ "pkg/snp-search-2.3.0.gem",
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  "snp-search.gemspec",
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  "spec/snp-search_spec.rb",
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  "spec/spec_helper.rb"
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  ]
39
- s.homepage = "http://github.com/hpa-bioinformatics/snp-search"
45
+ s.homepage = "http://github.com/phe-bioinformatics/snp-search"
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  s.licenses = ["MIT"]
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  s.require_paths = ["lib"]
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- s.rubygems_version = "1.8.10"
48
+ s.rubygems_version = "1.8.24"
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  s.summary = "Tool for generating SNP database"
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50
 
45
51
  if s.respond_to? :specification_version then
@@ -48,10 +54,9 @@ Gem::Specification.new do |s|
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  if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
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  s.add_runtime_dependency(%q<activerecord>, ["~> 3.1.3"])
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  s.add_runtime_dependency(%q<bio>, ["~> 1.4.2"])
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- s.add_runtime_dependency(%q<slop>, ["~> 3.3.1"])
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+ s.add_runtime_dependency(%q<slop>, ["~> 2.4.0"])
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  s.add_runtime_dependency(%q<sqlite3>, ["~> 1.3.4"])
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  s.add_runtime_dependency(%q<activerecord-import>, ["~> 0.2.8"])
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- s.add_runtime_dependency(%q<diff-lcs>, ["~> 1.1.3"])
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  s.add_development_dependency(%q<rspec>, ["~> 2.3.0"])
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  s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
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  s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
@@ -59,10 +64,9 @@ Gem::Specification.new do |s|
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  else
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  s.add_dependency(%q<activerecord>, ["~> 3.1.3"])
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  s.add_dependency(%q<bio>, ["~> 1.4.2"])
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- s.add_dependency(%q<slop>, ["~> 3.3.1"])
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+ s.add_dependency(%q<slop>, ["~> 2.4.0"])
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  s.add_dependency(%q<sqlite3>, ["~> 1.3.4"])
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  s.add_dependency(%q<activerecord-import>, ["~> 0.2.8"])
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- s.add_dependency(%q<diff-lcs>, ["~> 1.1.3"])
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  s.add_dependency(%q<rspec>, ["~> 2.3.0"])
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  s.add_dependency(%q<bundler>, ["~> 1.0.0"])
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  s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
@@ -71,10 +75,9 @@ Gem::Specification.new do |s|
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  else
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  s.add_dependency(%q<activerecord>, ["~> 3.1.3"])
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  s.add_dependency(%q<bio>, ["~> 1.4.2"])
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- s.add_dependency(%q<slop>, ["~> 3.3.1"])
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+ s.add_dependency(%q<slop>, ["~> 2.4.0"])
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  s.add_dependency(%q<sqlite3>, ["~> 1.3.4"])
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  s.add_dependency(%q<activerecord-import>, ["~> 0.2.8"])
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- s.add_dependency(%q<diff-lcs>, ["~> 1.1.3"])
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  s.add_dependency(%q<rspec>, ["~> 2.3.0"])
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  s.add_dependency(%q<bundler>, ["~> 1.0.0"])
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  s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
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  name: snp-search
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  version: !ruby/object:Gem::Version
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- version: 2.2.0
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+ version: 2.3.0
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  prerelease:
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  platform: ruby
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  authors:
@@ -10,11 +10,11 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-08-02 00:00:00.000000000Z
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+ date: 2013-04-19 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: activerecord
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- requirement: &2160033340 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -22,10 +22,15 @@ dependencies:
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  version: 3.1.3
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  type: :runtime
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  prerelease: false
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- version_requirements: *2160033340
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: 3.1.3
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  - !ruby/object:Gem::Dependency
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  name: bio
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- requirement: &2160032640 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -33,21 +38,31 @@ dependencies:
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  version: 1.4.2
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  type: :runtime
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  prerelease: false
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- version_requirements: *2160032640
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: 1.4.2
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  - !ruby/object:Gem::Dependency
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  name: slop
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- requirement: &2160031800 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: 3.3.1
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+ version: 2.4.0
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  type: :runtime
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  prerelease: false
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- version_requirements: *2160031800
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: 2.4.0
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  - !ruby/object:Gem::Dependency
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  name: sqlite3
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- requirement: &2160021660 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -55,10 +70,15 @@ dependencies:
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  version: 1.3.4
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  type: :runtime
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  prerelease: false
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- version_requirements: *2160021660
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: 1.3.4
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  - !ruby/object:Gem::Dependency
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  name: activerecord-import
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- requirement: &2160021080 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -66,21 +86,15 @@ dependencies:
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  version: 0.2.8
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  type: :runtime
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  prerelease: false
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- version_requirements: *2160021080
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- - !ruby/object:Gem::Dependency
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- name: diff-lcs
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- requirement: &2160020440 !ruby/object:Gem::Requirement
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+ version_requirements: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: 1.1.3
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- type: :runtime
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- prerelease: false
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- version_requirements: *2160020440
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+ version: 0.2.8
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  - !ruby/object:Gem::Dependency
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  name: rspec
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- requirement: &2160019880 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -88,10 +102,15 @@ dependencies:
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  version: 2.3.0
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  type: :development
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  prerelease: false
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- version_requirements: *2160019880
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
110
+ version: 2.3.0
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  - !ruby/object:Gem::Dependency
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  name: bundler
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- requirement: &2160019340 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -99,10 +118,15 @@ dependencies:
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  version: 1.0.0
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  type: :development
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  prerelease: false
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- version_requirements: *2160019340
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: 1.0.0
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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- requirement: &2160018780 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -110,10 +134,15 @@ dependencies:
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  version: 1.6.4
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  type: :development
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  prerelease: false
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- version_requirements: *2160018780
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
140
+ - - ~>
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+ - !ruby/object:Gem::Version
142
+ version: 1.6.4
114
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  - !ruby/object:Gem::Dependency
115
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  name: rcov
116
- requirement: &2160018240 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -121,10 +150,15 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
124
- version_requirements: *2160018240
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+ version_requirements: !ruby/object:Gem::Requirement
154
+ none: false
155
+ requirements:
156
+ - - ! '>='
157
+ - !ruby/object:Gem::Version
158
+ version: '0'
125
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  description: Use the snp-search tool to create, import, manipulate and query your
126
160
  SNP database
127
- email: ali.al-shahib@hpa.org.uk
161
+ email: ali.al-shahib@phe.gov.uk
128
162
  executables:
129
163
  - snp-search
130
164
  extensions: []
@@ -133,7 +167,6 @@ extra_rdoc_files:
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  - README
134
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  - README.rdoc
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  files:
136
- - .rspec
137
170
  - Gemfile
138
171
  - Gemfile.lock
139
172
  - LICENSE.txt
@@ -142,14 +175,21 @@ files:
142
175
  - Rakefile
143
176
  - VERSION
144
177
  - bin/snp-search
178
+ - lib/create_methods.rb
179
+ - lib/filter_ignore_snps_methods.rb
180
+ - lib/information_methods.rb
181
+ - lib/output_information_methods.rb
145
182
  - lib/snp-search.rb
146
183
  - lib/snp_db_connection.rb
147
184
  - lib/snp_db_models.rb
148
185
  - lib/snp_db_schema.rb
186
+ - pkg/snp-search-1.1.0.gem
187
+ - pkg/snp-search-1.2.0.gem
188
+ - pkg/snp-search-2.3.0.gem
149
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  - snp-search.gemspec
150
190
  - spec/snp-search_spec.rb
151
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  - spec/spec_helper.rb
152
- homepage: http://github.com/hpa-bioinformatics/snp-search
192
+ homepage: http://github.com/phe-bioinformatics/snp-search
153
193
  licenses:
154
194
  - MIT
155
195
  post_install_message:
@@ -164,7 +204,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  version: '0'
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  segments:
166
206
  - 0
167
- hash: -2122266153834504004
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+ hash: -4201119405686879786
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  required_rubygems_version: !ruby/object:Gem::Requirement
169
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  none: false
170
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  requirements:
@@ -173,7 +213,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  version: '0'
174
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  requirements: []
175
215
  rubyforge_project:
176
- rubygems_version: 1.8.10
216
+ rubygems_version: 1.8.24
177
217
  signing_key:
178
218
  specification_version: 3
179
219
  summary: Tool for generating SNP database
data/.rspec DELETED
@@ -1 +0,0 @@
1
- --color