parse_fasta 1.1.2 → 1.2.0
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- checksums.yaml +5 -13
- data/README.md +13 -0
- data/lib/parse_fasta/fastq_file.rb +1 -1
- data/lib/parse_fasta/quality.rb +11 -1
- data/lib/parse_fasta/version.rb +1 -1
- data/spec/lib/quality_spec.rb +8 -0
- metadata +16 -16
checksums.yaml
CHANGED
@@ -1,15 +1,7 @@
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---
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metadata.gz:
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data.tar.gz: !binary |-
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MWFlZTE2NmJkNTRjMDMyMjI4NDhmYzliY2JlZTY5NjY2ZjliZjIyOQ==
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SHA1:
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metadata.gz: b140f0d7d54cdb4f0938bbcd5aa2484f069fcb50
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data.tar.gz: 9ff3a6ace4f834da41b298075aa470cb730bd4f6
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SHA512:
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metadata.gz:
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ODgyMGI5YjQxNjBiYWUyMDZkMjgyNDNlMGFmMmM0YjRjM2JkMDM=
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data.tar.gz: !binary |-
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ZmQ1ODM2ZmIwMjgwMmE5NzRjYjhlMjAyZDhkNjJiNTc3ZDkxNzE1OTEyMzU4
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MmE2Y2VkYTI4NGNlMWI1MDAxYTU3NTVlYzFjOTI2Zjg2MGQwNjhmZDUzZDhh
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YTg2YzQ0Yjg4N2YxYjRiODNhZTlmYzk3OWJkNzYzYWUyMTE0Njk=
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metadata.gz: f9b9dd477b595a28970f2f299503f360c7fb353a62013b2e848f353a296ddebf1def65f5f6a5f02ea046d20041f28cfe0c32581cdc10793cd6ac75daec0576ec
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data.tar.gz: aa1e8e8aff902c6a16315fa6513f755f92887ae79c0c4cc8f42d7ae7c530e8885250885c7397cf1861d47136ceb6012deed7fab9be3d98da0d3d4c4d11720f60
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data/README.md
CHANGED
@@ -32,6 +32,8 @@ to see the full documentation.
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## Usage ##
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Some examples...
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A little script to print header and length of each record.
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require 'parse_fasta'
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@@ -54,6 +56,17 @@ Now we can parse fastq files as well!
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## Versions ##
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### 1.2.0 ###
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Added `mean_qual` method to the `Quality` class.
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### 1.1.2 ###
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Dropped Ruby requirement to 1.9.3
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(Note, if you want to build the docs with yard and you're using
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Ruby 1.9.3, you may have to install the redcarpet gem.)
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+
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### 1.1.0 ###
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Added: Fastq and Quality classes
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@@ -35,7 +35,7 @@ class FastqFile < File
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# @yieldparam sequence [Sequence] The sequence of the fastq record
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# @yieldparam description [String] The description line of the fastq
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# record without the leading '+'
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-
# @yieldparam
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# @yieldparam quality_string [Quality] The quality string of the
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# fastq record
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def each_record
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count = 0
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data/lib/parse_fasta/quality.rb
CHANGED
@@ -19,9 +19,19 @@
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# Provide some methods for dealing with common tasks regarding
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# quality strings.
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class Quality < String
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# Returns the mean quality for the record. This will be a good deal
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# faster than getting the average with `qual_scores` and reduce.
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#
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# @example Get mean quality score for a record
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# Quality.new("!+5?I").mean_qual #=> 20.0
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#
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# @return [Float] Mean quality score for record
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def mean_qual
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(self.sum - (self.length * 33)) / self.length.to_f
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end
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# Returns an array of illumina style quality scores. The quality
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# scores generated will be Phred+33.
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# scores generated will be Phred+33 (i.e., new Illumina).
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#
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# @example Get quality score array of a Quality
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# Quality.new("!+5?I").qual_scores #=> [0, 10, 20, 30, 40]
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data/lib/parse_fasta/version.rb
CHANGED
data/spec/lib/quality_spec.rb
CHANGED
@@ -32,4 +32,12 @@ describe Quality do
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end
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end
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end
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describe "#mean_qual" do
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it "returns the mean quality for the quality string" do
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len = qual_string.length.to_f
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mean_quality = qual_string.qual_scores.reduce(:+) / len
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expect(qual_string.mean_qual).to eq mean_quality
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end
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end
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end
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metadata
CHANGED
@@ -1,83 +1,83 @@
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1
1
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--- !ruby/object:Gem::Specification
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name: parse_fasta
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version: !ruby/object:Gem::Version
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version: 1.
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version: 1.2.0
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platform: ruby
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authors:
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- Ryan Moore
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2014-07-
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date: 2014-07-03 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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requirement: !ruby/object:Gem::Requirement
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requirements:
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-
- - ~>
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- - "~>"
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- !ruby/object:Gem::Version
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version: '1.6'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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-
- - ~>
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- - "~>"
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- !ruby/object:Gem::Version
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version: '1.6'
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- !ruby/object:Gem::Dependency
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name: rake
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requirement: !ruby/object:Gem::Requirement
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requirements:
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-
- - ~>
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- - "~>"
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- !ruby/object:Gem::Version
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version: '10.3'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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-
- - ~>
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- - "~>"
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- !ruby/object:Gem::Version
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version: '10.3'
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- !ruby/object:Gem::Dependency
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name: rspec
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requirement: !ruby/object:Gem::Requirement
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requirements:
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-
- - ~>
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- - "~>"
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- !ruby/object:Gem::Version
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version: '2.14'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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-
- - ~>
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+
- - "~>"
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- !ruby/object:Gem::Version
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version: '2.14'
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- !ruby/object:Gem::Dependency
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name: bio
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requirement: !ruby/object:Gem::Requirement
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requirements:
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-
- - ~>
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- - "~>"
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- !ruby/object:Gem::Version
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version: '1.4'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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-
- - ~>
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- - "~>"
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- !ruby/object:Gem::Version
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version: '1.4'
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- !ruby/object:Gem::Dependency
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name: yard
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - ~>
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- - "~>"
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- !ruby/object:Gem::Version
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version: '0.8'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ~>
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- - "~>"
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- !ruby/object:Gem::Version
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version: '0.8'
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description: So you want to parse a fasta file...
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@@ -87,7 +87,7 @@ executables: []
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extensions: []
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extra_rdoc_files: []
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files:
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-
- .gitignore
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- ".gitignore"
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- COPYING
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- Gemfile
|
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- README.md
|
@@ -109,7 +109,7 @@ files:
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- test_files/test.fq
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homepage: https://github.com/mooreryan/parse_fasta
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licenses:
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-
-
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- 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
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metadata: {}
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post_install_message:
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rdoc_options: []
|
@@ -117,12 +117,12 @@ require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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requirements:
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-
- -
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+
- - ">="
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- !ruby/object:Gem::Version
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version: 1.9.3
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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-
- -
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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