bio-ngs 0.4.4.alpha.01 → 0.4.5.alpha.01

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (3) hide show
  1. data/VERSION +1 -1
  2. data/bio-ngs.gemspec +4 -2
  3. metadata +66 -66
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.4.4.alpha.01
1
+ 0.4.5.alpha.01
data/bio-ngs.gemspec CHANGED
@@ -5,11 +5,11 @@
5
5
 
6
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  Gem::Specification.new do |s|
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  s.name = "bio-ngs"
8
- s.version = "0.4.2.alpha.01"
8
+ s.version = "0.4.4.alpha.01"
9
9
 
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  s.required_rubygems_version = Gem::Requirement.new("> 1.3.1") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Francesco Strozzi", "Raoul J.P. Bonnal"]
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- s.date = "2012-03-19"
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+ s.date = "2012-03-21"
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  s.description = "bio-ngs provides a framework for handling NGS data with BioRuby"
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  s.email = "francesco.strozzi@gmail.com"
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  s.executables = ["biongs"]
@@ -30,6 +30,7 @@ Gem::Specification.new do |s|
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  "bio-ngs.gemspec",
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  "ext/mkrf_conf.rb",
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  "lib/bio-ngs.rb",
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+ "lib/bio/appl/ngs/bcftools.rb",
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  "lib/bio/appl/ngs/bcl2qseq.rb",
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  "lib/bio/appl/ngs/blast.rb",
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  "lib/bio/appl/ngs/bowtie-inspect.rb",
@@ -67,6 +68,7 @@ Gem::Specification.new do |s|
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  "lib/enumerable.rb",
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  "lib/tasks/bwa.thor",
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  "lib/tasks/convert.thor",
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+ "lib/tasks/filter.thor",
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  "lib/tasks/history.thor",
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  "lib/tasks/homology.thor",
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  "lib/tasks/ontology.thor",
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
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  name: bio-ngs
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  version: !ruby/object:Gem::Version
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- version: 0.4.4.alpha.01
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+ version: 0.4.5.alpha.01
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  prerelease: 6
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  platform: ruby
7
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  authors:
@@ -14,7 +14,7 @@ date: 2012-03-21 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bio
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- requirement: &2154269220 !ruby/object:Gem::Requirement
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+ requirement: &2157544880 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -22,10 +22,10 @@ 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: *2154269220
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+ version_requirements: *2157544880
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  - !ruby/object:Gem::Dependency
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  name: bio-samtools
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- requirement: &2154267300 !ruby/object:Gem::Requirement
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+ requirement: &2157542920 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
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  version: 0.3.2
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  type: :runtime
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  prerelease: false
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- version_requirements: *2154267300
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+ version_requirements: *2157542920
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  - !ruby/object:Gem::Dependency
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  name: thor
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- requirement: &2154282240 !ruby/object:Gem::Requirement
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+ requirement: &2157557820 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
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  version: 0.14.6
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  type: :runtime
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  prerelease: false
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- version_requirements: *2154282240
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+ version_requirements: *2157557820
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  - !ruby/object:Gem::Dependency
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  name: rubyvis
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- requirement: &2154281240 !ruby/object:Gem::Requirement
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+ requirement: &2157556680 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
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  version: 0.5.0
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  type: :runtime
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  prerelease: false
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- version_requirements: *2154281240
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+ version_requirements: *2157556680
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  - !ruby/object:Gem::Dependency
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  name: daemons
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- requirement: &2154280320 !ruby/object:Gem::Requirement
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+ requirement: &2157555760 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -66,10 +66,10 @@ dependencies:
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  version: 1.1.0
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  type: :runtime
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  prerelease: false
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- version_requirements: *2154280320
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+ version_requirements: *2157555760
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  - !ruby/object:Gem::Dependency
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  name: ruby-ensembl-api
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- requirement: &2154278980 !ruby/object:Gem::Requirement
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+ requirement: &2157554600 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -77,10 +77,10 @@ dependencies:
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  version: 1.0.1
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  type: :runtime
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  prerelease: false
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- version_requirements: *2154278980
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+ version_requirements: *2157554600
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  - !ruby/object:Gem::Dependency
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  name: activerecord
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- requirement: &2154277960 !ruby/object:Gem::Requirement
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+ requirement: &2157553420 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -88,10 +88,10 @@ dependencies:
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  version: 3.0.5
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  type: :runtime
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  prerelease: false
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- version_requirements: *2154277960
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+ version_requirements: *2157553420
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  - !ruby/object:Gem::Dependency
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  name: sqlite3
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- requirement: &2154277080 !ruby/object:Gem::Requirement
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+ requirement: &2157552540 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -99,10 +99,10 @@ dependencies:
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  version: 1.3.3
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  type: :runtime
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  prerelease: false
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- version_requirements: *2154277080
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+ version_requirements: *2157552540
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  - !ruby/object:Gem::Dependency
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  name: bio-blastxmlparser
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- requirement: &2154276060 !ruby/object:Gem::Requirement
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+ requirement: &2157551480 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -110,10 +110,10 @@ dependencies:
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  version: '0'
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  type: :runtime
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  prerelease: false
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- version_requirements: *2154276060
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+ version_requirements: *2157551480
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  - !ruby/object:Gem::Dependency
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  name: progressbar
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- requirement: &2154275100 !ruby/object:Gem::Requirement
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+ requirement: &2157550620 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -121,10 +121,10 @@ dependencies:
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  version: 0.9.0
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  type: :runtime
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  prerelease: false
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- version_requirements: *2154275100
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+ version_requirements: *2157550620
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  - !ruby/object:Gem::Dependency
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  name: rake
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- requirement: &2154290640 !ruby/object:Gem::Requirement
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+ requirement: &2157566100 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - =
@@ -132,10 +132,10 @@ dependencies:
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  version: 0.9.2.2
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  type: :runtime
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  prerelease: false
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- version_requirements: *2154290640
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+ version_requirements: *2157566100
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  - !ruby/object:Gem::Dependency
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  name: json
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- requirement: &2154288840 !ruby/object:Gem::Requirement
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+ requirement: &2157564540 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -143,10 +143,10 @@ dependencies:
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  version: '0'
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  type: :runtime
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  prerelease: false
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- version_requirements: *2154288840
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+ version_requirements: *2157564540
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  - !ruby/object:Gem::Dependency
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  name: parallel
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- requirement: &2154285720 !ruby/object:Gem::Requirement
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+ requirement: &2157561780 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -154,10 +154,10 @@ dependencies:
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  version: '0'
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  type: :runtime
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  prerelease: false
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- version_requirements: *2154285720
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+ version_requirements: *2157561780
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  - !ruby/object:Gem::Dependency
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  name: shoulda
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- requirement: &2154299000 !ruby/object:Gem::Requirement
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+ requirement: &2157574380 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -165,10 +165,10 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *2154299000
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+ version_requirements: *2157574380
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  - !ruby/object:Gem::Dependency
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  name: bundler
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- requirement: &2154297180 !ruby/object:Gem::Requirement
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+ requirement: &2157572660 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -176,10 +176,10 @@ dependencies:
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  version: 1.1.0
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  type: :development
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  prerelease: false
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- version_requirements: *2154297180
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+ version_requirements: *2157572660
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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- requirement: &2154296480 !ruby/object:Gem::Requirement
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+ requirement: &2157571880 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -187,10 +187,10 @@ dependencies:
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  version: 1.8.3
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  type: :development
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  prerelease: false
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- version_requirements: *2154296480
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+ version_requirements: *2157571880
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  - !ruby/object:Gem::Dependency
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  name: rcov
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- requirement: &2154295940 !ruby/object:Gem::Requirement
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+ requirement: &2157571380 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -198,10 +198,10 @@ dependencies:
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  version: 0.9.11
199
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  type: :development
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  prerelease: false
201
- version_requirements: *2154295940
201
+ version_requirements: *2157571380
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  - !ruby/object:Gem::Dependency
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  name: bio
204
- requirement: &2154302280 !ruby/object:Gem::Requirement
204
+ requirement: &2157578140 !ruby/object:Gem::Requirement
205
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  none: false
206
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  requirements:
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  - - ! '>='
@@ -209,10 +209,10 @@ dependencies:
209
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  version: 1.4.2
210
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  type: :development
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  prerelease: false
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- version_requirements: *2154302280
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+ version_requirements: *2157578140
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  - !ruby/object:Gem::Dependency
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  name: thor
215
- requirement: &2154300720 !ruby/object:Gem::Requirement
215
+ requirement: &2157576920 !ruby/object:Gem::Requirement
216
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  none: false
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  requirements:
218
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  - - ! '>='
@@ -220,10 +220,10 @@ dependencies:
220
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  version: 0.14.6
221
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  type: :development
222
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  prerelease: false
223
- version_requirements: *2154300720
223
+ version_requirements: *2157576920
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  - !ruby/object:Gem::Dependency
225
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  name: ffi
226
- requirement: &2154314940 !ruby/object:Gem::Requirement
226
+ requirement: &2157590920 !ruby/object:Gem::Requirement
227
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  none: false
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  requirements:
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  - - ! '>='
@@ -231,10 +231,10 @@ dependencies:
231
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  version: 1.0.6
232
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  type: :development
233
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  prerelease: false
234
- version_requirements: *2154314940
234
+ version_requirements: *2157590920
235
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  - !ruby/object:Gem::Dependency
236
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  name: rubyvis
237
- requirement: &2154313100 !ruby/object:Gem::Requirement
237
+ requirement: &2157589180 !ruby/object:Gem::Requirement
238
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  none: false
239
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  requirements:
240
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  - - ! '>='
@@ -242,10 +242,10 @@ dependencies:
242
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  version: 0.5.0
243
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  type: :development
244
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  prerelease: false
245
- version_requirements: *2154313100
245
+ version_requirements: *2157589180
246
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  - !ruby/object:Gem::Dependency
247
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  name: rspec
248
- requirement: &2154311240 !ruby/object:Gem::Requirement
248
+ requirement: &2157587220 !ruby/object:Gem::Requirement
249
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  none: false
250
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  requirements:
251
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  - - ! '>='
@@ -253,10 +253,10 @@ dependencies:
253
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  version: 2.5.0
254
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  type: :development
255
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  prerelease: false
256
- version_requirements: *2154311240
256
+ version_requirements: *2157587220
257
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  - !ruby/object:Gem::Dependency
258
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  name: daemons
259
- requirement: &2154309900 !ruby/object:Gem::Requirement
259
+ requirement: &2157585680 !ruby/object:Gem::Requirement
260
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  none: false
261
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  requirements:
262
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  - - ! '>='
@@ -264,10 +264,10 @@ dependencies:
264
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  version: 1.1.0
265
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  type: :development
266
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  prerelease: false
267
- version_requirements: *2154309900
267
+ version_requirements: *2157585680
268
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  - !ruby/object:Gem::Dependency
269
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  name: bio-samtools
270
- requirement: &2154309200 !ruby/object:Gem::Requirement
270
+ requirement: &2157584920 !ruby/object:Gem::Requirement
271
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  none: false
272
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  requirements:
273
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  - - ! '>='
@@ -275,10 +275,10 @@ dependencies:
275
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  version: 0.3.2
276
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  type: :development
277
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  prerelease: false
278
- version_requirements: *2154309200
278
+ version_requirements: *2157584920
279
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  - !ruby/object:Gem::Dependency
280
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  name: ruby-ensembl-api
281
- requirement: &2154308560 !ruby/object:Gem::Requirement
281
+ requirement: &2157584240 !ruby/object:Gem::Requirement
282
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  none: false
283
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  requirements:
284
284
  - - ! '>='
@@ -286,10 +286,10 @@ dependencies:
286
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  version: 1.0.1
287
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  type: :development
288
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  prerelease: false
289
- version_requirements: *2154308560
289
+ version_requirements: *2157584240
290
290
  - !ruby/object:Gem::Dependency
291
291
  name: activerecord
292
- requirement: &2154323680 !ruby/object:Gem::Requirement
292
+ requirement: &2157583260 !ruby/object:Gem::Requirement
293
293
  none: false
294
294
  requirements:
295
295
  - - ! '>='
@@ -297,10 +297,10 @@ dependencies:
297
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  version: 3.0.5
298
298
  type: :development
299
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  prerelease: false
300
- version_requirements: *2154323680
300
+ version_requirements: *2157583260
301
301
  - !ruby/object:Gem::Dependency
302
302
  name: sqlite3
303
- requirement: &2154322400 !ruby/object:Gem::Requirement
303
+ requirement: &2157598260 !ruby/object:Gem::Requirement
304
304
  none: false
305
305
  requirements:
306
306
  - - ! '>='
@@ -308,10 +308,10 @@ dependencies:
308
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  version: 1.3.3
309
309
  type: :development
310
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  prerelease: false
311
- version_requirements: *2154322400
311
+ version_requirements: *2157598260
312
312
  - !ruby/object:Gem::Dependency
313
313
  name: bio-blastxmlparser
314
- requirement: &2154320940 !ruby/object:Gem::Requirement
314
+ requirement: &2157597220 !ruby/object:Gem::Requirement
315
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  none: false
316
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  requirements:
317
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  - - ! '>='
@@ -319,10 +319,10 @@ dependencies:
319
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  version: '0'
320
320
  type: :development
321
321
  prerelease: false
322
- version_requirements: *2154320940
322
+ version_requirements: *2157597220
323
323
  - !ruby/object:Gem::Dependency
324
324
  name: progressbar
325
- requirement: &2154320180 !ruby/object:Gem::Requirement
325
+ requirement: &2157595700 !ruby/object:Gem::Requirement
326
326
  none: false
327
327
  requirements:
328
328
  - - ! '>='
@@ -330,10 +330,10 @@ dependencies:
330
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  version: 0.9.0
331
331
  type: :development
332
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  prerelease: false
333
- version_requirements: *2154320180
333
+ version_requirements: *2157595700
334
334
  - !ruby/object:Gem::Dependency
335
335
  name: json
336
- requirement: &2154319540 !ruby/object:Gem::Requirement
336
+ requirement: &2157595000 !ruby/object:Gem::Requirement
337
337
  none: false
338
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  requirements:
339
339
  - - ! '>='
@@ -341,10 +341,10 @@ dependencies:
341
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  version: '0'
342
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  type: :development
343
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  prerelease: false
344
- version_requirements: *2154319540
344
+ version_requirements: *2157595000
345
345
  - !ruby/object:Gem::Dependency
346
346
  name: rake
347
- requirement: &2154318340 !ruby/object:Gem::Requirement
347
+ requirement: &2157593700 !ruby/object:Gem::Requirement
348
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  none: false
349
349
  requirements:
350
350
  - - =
@@ -352,10 +352,10 @@ dependencies:
352
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  version: 0.9.2.2
353
353
  type: :development
354
354
  prerelease: false
355
- version_requirements: *2154318340
355
+ version_requirements: *2157593700
356
356
  - !ruby/object:Gem::Dependency
357
357
  name: parallel
358
- requirement: &2154317580 !ruby/object:Gem::Requirement
358
+ requirement: &2157592960 !ruby/object:Gem::Requirement
359
359
  none: false
360
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  requirements:
361
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  - - ! '>='
@@ -363,7 +363,7 @@ dependencies:
363
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  version: '0'
364
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  type: :development
365
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  prerelease: false
366
- version_requirements: *2154317580
366
+ version_requirements: *2157592960
367
367
  description: bio-ngs provides a framework for handling NGS data with BioRuby
368
368
  email: francesco.strozzi@gmail.com
369
369
  executables:
@@ -469,7 +469,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
469
469
  version: '0'
470
470
  segments:
471
471
  - 0
472
- hash: 1080687296344900764
472
+ hash: 1893794030483247013
473
473
  required_rubygems_version: !ruby/object:Gem::Requirement
474
474
  none: false
475
475
  requirements: