fastq-factory 0.1.5 → 0.1.6
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- data/VERSION +1 -1
- data/bin/fastq-factory +2 -2
- data/fastq-factory.gemspec +2 -2
- metadata +3 -3
data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.1.
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1
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+
0.1.6
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data/bin/fastq-factory
CHANGED
@@ -8,7 +8,7 @@ require 'trollop'
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8
8
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options = Trollop::options do
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9
9
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opt :trim, "Trim fastq files"
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10
10
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opt :metrics, "Produce quality metrics"
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11
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-
opt :directory, "The full path to
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11
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+
opt :directory, "The full path to the directory where the fastq and sample map files are stored", :type => :string, :required => true
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12
12
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opt :sample_map_file, "A file that where each line is tab-delimited filename_prefix and sample name e.g H113880160-S2-E1_S3_L001\\tH113880160", :type => :string, :required => true
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13
13
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opt :forward_reads_suffix, "The suffix for the forward read files such that the prefix listed in the sample map file and the suffic combined will make up the complete fastq filename", :type => :string, :required => true
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14
14
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opt :reverse_reads_suffix, "The suffix for the forward read files such that the prefix listed in the sample map file and the suffic combined will make up the complete fastq filename", :type => :string, :required => true
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@@ -17,7 +17,7 @@ options = Trollop::options do
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17
17
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opt :quake_dir, "The directory where the quake executable can be found", :short => "-Q", :type => :string
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18
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opt :trim_point_fraction, "The fraction of the read length below which a read will be discarded if it is shorter than teh value after trimming", :short => "-T", :type => :float, :default => 0.6
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19
19
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opt :trim_quality_cutoff, "The quality used as a cutoff with which to trim a read from the 3' end", :short => "-E", :type => :integer, :default => 20
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20
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-
opt :metrics_quality_cutoff, "The quality value which will be used to determine at which position the read falls below this
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20
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+
opt :metrics_quality_cutoff, "The quality value which will be used to determine at which position the read falls below this value in a 5 position window", :short => "-W", :type => :integer, :default => 30
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21
21
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end
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22
22
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23
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forward_reads_suffix, forward_reads_file_extension = options[:forward_reads_suffix].match(/(.+)\.(.+?)$/).captures
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data/fastq-factory.gemspec
CHANGED
@@ -5,11 +5,11 @@
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5
5
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6
6
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Gem::Specification.new do |s|
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7
7
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s.name = "fastq-factory"
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8
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-
s.version = "0.1.
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8
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+
s.version = "0.1.6"
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9
9
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10
10
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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11
11
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s.authors = ["Anthony Underwood"]
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12
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-
s.date = "2012-08-
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12
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+
s.date = "2012-08-31"
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13
13
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s.description = "This tool can process fastq files, using fastq_quality_trimmer and quake to correct fastq files and then provide a quality asssessment of the data"
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14
14
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s.email = "anthony.underwood@hpa.org.uk"
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15
15
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s.executables = ["fastq-factory"]
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: fastq-factory
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 0.1.
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4
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+
version: 0.1.6
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5
5
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prerelease:
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6
6
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platform: ruby
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7
7
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authors:
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@@ -9,7 +9,7 @@ authors:
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9
9
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autorequire:
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10
10
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bindir: bin
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11
11
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cert_chain: []
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12
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-
date: 2012-08-
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12
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+
date: 2012-08-31 00:00:00.000000000 Z
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13
13
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dependencies:
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14
14
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- !ruby/object:Gem::Dependency
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15
15
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name: trollop
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@@ -165,7 +165,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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165
165
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version: '0'
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166
166
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segments:
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167
167
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- 0
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168
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-
hash:
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168
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+
hash: -2993436781626522659
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169
169
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required_rubygems_version: !ruby/object:Gem::Requirement
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170
170
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none: false
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171
171
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requirements:
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