Class: CagnutBwa::Util

Inherits:
Object
  • Object
show all
Defined in:
lib/cagnut_bwa/util.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(config) ⇒ Util

Returns a new instance of Util.



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# File 'lib/cagnut_bwa/util.rb', line 5

def initialize config
  @config = config
  @bwa = CagnutBwa::Base.new
end

Instance Attribute Details

#bwa ⇒ Object

Returns the value of attribute bwa.



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# File 'lib/cagnut_bwa/util.rb', line 3

def bwa
  @bwa
end

#config ⇒ Object

Returns the value of attribute config.



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# File 'lib/cagnut_bwa/util.rb', line 3

def config
  @config
end

Instance Method Details

#aln(dirs, order = 1, previous_job_id = nil, filename = nil) ⇒ Object 



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# File 'lib/cagnut_bwa/util.rb', line 20

def aln dirs, order=1, previous_job_id = nil, filename=nil
  job_name = bwa.aln dirs, order, previous_job_id, filename
  [job_name, order+1]
end

#aln_one_fastq(dirs, order = 1, filename = nil) ⇒ Object 



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# File 'lib/cagnut_bwa/util.rb', line 10

def aln_one_fastq dirs, order=1, filename=nil
  job_name = bwa.aln_one_fastq dirs, order, filename
  [job_name, order+1]
end

#mem(dirs, order = 1, filename = nil) ⇒ Object 



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# File 'lib/cagnut_bwa/util.rb', line 30

def mem dirs, order=1, filename = nil
  job_name, filename = bwa.mem dirs, order, filename
  [job_name, filename, order+1]
end

#samp(dirs, order = 1, previous_job_id = nil, filename = nil) ⇒ Object 



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# File 'lib/cagnut_bwa/util.rb', line 25

def samp dirs, order=1, previous_job_id=nil, filename=nil
  job_name, filename = bwa.samp dirs, order, previous_job_id, filename
  [job_name, filename, order+1]
end

#samp_one_fastq(dirs, order = 1, previous_job_id = nil, filename = nil) ⇒ Object 



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# File 'lib/cagnut_bwa/util.rb', line 15

def samp_one_fastq dirs, order=1, previous_job_id=nil, filename=nil
  job_name, filename = bwa.samp_one_fastq dirs, order, previous_job_id, filename
  [job_name, filename, order+1]
end