Class: CagnutSamtools::Util

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(config = nil) ⇒ Util

Returns a new instance of Util.



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

def initialize config=nil
  @config = config
  @samtools = CagnutSamtools::Base.new
end

Instance Attribute Details

#config ⇒ Object

Returns the value of attribute config.



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

def config
  @config
end

#samtools ⇒ Object

Returns the value of attribute samtools.



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

def samtools
  @samtools
end

Instance Method Details

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



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

def do_flag_stat dirs, order=1, previous_job_id=nil, filename = nil
  samtools.do_flag_stat dirs, order, previous_job_id, filename
  order+1
end

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



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

def merge_bam dirs, order=1, previous_job_id=nil, filename = nil
  job_name, filename = samtools.merge_bam dirs, order, previous_job_id, filename
  [job_name, filename, order+1]
end

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



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

def mg_bam_soft_link dirs, order=1, previous_job_id=nil, filename = nil
  job_name, filename = samtools.mg_bam_soft_link dirs, order, previous_job_id, filename
  [job_name, filename, order+1]
end