Class: CagnutSamtools::MergeBam

Inherits:
Object
  • Object
show all
Extended by:
Forwardable
Defined in:
lib/cagnut_samtools/functions/merge_bam.rb

Instance Method Summary collapse

Constructor Details

#initialize(opts = {}) ⇒ MergeBam

Returns a new instance of MergeBam.



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# File 'lib/cagnut_samtools/functions/merge_bam.rb', line 9

def initialize opts = {}
  @order = sprintf '%02i', opts[:order]
  @sam_dir = opts[:dirs][:input]
  @bam_dir = opts[:dirs][:output]
  @job_name = "#{prefix_name}_mgBam_#{sample_name}"
  @input = opts[:input].nil? ? "#{@bam_dir}/*.bam" : opts[:input]
  @output = "#{@bam_dir}/#{sample_name}_merged.bam"
  @output_bai = "#{@bam_dir}/#{sample_name}_merged.bai"
end

Instance Method Details

#generate_script ⇒ Object 



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# File 'lib/cagnut_samtools/functions/merge_bam.rb', line 34

def generate_script
  script_name = "#{@order}_samtools_merge_bam"
  file = File.join jobs_dir, "#{script_name}.sh"
  path = File.expand_path '../templates/merge_bam.sh', __FILE__
  template = Tilt.new path
  File.open(file, 'w') do |f|
    f.puts template.render Object.new, job_params(script_name)
  end
  File.chmod(0700, file)
  script_name
end

#job_params(script_name) ⇒ Object 



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# File 'lib/cagnut_samtools/functions/merge_bam.rb', line 46

def job_params script_name
  {
    bam_dir: @bam_dir,
    samtools_path: samtools_path,
    magic28: magic28,
    jobs_dir: jobs_dir,
    input: @input,
    output: @output,
    output_bai: @output_bai,
    sam_dir: @sam_dir,
    script_name: script_name,
    run_local: ::Cagnut::JobManage.run_local
  }
end

#queuing_options(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_samtools/functions/merge_bam.rb', line 26

def queuing_options previous_job_id = nil
  {
    previous_job_id: previous_job_id,
    adjust_memory: ['h_vmem=1G'],
    tools: ['samtools', 'merge_bam']
  }
end

#run(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_samtools/functions/merge_bam.rb', line 19

def run previous_job_id = nil
  puts "Submitting samtoolsMergeBam #{sample_name}"
  script_name = generate_script
  ::Cagnut::JobManage.submit  script_name, @job_name, queuing_options(previous_job_id)
  [@job_name, @output]
end