Class: CagnutGatk::PrintReads

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

Instance Method Summary collapse

Constructor Details

#initialize(opts = {}) ⇒ PrintReads

Returns a new instance of PrintReads.



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# File 'lib/cagnut_gatk/functions/print_reads.rb', line 9

def initialize opts = {}
  @order = sprintf '%02i', opts[:order]
  @job_name = "#{prefix_name}_PrintReads_#{sample_name}"
  @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_realn.bam" : opts[:input]
  @output = "#{opts[:dirs][:output]}/#{output_file}"
  @bqsr_file = "#{opts[:dirs][:contrast]}/#{replace_filename('_recal.csv')}"
end

Instance Method Details

#cluster_options(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_gatk/functions/print_reads.rb', line 38

def cluster_options previous_job_id = nil
  {
    previous_job_id: previous_job_id,
    adjust_memory: ['h_vmem=6G'],
    tools: ['gatk', 'print_reads']
  }
end

#file_basename ⇒ Object 



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# File 'lib/cagnut_gatk/functions/print_reads.rb', line 17

def file_basename
  @basename ||= File.basename @input
end

#generate_script ⇒ Object 



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# File 'lib/cagnut_gatk/functions/print_reads.rb', line 46

def generate_script
  script_name = "#{@order}_gatk_print_reads"
  file = File.join jobs_dir, "#{script_name}.sh"
  path = File.expand_path '../templates/print_reads.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_gatk/functions/print_reads.rb', line 81

def job_params script_name
  {
    script_name: script_name,
    jobs_dir: jobs_dir,
    output: @output,
    bqsr_file: @bqsr_file,
    print_reads_params: params_combination,
    run_local: ::Cagnut::JobManage.run_local,
  }
end

#modified_java_array ⇒ Object 



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# File 'lib/cagnut_gatk/functions/print_reads.rb', line 69

def modified_java_array
  array = print_reads_params['java'].dup
  array.unshift(java_path).uniq
end

#output_file ⇒ Object 



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# File 'lib/cagnut_gatk/functions/print_reads.rb', line 25

def output_file
  output = replace_filename '_recal.bam'
  return output unless output == file_basename
  abort 'Input file is not correctly'
end

#params_combination ⇒ Object 



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# File 'lib/cagnut_gatk/functions/print_reads.rb', line 74

def params_combination
  {
    'java' => modified_java_array,
    'params' => print_reads_options
  }
end

#print_reads_options ⇒ Object 



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# File 'lib/cagnut_gatk/functions/print_reads.rb', line 58

def print_reads_options
  ary = print_reads_params['params'].dup
  ary << "-T PrintReads"
  ary << "-R #{ref_fasta}"
  ary << "-I #{@input}"
  ary << "-o #{@output}"
  ary << "-BQSR #{@bqsr_file}"
  ary << "-L #{target_flanks_file}" if target_flanks_file
  ary.uniq
end

#replace_filename(target) ⇒ Object 



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# File 'lib/cagnut_gatk/functions/print_reads.rb', line 21

def replace_filename target
  file_basename.gsub '_realn.bam', target
end

#run(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_gatk/functions/print_reads.rb', line 31

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