Class: CagnutSamtools::MgBamSoftLink

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

Instance Method Summary collapse

Constructor Details

#initialize(opts = {}) ⇒ MgBamSoftLink

Returns a new instance of MgBamSoftLink.



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

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

Instance Method Details

#generate_script ⇒ Object 



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# File 'lib/cagnut_samtools/functions/mg_bam_soft_link.rb', line 31

def generate_script
  script_name = "#{@order}_samtools_mg_bam_soft_link"
  file = File.join jobs_dir, "#{script_name}.sh"
  File.open(file, 'w') do |f|
    f.puts <<-BASH.strip_heredoc
      #!/bin/bash

      cd "#{jobs_dir}/../"
      echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
      rm -f #{@output} #{@output_bai}
      ln -s #{@input}  #{@output}

      # Check BAM EOF
      BAM_28=$(tail -c 28 #{@output}|xxd -p)
      if [ "#{magic28}" != "$BAM_28" ]
      then
        echo "Error with BAM EOF" 1>&2
        exit 100
      fi

      #{samtools_path} index #{@output} \\
        #{::Cagnut::JobManage.run_local}
      mv #{output}.bai #{@output_bai}

      if [ !  -s "#{@output_bai}" ]
      then
        echo "Incorrect Output!"
        exit 100
      fi
      echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"

      exit $EXITSTATUS
    BASH
  end
  File.chmod(0700, file)
  script_name
end

#queuing_options(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_samtools/functions/mg_bam_soft_link.rb', line 24

def queuing_options previous_job_id = nil
  {
    previous_job_id: previous_job_id,
    tools: ['samtools', 'mg_bam_soft_link']
  }
end

#run(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_samtools/functions/mg_bam_soft_link.rb', line 17

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