class CagnutPicard::AddOrReplaceReadGroups

Public Class Methods

new(opts = {}) click to toggle source
# File lib/cagnut_picard/functions/add_or_replace_readgroups.rb, line 9
def initialize opts = {}
  @order = sprintf '%02i', opts[:order]
  @tmp_dir = opts[:dirs][:tmp_dir]
  @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_aligned.sam.gz" : opts[:input]
  @output = "#{opts[:dirs][:output]}/#{sample_name}.bam"
  @job_name = "#{prefix_name}_addRG_#{sample_name}_addrg"
end

Public Instance Methods

add_read_group_options() click to toggle source
# File lib/cagnut_picard/functions/add_or_replace_readgroups.rb, line 32
def add_read_group_options
  array = add_or_replace_readgroups_params['params'].dup
  array << "INPUT=#{@input}"
  array << "OUTPUT=#{@output}"
  array << "TMP_DIR=#{@tmp_dir} "
  array << "#{rg_str_picard}"
  array.uniq
end
generate_script() click to toggle source
# File lib/cagnut_picard/functions/add_or_replace_readgroups.rb, line 54
    def generate_script
      script_name = "#{@order}_picard_add_or_replace_readgroups"
      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"
          #{params_combination_hash['java'].join("\s")} \\
            #{params_combination_hash['params'].join(" \\\n            ")} \\
            #{::Cagnut::JobManage.run_local}

          EXITSTATUS=$?

          if [ ! -e "#{@output}" ]
          then
            echo "Missing output: #{@output}"
            exit 100
          fi

          # 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

          if [ $EXITSTATUS -ne 0 ];then exit $EXITSTATUS;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
modified_java_array() click to toggle source
# File lib/cagnut_picard/functions/add_or_replace_readgroups.rb, line 41
def modified_java_array
  array = add_or_replace_readgroups_params['java'].dup
  array << 'AddOrReplaceReadGroups'
  array.unshift(java_path).uniq
end
params_combination_hash() click to toggle source
# File lib/cagnut_picard/functions/add_or_replace_readgroups.rb, line 47
def params_combination_hash
  @params_combination_hash ||= {
    'java' => modified_java_array,
    'params' => add_read_group_options
  }
end
queuing_options(previous_job_id = nil) click to toggle source
# File lib/cagnut_picard/functions/add_or_replace_readgroups.rb, line 24
def queuing_options previous_job_id = nil
  {
    previous_job_id: previous_job_id,
    adjust_memory: ['h_vmem=10G'],
    tools: ['picard', 'add_or_replace_readgroups']
  }
end
run(previous_job_id = nil) click to toggle source
# File lib/cagnut_picard/functions/add_or_replace_readgroups.rb, line 17
def run previous_job_id = nil
  puts "Submitting addReadGroup #{sample_name}"
  script_name = generate_script
  ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
  [@job_name, @output]
end