Class: CagnutGatk::IndelRealigner

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

Instance Method Summary collapse

Constructor Details

#initialize(opts = {}) ⇒ IndelRealigner

Returns a new instance of IndelRealigner.



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# File 'lib/cagnut_gatk/functions/indel_realigner.rb', line 10

def initialize opts = {}
  @order = sprintf '%02i', opts[:order]
  @job_name = "#{prefix_name}_indelRealigner_#{sample_name}"
  @interval_list = opts[:interval_list]
  @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_markdup.bam" : opts[:input]
  @output = "#{opts[:dirs][:output]}/#{sample_name}_realn.bam"
end

Instance Method Details

#cluster_options(previous_job_id = nil) ⇒ Object 



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

def cluster_options previous_job_id = nil
  {
    previous_job_id: previous_job_id,
    adjust_memory: ['h_vmem=8G'],
    tools: ['gatk', 'indel_realigner']
  }
end

#generate_script ⇒ Object 



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# File 'lib/cagnut_gatk/functions/indel_realigner.rb', line 57

def generate_script
  script_name = "#{@order}_gatk_indel_realigner"
  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"
      # Check for intervals file
      if [ ! -s "#{@interval_list}" ];then
        echo "Error: Missing interval file: "#{@interval_list}" from realignTargetCreator_#{sample_name}"
        exit 100
      fi

      #{params_combination['java'].join("\s")} \\
        #{params_combination['params'].join(" \\\n            ")} \\
        #{::Cagnut::JobManage.run_local}

      EXITSTATUS=$?

      #force error when missing @output
      if [ ! -s "#{@output}" ]
      then
        echo "Missing @output BAM #{@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
      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

#indel_realigner_options ⇒ Object 



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# File 'lib/cagnut_gatk/functions/indel_realigner.rb', line 33

def indel_realigner_options
  array = indel_realigner_params['params'].dup
  array << "-T IndelRealigner"
  array << "-R #{ref_fasta}"
  array << "-targetIntervals #{@interval_list}"
  array << "-I #{@input}"
  array << "-o #{@output}"
  array << "-known #{dbsnp_ref_indels}" if dbsnp_ref_indels
  array.uniq!
  array.uniq
end

#modified_java_array ⇒ Object 



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# File 'lib/cagnut_gatk/functions/indel_realigner.rb', line 45

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

#params_combination ⇒ Object 



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# File 'lib/cagnut_gatk/functions/indel_realigner.rb', line 50

def params_combination
  @params_combination_hash ||= {
    'java' => modified_java_array,
    'params' => indel_realigner_options
  }
end

#run(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_gatk/functions/indel_realigner.rb', line 18

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