Class: CagnutGatk::HaplotypeCaller

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

Instance Method Summary collapse

Constructor Details

#initialize(opts = {}) ⇒ HaplotypeCaller

Returns a new instance of HaplotypeCaller.



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

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

Instance Method Details

#cluster_options(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_gatk/functions/haplotype_caller.rb', line 23

def cluster_options previous_job_id = nil
  core_num = 6
  job_mem1 = "adjustWorkingMem 256M #{core_num}"
  job_mem2 = "adjustWorkingMem 10G #{core_num}"
  {
    previous_job_id: previous_job_id,
    var_env: [core_num, target],
    adjust_memory: ["h_stack=#{job_mem1}", "h_vmem=#{job_mem2}"],
    parallel_env: [core_num],
    tools: ['gatk', 'haplotype_caller']
  }
end

#generate_script ⇒ Object 



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

def generate_script
  script_name = "#{@order}_gatk_haplotype_caller"
  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['java'].join("\s")} \\
        #{params_combination['params'].join(" \\\n            ")} \\
        #{::Cagnut::JobManage.run_local}

      EXITSTATUS=$?

      if [ ! -s "#{@output}" ]
      then
        echo "vcf incomplete!"
        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"

    BASH
  end
  File.chmod(0700, file)
  script_name
end

#haplotype_caller_options ⇒ Object 



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# File 'lib/cagnut_gatk/functions/haplotype_caller.rb', line 36

def haplotype_caller_options
  array = haplotype_caller_params['params'].dup
  array << "-T HaplotypeCaller"
  array << "-R #{ref_fasta}"
  array << "-I #{@input}"
  array << "-o #{@output}"
  array << "-L #{target_flanks_file}" if target_flanks_file
  array.uniq
end

#modified_java_array ⇒ Object 



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

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

#params_combination ⇒ Object 



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# File 'lib/cagnut_gatk/functions/haplotype_caller.rb', line 51

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

#run(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_gatk/functions/haplotype_caller.rb', line 16

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