Class: CagnutGatk::RealignerTargetCreator

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

Instance Method Summary collapse

Constructor Details

#initialize(opts = {}) ⇒ RealignerTargetCreator

Returns a new instance of RealignerTargetCreator.



10
11
12
13
14
15
 
# File 'lib/cagnut_gatk/functions/realigner_target_creator.rb', line 10

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

Instance Method Details

#cluster_options(previous_job_id = nil) ⇒ Object 



24
25
26
27
28
29
30
31
32
33
34
35
 
# File 'lib/cagnut_gatk/functions/realigner_target_creator.rb', line 24

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],
    adjust_memory: ["h_stack=#{job_mem1}", "h_vmem=#{job_mem2}"],
    parallel_env: [core_num],
    tools: ['gatk', 'realigner_target_creator']
  }
end

#generate_script ⇒ Object 



61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
 
# File 'lib/cagnut_gatk/functions/realigner_target_creator.rb', line 61

def generate_script
  script_name = "#{@order}_gatk_realigner_target_creator"
  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=$?

      #force error when missing output
      if [ ! -s "#{@output}" ]
      then
        echo "Missing indel_calls #{@output}, can not continue"
        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

#modified_java_array ⇒ Object 



49
50
51
52
 
# File 'lib/cagnut_gatk/functions/realigner_target_creator.rb', line 49

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

#params_combination ⇒ Object 



54
55
56
57
58
59
 
# File 'lib/cagnut_gatk/functions/realigner_target_creator.rb', line 54

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

#realigner_target_creator_options ⇒ Object 



37
38
39
40
41
42
43
44
45
46
47
 
# File 'lib/cagnut_gatk/functions/realigner_target_creator.rb', line 37

def realigner_target_creator_options
  array = realigner_target_creator_params['params'].dup
  array << "-T RealignerTargetCreator"
  array << "-R #{ref_fasta}"
  array << "--known #{snpdb}"
  array << "-I #{@input}"
  array << "-o #{@output}"
  array << "-L #{target_flanks_file}" if target_flanks_file
  array.uniq!
  array.uniq
end

#run(previous_job_id = nil) ⇒ Object 



17
18
19
20
21
22
 
# File 'lib/cagnut_gatk/functions/realigner_target_creator.rb', line 17

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