Class: CagnutGatk::Util

Inherits:
Object
  • Object
show all
Defined in:
lib/cagnut_gatk/util.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(config) ⇒ Util

Returns a new instance of Util.



5
6
7
8
 
# File 'lib/cagnut_gatk/util.rb', line 5

def initialize config
  @config = config
  @gatk = CagnutGatk::Base.new
end

Instance Attribute Details

#config ⇒ Object

Returns the value of attribute config.



3
4
5
 
# File 'lib/cagnut_gatk/util.rb', line 3

def config
  @config
end

#gatk ⇒ Object

Returns the value of attribute gatk.



3
4
5
 
# File 'lib/cagnut_gatk/util.rb', line 3

def gatk
  @gatk
end

Instance Method Details

#analyze_covariates(dirs, order = 1, previous_job_id = nil, filename = nil) ⇒ Object 



50
51
52
53
 
# File 'lib/cagnut_gatk/util.rb', line 50

def analyze_covariates dirs, order=1, previous_job_id=nil, filename=nil
  job_name = @gatk.analyze_covariates dirs, order, previous_job_id, filename
  [job_name, order+1]
end

#base_recalibrator(dirs, order = 1, previous_job_id = nil, filename = nil) ⇒ Object 



43
44
45
46
47
48
 
# File 'lib/cagnut_gatk/util.rb', line 43

def base_recalibrator dirs, order=1, previous_job_id=nil, filename=nil
  before_and_after_generated_bqsr_file.each do |option|
    previous_job_id = @gatk.base_recalibrator dirs, order, previous_job_id, filename, option
  end
  [previous_job_id, order+1]
end

#count_read(dirs, order = 1, previous_job_id = nil, filename = nil) ⇒ Object 



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

def count_read dirs, order=1, previous_job_id=nil, filename=nil
  count_read_params(filename).each do |option|
    gatk.count_read dirs, order, previous_job_id, option
  end
  order+1
end

#depth_of_coverage(dirs, order = 1, previous_job_id = nil, filename = nil) ⇒ Object 



60
61
62
63
64
65
 
# File 'lib/cagnut_gatk/util.rb', line 60

def depth_of_coverage dirs, order=1, previous_job_id=nil, filename=nil
  depth_of_coverage_params.each do |option|
    @gatk.depth_of_coverage dirs, order, previous_job_id, filename, option
  end
  order+1
end

#haplotype_caller(dirs, order = 1, previous_job_id = nil, file_name = nil) ⇒ Object 



67
68
69
70
 
# File 'lib/cagnut_gatk/util.rb', line 67

def haplotype_caller dirs, order=1, previous_job_id=nil, file_name=nil
  job_name, filename = @gatk.haplotype_caller dirs, order, previous_job_id, file_name
  [job_name, filename, order+1]
end

#indel_realigner(dirs, order = 1, previous_job_id = nil, filename = nil, interval_list = nil) ⇒ Object 



38
39
40
41
 
# File 'lib/cagnut_gatk/util.rb', line 38

def indel_realigner dirs, order=1, previous_job_id=nil, filename=nil, interval_list=nil
  job_name, filename = @gatk.indel_realigner dirs, order, previous_job_id, filename, interval_list
  [job_name, filename, order+1]
end

#print_reads(dirs, order = 1, previous_job_id = nil, file_name = nil) ⇒ Object 



55
56
57
58
 
# File 'lib/cagnut_gatk/util.rb', line 55

def print_reads dirs, order=1, previous_job_id=nil, file_name=nil
  job_name, filename = @gatk.print_reads dirs, order, previous_job_id, file_name
  [job_name, filename, order+1]
end

#realigner_target_creator(dirs, order = 1, previous_job_id = nil, filename = nil) ⇒ Object 



33
34
35
36
 
# File 'lib/cagnut_gatk/util.rb', line 33

def realigner_target_creator dirs, order=1, previous_job_id=nil, filename=nil
  job_name, interval_list = @gatk.realigner_target_creator dirs, order, previous_job_id, filename
  [job_name, interval_list, order+1]
end

#recal(dirs, order = 1, previous_job_id = nil, filename = nil) ⇒ Object 



17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
 
# File 'lib/cagnut_gatk/util.rb', line 17

def recal dirs, order=1, previous_job_id=nil, filename = nil
  # if (@config['cagnut']['ref_fasta'].scan 'hg').empty?
  #   # filename = "s_#{@config['line']}_merged_markdup.bam"
  #   filename = "#{line}_realn.bam"
  # else
  #   previous_job_id, target_interval = realigner_target_creator previous_job_id, filename
  #   previous_job_id, filename = indel_realigner previous_job_id, filename, target_interval
  # end

  previous_job_id, interval_list, order = realigner_target_creator dirs, order, previous_job_id, filename
  previous_job_id, filename, order = indel_realigner dirs, order, previous_job_id, filename, interval_list
  previous_job_id, order = base_recalibrator dirs, order, previous_job_id, filename
  previous_job_id, filename = print_reads dirs, order, previous_job_id, filename
  [previous_job_id, filename, order+1]
end

#snpcal(dirs, order = 1, previous_job_id = nil, filename = nil) ⇒ Object 



77
78
79
80
 
# File 'lib/cagnut_gatk/util.rb', line 77

def snpcal dirs, order=1, previous_job_id=nil, filename = nil
  previous_job_id, filename, order = variant_filtration dirs, order, previous_job_id, filename
  variant_eval dirs, order, previous_job_id, filename
end

#unified_genotyper(dirs, order = 1, previous_job_id = nil, file_name = nil) ⇒ Object 



72
73
74
75
 
# File 'lib/cagnut_gatk/util.rb', line 72

def unified_genotyper dirs, order=1, previous_job_id=nil, file_name=nil
  job_name, filename = @gatk.unified_genotyper dirs, order, previous_job_id, file_name
  [job_name, filename, order+1]
end

#variant_eval(dirs, order = 1, previous_job_id = nil, filename = nil) ⇒ Object 



87
88
89
90
 
# File 'lib/cagnut_gatk/util.rb', line 87

def variant_eval dirs, order=1, previous_job_id=nil, filename=nil
  job_name, filename = gatk.variant_eval dirs, order, previous_job_id, filename
  [job_name, filename, order+1]
end

#variant_filtration(dirs, order = 1, previous_job_id = nil, filename = nil) ⇒ Object 



82
83
84
85
 
# File 'lib/cagnut_gatk/util.rb', line 82

def variant_filtration dirs, order=1, previous_job_id=nil, filename=nil
  job_name, filename = gatk.variant_filtration dirs, order, previous_job_id, filename
  [job_name, filename, order+1]
end