class CagnutGatk::Util
Attributes
config[RW]
gatk[RW]
Public Class Methods
new(config)
click to toggle source
# File lib/cagnut_gatk/util.rb, line 5 def initialize config @config = config @gatk = CagnutGatk::Base.new end
Public Instance Methods
analyze_covariates(dirs, order=1, previous_job_id=nil, filename=nil)
click to toggle source
# 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)
click to toggle source
# 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)
click to toggle source
# 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)
click to toggle source
# 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)
click to toggle source
# 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)
click to toggle source
# 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)
click to toggle source
# 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)
click to toggle source
# 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)
click to toggle source
# 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)
click to toggle source
# 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)
click to toggle source
# 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)
click to toggle source
# 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)
click to toggle source
# 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
Private Instance Methods
before_and_after_generated_bqsr_file()
click to toggle source
# File lib/cagnut_gatk/util.rb, line 94 def before_and_after_generated_bqsr_file [{ has_bqsr_file: false }, { has_bqsr_file: true }] end
count_read_params(filename)
click to toggle source
# File lib/cagnut_gatk/util.rb, line 98 def count_read_params filename ary = [{ input: filename }] if @config['refs']['targets_file'] ary << { input: filename, target: @config['refs']['targets_file'] } end ary end
depth_of_coverage_params()
click to toggle source
# File lib/cagnut_gatk/util.rb, line 107 def depth_of_coverage_params ary = [{ suffix: 'genome' }] if @config['refs']['targets_file'] ary << { suffix: 'target', target: @config['refs']['targets_file'] } end if @config['refs']['target_flanks_file'] ary << { suffix: 'flank', target: @config['refs']['target_flanks_file'] } end ary end