class CagnutBwa::Configuration
Attributes
aln_params[RW]
mem_params[RW]
rg_str[RW]
samp_params[RW]
Public Class Methods
load(config, params)
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# File lib/cagnut_bwa/configuration.rb, line 9 def load config, params instance.load config, params end
Public Instance Methods
add_bwa_path_in_params(method_params)
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# File lib/cagnut_bwa/configuration.rb, line 32 def add_bwa_path_in_params method_params return if method_params.blank? array = method_params['params'].dup array.unshift "#{@config['tools']['bwa']}" end
attributes()
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# File lib/cagnut_bwa/configuration.rb, line 23 def attributes { rg_str: @config['sample']['rg_str'], mem_params: add_bwa_path_in_params(@params['mem']), aln_params: add_bwa_path_in_params(@params['aln']), samp_params: add_bwa_path_in_params(@params['samp']) } end
generate_rg_str()
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# File lib/cagnut_bwa/configuration.rb, line 38 def generate_rg_str @config['samples'].each do |sample| arg = %W( @RG ID:#{sample['rgid']} SM:#{sample['name']} PL:#{@config['info']['pl']} PU:#{sample['pu']} LB:#{@config['info']['lb']} DS:#{@config['info']['ds']} CN:#{@config['info']['cn']} DT:#{@config['info']['dt']} ) rg_str = { 'rg_str' => arg.join('\t') } sample.merge! rg_str end end
load(config, params)
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# File lib/cagnut_bwa/configuration.rb, line 14 def load config, params @config = config @params = params generate_rg_str attributes.each do |name, value| send "#{name}=", value if respond_to? "#{name}=" end end