class CagnutBwa::Configuration

Attributes

aln_params[RW]
mem_params[RW]
rg_str[RW]
samp_params[RW]

Public Class Methods

load(config, params) click to toggle source
# 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) click to toggle source
# 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() click to toggle source
# 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() click to toggle source
# 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) click to toggle source
# 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