class CagnutGatk::Configuration

Attributes

analyze_covariates_params[RW]
base_recalibrator_params[RW]
count_reads_params[RW]
depth_of_coverage_params[RW]
haplotype_caller_params[RW]
indel_realigner_params[RW]
print_reads_params[RW]
realigner_target_creator_params[RW]
unified_genotyper_params[RW]
variant_eval_params[RW]
variant_filtration_params[RW]

Public Class Methods

load(config, params) click to toggle source
# File lib/cagnut_gatk/configuration.rb, line 15
def load config, params
  instance.load config, params
end

Public Instance Methods

add_java_params(method_params, verbose=false) click to toggle source
# File lib/cagnut_gatk/configuration.rb, line 44
def add_java_params method_params, verbose=false
  return if method_params.blank?
  array = method_params['java'].dup
  array << "-verbose:sizes" if verbose
  array << "-jar #{@config['tools']['gatk']}"
  {
    'java' => array,
    'params' => method_params['params']
  }
end
attributes() click to toggle source
# File lib/cagnut_gatk/configuration.rb, line 28
def attributes
  {
    analyze_covariates_params: add_java_params(@params['analyze_covariates']),
    base_recalibrator_params: add_java_params(@params['base_recalibrator']),
    count_reads_params: add_java_params(@params['count_reads']),
    depth_of_coverage_params: add_java_params(@params['depth_of_coverage'], true),
    haplotype_caller_params: add_java_params(@params['haplotype_caller']),
    indel_realigner_params: add_java_params(@params['indel_realigner']),
    print_reads_params: add_java_params(@params['print_reads']),
    realigner_target_creator_params: add_java_params(@params['realigner_target_creator']),
    unified_genotyper_params: add_java_params(@params['unified_genotyper']),
    variant_eval_params: add_java_params(@params['variant_eval']),
    variant_filtration_params: add_java_params(@params['variant_filtration'])
  }
end
load(config, params) click to toggle source
# File lib/cagnut_gatk/configuration.rb, line 20
def load config, params
  @config = config
  @params = params
  attributes.each do |name, value|
    send "#{name}=", value if respond_to? "#{name}="
  end
end