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)
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# 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)
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# 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()
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# 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)
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# 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