class CagnutPicard::Configuration
Attributes
add_or_replace_readgroups_params[RW]
build_bam_index_params[RW]
collect_gc_bias_metrics_params[RW]
collect_insert_size_metrics_params[RW]
collect_multiple_metrics_params[RW]
markduplicate_params[RW]
mean_quality_by_cycle_params[RW]
quailty_score_distribution_params[RW]
rg_str_picard[RW]
sort_sam_params[RW]
Public Class Methods
load(config, params)
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# File lib/cagnut_picard/configuration.rb, line 13 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_picard/configuration.rb, line 42 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']['picard']}" { 'java' => array, 'params' => method_params['params'] } end
attributes()
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# File lib/cagnut_picard/configuration.rb, line 27 def attributes { rg_str_picard: @config['sample']['rg_str_picard'], add_or_replace_readgroups_params: add_java_params(@params['add_or_replace_readgroups'], true), build_bam_index_params: add_java_params(@params['build_bam_index']), collect_gc_bias_metrics_params: add_java_params(@params['collect_gc_bias_metrics']), collect_insert_size_metrics_params: add_java_params(@params['collect_insert_size_metrics']), collect_multiple_metrics_params: add_java_params(@params['collect_multiple_metrics']), markduplicate_params: add_java_params(@params['markduplicate']), mean_quality_by_cycle_params: add_java_params(@params['mean_quality_by_cycle']), quailty_score_distribution_params: add_java_params(@params['quailty_score_distribution']), sort_sam_params: add_java_params(@params['sort_sam']) } end
generate_rg_str()
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# File lib/cagnut_picard/configuration.rb, line 53 def generate_rg_str @config['samples'].each do |sample| arg = %W( 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']} ) rg_str_picard = { 'rg_str_picard' => arg.join(' ') } sample.merge! rg_str_picard end end
load(config, params)
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# File lib/cagnut_picard/configuration.rb, line 18 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