module CagnutPicard::CheckTools
Public Instance Methods
check_Picard(path)
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# File lib/cagnut_picard/check_tools.rb, line 9 def check_Picard path check_tool_ver 'Picard' do `#{@java} -jar #{path} AddOrReplaceReadGroups --version 2>&1` if path end end
check_picard_dict(ref_path)
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# File lib/cagnut_picard/check_tools.rb, line 15 def check_picard_dict ref_path tool = 'Sequence Dictionary' file = ref_path.gsub '.fasta', '.dict' command = "#{@java} -jar #{@config['tools']['picard']} CreateSequenceDictionary REFERENCE=#{ref_path} OUTPUT=#{file}" check_ref_related file, tool, command end
check_tool(tools_path, refs=nil)
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Calls superclass method
# File lib/cagnut_picard/check_tools.rb, line 3 def check_tool tools_path, refs=nil super if defined?(super) ver = check_Picard tools_path['picard'] if @java check_picard_dict refs['ref_fasta'] if !ver.blank? end