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# File 'lib/transrate/cmdline.rb', line 20
def run
results = []
assemblies = @opts.assembly.split(',')
result_paths = assembly_result_paths assemblies
r = @opts.reference ? Assembly.new(File.expand_path @opts.reference) : nil
@opts.output = File.expand_path @opts.output
FileUtils.mkdir_p @opts.output
Dir.chdir @opts.output do
if @opts.merge_assemblies
assemblies = concatenate_assemblies assemblies
end
assemblies.zip(result_paths) do |assembly, result_path|
results << analyse_assembly(assembly, r, result_path)
end
write_assembly_csv results
end
end
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