+ # Method to execute uchime chimera detection.
+ def uchime
+ @command << "usearch --uchime #{@infile} --db #{@options[:database]} --uchimeout #{@outfile}"
+
+ execute
+ end
+
+ # Method to execute ustar alignment.
+ def ustar
+ command = %Q{grep "^[SH]" #{@outfile} > #{@outfile}.sub}
+ system(command)
+ raise "Command failed: #{command}" unless $?.success?
+
+ File.rename "#{@outfile}.sub", @outfile
+
+ @command << "usearch --uc2fastax #{@outfile} --input #{@infile} --output #{@infile}.sub"
+
+ execute
+
+ @command << "usearch --staralign #{@infile}.sub --output #{@outfile}"
+
+ execute
+
+ File.delete "#{@infile}.sub"
+ end
+