By default, the output mapping refers to one or all of the reference files in the input cas file. It refers to just one of the files when it has been selected using the `-d' option or when a single reference sequence has been selected with the `-s' option.
If the `-g' option is used, an output file is made with only the reference sequences of the output mapping. The new mapping automatically refers to this reference sequence file. This is typically useful when selecting only a single reference sequence and the input alignment contains many reference sequences in the same file. That way the output only contains the relevant reference sequence instead of many references with no matches. It makes the output easier and faster to work with.
If a position range was specified, the output reference file only contains these positions.