By default, the output refers to one or all of the read files in the input. It refers to just one of the files when it has been selected using the `-q' option.
Using the `-f' option, a new read file is made instead containing only the reads that match. The output automatically refers to this new read file instead of the originals.
This is very useful when making a sub mapping that only covers a small part of the original reference sequences. That way a much smaller number of reads come into play when working with the sub mapping, making subsequent analyses more efficient.
When the reads are from a paired experiment, the read mapper expects read one to pair with read two, read three to pair with read four, etc. If one read out of a pair is removed with the clc_submapping program, the paired read order is disrupted. Because of this, the `-p' option should be used when the reads are from a paired experiment. It works by retaining reads that do not match the clc_submapping criteria if the counterpart does match the criteria. Without the `-p' option, the read file will contain no unassembled reads, but with this option some reads may be unassembled because the other member of their pair is part of the assembly.