The `-s' option is used for making a new mapping with only matches to a single reference sequence. The `-d' option makes a new mapping with only matches to the reference sequences of a single file. The sequence or file must be specified as its number in the list of reference sequences or files in the input. You can use clc_mapping_info to see the contents of the input mappings is needed.
These options are useful when working with a large mappings such as the human genome. Extracting sub mappings for each chromosome may make it easier to work with.