When you use the -cos option with a MAF utility, and supply MAF with an input file name group, and a substructure suffix subsuffix, then MAF will either generate (if you are running automata, gptcenum, or one of the KBMAG compatibility programs), or open (all other utilities) an input file for a coset system named group.cossuffix, created from the input file group, and the substructure file group.subsuffix
Here cossuffix is defined as follows. If (as is recommended), subsuffix has the form substring for some (possibly empty) string string, then cossuffix is cosstring. Otherwise, cossuffix is subsuffix_cos. The default for subsuffix is just sub, and then cossuffix is just cos. If the file containing the coset rewriting system is named group.cossuffix, then most automata and other output files created from it will have names of the form group.cossuffix.suffix. However, a few files will have names of the form group.subsuffix.suffix. This applies in particular to the presentation that may be generated for the subgroup, and to the word-acceptor for the subgroup.
If the subgroup suffix is substring string should not itself contain either cos or sub. Doing this is likely to cause MAF to become confused about your intentions.
MAF, but not KBMAG, will allow you to open a coset system file directly. Thus, if the file group.cossuffix already exists, the following two commands will have almost the same effect:
automata -cos group subsuffix
Never rename a coset system to use some other filename. MAF must be able to deduce the names of both the original input file for the group, and of the substructure file, since these files, or files related to them, may be needed for some computations for the coset system.
The only difference between the two commands, is that in the first case the coset system file will be generated, even if it already exists, whereas in the second case, the existing coset system file will be used (and the command will fail if the file does not yet exist). Therefore, if you need to modify a coset system input file created by MAF for some reason, then you should use the second command. This command will also be marginally quicker.
Some utilities that accept the -cos option will expect the coset system to have been generated previously, since it only makes sense to use them once automata have been computed for the coset system. If you invoke them before the coset system input file is created they will complain.
MAF will also allow you to use the -cos option in the following manner:
automata -cos group cossuffix
If MAF sees the -cos option being used like this, it will interpret the command line just as though subsuffix had been supplied. This is because KBMAG's kbprogcos expects cossuffix whereas autcos expects a subsuffix. As this is confusing for the user MAF attempts to be flexible. This is the reason why you should follow the advice given above when choosing a subgroup suffix.