The change_cas_paths Program

This program allows you to change the file names in a mapping file. It is useful if you have moved the sequence files after the assembly was made. Or if you for example made the mapping with relative file names and want to change the file names to absolute names (or vice versa). It is also possible to change the file format, for example from fasta to GenBank format if you wish a richer representation of the sequence. For the operation to be a success, however, the actual sequences and their order must remain unchanged.

With the change_cas_paths program, file names are specified like they are when making the original reference assembly, i.e. using the `-d', `-q', and `-i' options. The output cas file is specified with the `-o' option and the input cas file is specified with the `-a' option.

To make the change in place, use the same cas file name for input and for output. It is of course slightly safer to use different file names, so a backup of the original is kept.

By default, the program compares the sequence files to make sure they contain the same data. This takes some time, so the `-n' option is included to avoid this check. The `-n' option is also useful if the old sequence files does not exist any more.

For options see Options for All Programs.