Options for clc_change_cas_paths
usage: clc_change_cas_paths <options> Change the sequence file names in a cas file. Can be used for the reference files, the read files, or both. Options: -h / --help: Display this message. -a <file> / --cas <file>: Give the cas file (required). -o <file> / --output <file>: Give the output cas file (required). -q / --reads: The files following this option are read files. (may be used several times). -d / --reference: The files following this option are reference files. Fasta and GenBank formats are allowed (may be used several times). -i <file1> <file2> / --interleave <file1> <file2>: Interleave the sequences in two files, alternating between the files when reading the sequences. Only valid for read files (may be used several times). -n / --nocheck: Do not check if the sequence files match. This is useful if the old files do not exist any more, or to get a fast result if the files are known to match.