The clc_change_cas_paths Program
Cas files contain information about the files containing the reference and read data used in the mapping. This includes the paths to those files. The clc_change_cas_paths program allows you to change the file names and paths for the read and reference data files referred to in a cas file. This is useful if you have moved the sequence data files, and also can be useful when sharing cas files and the constituent data (reads and references) with others.
In addition to changing the locations of the data files, this tool can also be useful for changing relative file paths to absolute paths or vice versa.
The data file information is provided to this tool using the same parameters used with the clc_mapper tool. That is, using the `-d', `-q', and `-i' options. The input cas file is specified with the `-a' option and the cas file to be generated, containing the updated file locations, is specified with the `-o' option.
By default, the clc\_change\_cas\_paths program compares the sequence files to make sure they contain the same data. If the original read files (in their original location) no longer exist, or if you are certain you are working with the correct data files and wish to skip this check, you can use the n flag.
For the clc\_change\_cas\_paths command to succeed, you must provide the (new) locations of the data in the same order as they were used when creating the cas file originally. If you do not already know what this order is, then you can find out by running the clc\_mapping\_info program on the cas file. Providing the s flag to that tool skips checks of the contigs and thus can save some time here.
clc_mapping_info -s myassembly.cas
The order of the reads and reference files listed in that output is the same order they should be provided to the clc\_change\_cas\_paths tool.
Generally speaking it is a good idea to use different file names for the input cas file and the output cas file so the original is retained as backup. However changes can be made in place if the same cas file name is used for both the input and output.
For a full list of parameters, please refer to Options for All Programs.