The clc_sam_to_cas Program
This tool converts a read mapping in sam or bam format to a cas format file.
The clc_sam_to_cas tool converts SAM or BAM files to cas format. Like cas format files, SAM and BAM files do not contain the reference sequence data, so the reference sequences need to be provided when running this command. This is so that the required information can be generated for the cas file.
You also need to provide a destination for the sequencing read data to be written to when running this program.
Further details of the command line options for this tool are provided in Options for All Programs.