Options for clc_cas_to_sam
usage: clc_cas_to_sam <options>
Convert a cas file to sam or bam format.
Options:
-h / --help: Display this message
-a <file> / --cas <file>: Set the input cas file (required).
-o <file> / --output <file>: Set the output sam or bam file. Sam format is
assumed unless the file ends with ".bam" or ".BAM" (required).
-f <offset> / --qualityoffset <offset>: Set the ascii offset value in fastq
files. If not specified, the offset is estimated by examining the input files.
-u / --discardunmapped: Discard the unmapped reads
-m / --multimatch: Output all available alignments in each match
--no-progress: Disable progress bar.
Example:
Convert a cas file to bam format:
clc_cas_to_sam -a assembly.cas -o assembly.bam