In the case of human genome and mitochondrial references then, the input command would look like this:
clc_mapper -o assembly.cas -d human.gb -q reads1.fasta reads2.fasta -d -z mito.gb
This will cause the mapper to map reads spanning the start point of the circular reference sequence as if they were mapped to a contiguous reference sequence. Note that the `-d' option is used twice in the example above to achieve this.
* Please note this functionality is not available for the legacy read mapper.