Support for Multiple Restriction Sites in 3D-CARTA

[doubtfuldex]

I’m currently working with Hi-C data generated using the Arima protocol, which recognizes two restriction sites: GATC and GANTC. I’m interested in using 3D-CARTA to generate a chromosome-length genome assembly, but I’ve encountered a potential issue.

The -r option in the 3D-CARTA command allows specifying a restriction sequence, but the documentation and help output seem to suggest that only a single sequence can be provided. Given that the Arima protocol involves two restriction sites, I’m wondering:

Does 3D-CARTA support specifying multiple restriction sequences via the -r flag (e.g., by listing them or separating them with commas)?
If not, do you recommend a particular approach to handle this situation? For example, should I preprocess the data in some way to account for both restriction sites, or is there a workaround within the current version of 3D-CARTA?