Masking regions for chaining?

[rlorigro]

Hi,

I am using minigraph in a local context (<20Kbp) where I have a highly variable region flanked by reasonably conserved regions, and I would like to anchor my query sequences on the flanks and compute optimal base-level alignments in the variable region. Do you see it possible as a additional feature to mask out regions for chaining in my graph? Essentially, I just want to build the index and do minimizer chaining on the flanks, and then bridge them with gWFA.

Alternatively, if you have any recommendations for manually building an index, or any combination of existing parameters that would help with long range gWFA, that would be great too.

Thanks