I wanted to generate bisulfite alignments with gmapR, but cannot get it to work. I can generate a normal alignment similar to how it is described in the documentation.

Running gsnap on the command line, you normally have to run cmetindex in order to prepare a normal genomic index for bisulfite alignments. Do you need to do this within gmapR as well?

Looking to the code-base, there are empty wrappers for both cmetindex and atoiindex. They are not visible within R. Is there a plan to add this functionality? Or am I just missing something obvious?

I guess we were waiting for a post like this to motivate support for those. They look like they've been implemented, but they've never been tested. You could try calling them, passing the GmapGenome object. Let me know how it goes. Eventually we can export and document them.