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?