nucleoatac occ requires FASTA?

[vreuter]

Does nucleoatac occ require a FASTA as run does? It looks like this may be implicit through run_occ making an OccupancyParameters, for which the constructor calls into read_chrom_sizes_from_fasta. It looks like that needs a valid FASTA to pass to pysam.

If this is the case, could the documentation be updated to reflect that requirement?
Separate but related, defining a subparser for each subcommand and declaring required arguments that way could make such requirements more apparent, bubbling an guaranteed failure to the surface and saving users some runtime before the inevitable exception.

[AliciaSchep]

I think this is a bug -- e.g. the intention is that occ can be run without fasta (in which case no Tn5 bias correction is performed) but that there is at the moment a call in at least one place that will throw an error in that case...

Each subcommand has a subparser defined for it, and in general required arguments should be flagged as such there. However, there may be cases where something that should be required is presently not marked as required as it should be. However, in the case above, the argument is not intended to be required and the error when it is missing is a bug.