`REF_PATH` differs from samtools behaviour
It's difficult for me to identify how or if samtools even uses the `REF_PATH` variable, because it seems to use the `.fai` for this purpose. But in any case, the supposed behaviour is documented here: https://www.htslib.org/workflow/cram.html. In this case, `REF_PATH` is one or more paths that point to a reference *cache*, which is a series of directories containing MD5 hashes of the different contigs, e.g. `/some_dir/cache/%2s/%2s/%s`. 

On the other hand, `mosdepth` definitively treats `REF_PATH` as the path to the reference fasta file, ie analogous to `--fasta`.

I don't believe this is part of the CRAM standard, so mosdepth isn't doing anything objectively wrong here, but it does lead to confusion if e.g. `samtools` and `mosdepth` are used in the same environment/workflow, where you might think that setting `REF_PATH` to one single value would satisfy both programs, but this doesn't seem to be the case.