Input full path to cache directory

[nuno-agostinho]

Add new --full_cache_dir option to set cache directory directly and check if given directory exists

@nakib103, should we improve the logic to check if the directory is a VEP cache dir? How would we do this?

Testing

Run VEP with:

• --full_cache_dir with a non-existing directory: should raise error
• --full_cache_dir with a VEP cache dir: should work as expected
• --cache_dir and --full_cache_dir with a VEP cache dir: should ignore --cache_dir
• --cache_dir as usual: should work as expected

[nakib103]

Hi @nuno-agostinho,

Everything is working as expected, thanks!

As for the checking if the --full_cache_dir is actually cache dir - we do not check for that with --dir_cache either. It would be nice but not mandatory I would say. User currently get warning -

variant .. not found in annotation sources or synonyms

But a clear warning of it happened because of faulty cache directory would be better.

We can add checking for the presence of info.txt file here and further checking if species and assembly matches if present in config.

[nakib103]

Checking if the cache dir is a proper is not mandatory. Something that can be added later on. LOTM!~