CSN, GeneSplicer and MaxEntScan plugins do not use default fasta

[davmlaw]

docs say

files set up using the installer are automatically detected by VEP when using --cache or --offline; you should not need to use --fasta manually specify them.

However the following plugins check for the parameter being passed (not the default fasta being loaded)

Eg code from MaxEntScan.pm

  die("ERROR: cannot function in offline mode without a FASTA file\n") if $self->{config}->{offline} && !$self->{config}->{fasta};

• CSN
• GeneSplicer
• MaxEntScan

UTRAnnotator gives a warning about not being passed "--fasta" but still works

[davmlaw]

Workaround is of course to just explicitly pass the auto downloaded fasta, so for 38 you'd add:

--fasta ${VEP_CACHE_DIR}/Homo_sapiens.GRCh38.dna.toplevel.fa.gz

[jamie-m-a]

Thanks for the suggestions @davmlaw we will check them out and update the impacted plugins as needed.