[ensembl-dev] Required to use --fasta flag with --refseq?

[Matt Wood]

I've installed the following caches:

homo_sapiens_refseq_vep_75.tar.gz
homo_sapiens_vep_75.tar.gz

and the FASTA file for homo_sapiens.

I'm trying to get access to the ref sequence from a VEP plugin when running
with the refseq flag. I have no problems when running without the flag. My
args are:

-dir ~/.vep --force_overwrite --refseq -offline --vcf --plugin RSTest -i
test.vcf -o test.out

In my RSTest plugin I do the following:

my $subslice = $vf->slice->sub_Slice($start, $end)->seq;

But, my $subslice is always "NNNNNNNNNNN". If I remove the refseq flag I
get what I expect.

I found that if I add a --fasta flag and point explicitly to the fasta file
that was downloaded by the VEP install process things work as expected.

Is this expected behavior? Or is there some way for the fasta file to be
recognized implicitly like when running without the refseq flag?

Thanks.
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