[ensembl-dev] VEP offline script: Checking/creating FASTA index fails to find existing index

Cyriac Kandoth kandoth at cbio.mskcc.org
Sat Oct 18 02:33:15 BST 2014


Hi Devs,

The code to check whether a FASTA index needs to be created, looks for a
file with extension ".fa.index". However, (and this may be recent) the
indexes created are files named ".fa.index.dir" and ".fa.index.pag". I
haven't checked the code to confirm this. I'm assuming this is the case,
since VEP appears to index the FASTA everytime it runs, unless I create a
copy of ".fa.index.pag" with extension ".fa.index".

Cheers!

~Cyriac
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