VEP cache/plugin directory option not implemented

[Jason M. Wood]

According to the README, there is an option to provide the location of the VEP cache/plugin directory for the indels annotation phase. However, this option is not currently implemented:

usage: ScanNeo.py [-h] [-v] {indel,anno,hla,fasta} ...
ScanNeo.py: error: unrecognized arguments: -d /mnt/store3/clustcrilab/tools/scanneo/vep/

usage: ScanNeo.py [-h] [-v] {indel,anno,hla,fasta} ...
ScanNeo.py: error: unrecognized arguments: --dir /mnt/store3/clustcrilab/tools/scanneo/vep/

[Carlos D. Wang]

I have fixed this bug. 56fe1d9
Thanks a lot.

[Jason M. Wood]

Thanks. I was working on a patch, but I'll revert my changes and use yours.