VEP plugins: retrieve data from specific Tabix-indexed files

[nuno-agostinho]

ENSVAR-2596

Required by Ensembl/VEP_plugins#681

Motivation

Currently, Tabix-indexed data in VEP plugins when using get_data is retrieved in conglomerate from all the files.

This update allows to retrieve data only from a specific file by changing how the cache mechanism is created when get_data gets a file:

• Nothing should change if the last argument of get_data is not defined, so this change should not affect any plugins
• If get_data defines a file:
  • Result cache are separated by filename
  • Data is only retrieved for the specified filename

Testing

1. Test with Improve Paralogues plugin VEP_plugins#681
2. Test with any plugin that uses get_data function to see if its results are as expected (such as CADD plugin).

[jamie-m-a]

Original functionality retained, new function added to support selection of specific input