Improve Paralogues plugin

[nuno-agostinho]

ENSVAR-2596

Requires Ensembl/ensembl-variation#1069

Changelog

1. Fetch paralogue variants from VEP cache; the source for paralogue variants is prioritised in this order:
   • From custom VCF file (if vcf option is defined)
   • From VEP cache (in cache/offline mode)
   • From Ensembl API (in database mode)
2. Simplify remote mode
   • Enable remote mode using paralogues=remote instead of a separate argument mode=remote
   • This change makes it clearer that remote mode is relative to paralogue annotation only
3. Support a VCF file of variants mapped to their paralogous regions
   • This can be created during the release process
   • New regions option allows to get paralogue regions (that are used to look up for paralogue variants)
4. Improve performance when using Tabix-indexed data by using get_data
   • Requires changes from VEP plugins: retrieve data from specific Tabix-indexed files ensembl-variation#1069
5. Fix using plugin with registry to access custom databases

Matches file

The file with variants mapped to paralogue regions can be created by running VEP with VCF output, a registry pointing to the next release databases (e112 in this case) and Paralogues plugin with the recommended options.

More information: refer to the Paralogues plugin page in Confluence.

Testing

Example of variants to test with this plugin:

1	939112	.	G	A
1	44827194-44827195	.	GT	AA
1	8871910	.	C	T
2	166073606	.	G	T
17	4833586	.	G	T

1. Test fetching variants in VEP cache by using the plugin in --offline or --cache mode (without using a custom VCF)
2. Check if paralogues=remote works as expected
3. Check if matches option works with ClinVar file (location to file in ENSVAR-2596)
   • Test regions=0 and regions=1

[jamie-m-a]

Thanks Nuno - those few fixes seem to be working.

Just a quick comment before merging - it's good practise to not leave big chunks of commented code in stuff we're merging to the repos. Can you remove (and keep locally if you think it might be code you want to use later), thanks!

[nuno-agostinho]

Thanks for the review, @jamie-m-a! I removed the commented code now.