Fix chromosome synonyms for breakends and custom annotation

[nuno-agostinho]

Fixes:

• issue with data from gff flag when upgrading to VEP110  #1570 (fix data when using custom annotation with chromosome synonyms)
• ENSVAR-5967 (add support for chromosome synonyms in breakends)

Requires Ensembl/ensembl-variation#1064

Motivation

When using chromosome synonyms (such as chr12 and NC_000012.12) with custom annotation or breakends, the comparison fails because it doesn't take synonyms into account.

Changelog

• Fetch chromosome synonyms when using --database
  • Move code from CreateDumpJobs to BaseVEP: new function _fetch_chr_synonyms()
  • Call _fetch_chr_synonyms() when in --database mode
• Look for chromosome synonyms when checking if a breakend or feature from a custom annotation is in a $min_max region
• Set global variable $CHROMOSOME_SYNONYMS in ensembl-variation
  • Support chromosome synonyms in breakends ensembl-variation#1064
• Add unit tests

Testing

Test if VEP cache dump works with the changes.

Run VEP with:

• a custom annotation containing chromosome synonyms (examples: GFF and VCF)
• an input containing breakend variants, for instance (this example has the same two variants using different chromosome synonyms):

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
2	29225144        bnd     G	G]2:42267610]   .	.	SVTYPE=BND
2	42267610        bnd     A	A]2:29225144]   .	.	SVTYPE=BND
chr2    29225144        bnd     G	G]chr2:42267610]        .	.       SVTYPE=BND
chr2    42267610        bnd     A	A]chr2:29225144]        .	.       SVTYPE=BND
NC_000002.12    29225144        bnd     G G]NC_000002.12:42267610]        . .       SVTYPE=BND
NC_000002.12    42267610        bnd     A A]NC_000002.12:29225144]        . .       SVTYPE=BND
CM000664.2    29225144        bnd     G G]CM000664.2:42267610]        . .       SVTYPE=BND
CM000664.2    42267610        bnd     A A]CM000664.2:29225144]        . .       SVTYPE=BND

[nakib103]

LGTM!~ thanks @nuno-agostinho!

[nakib103]

merged to main and release/112