Fix breakend consequences when using chr prefix

[nuno-agostinho]

Fixes Ensembl/ensembl-vep#1479

Simply ignore the chr prefix of breakend mates when checking if a mate is contained within an Ensembl feature.

In a future PR, we will also look into chromosome synonyms (ENSVAR-5967), such as CM000664.2 and NC_000002.12.

Testing

Run VEP with the following pairs of variants, the results should be the same whether they regions have a chr prefix or not:

#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

[nakib103]

LOTM!~