Parse END field in Manta breakend variants

[nuno-agostinho]

Fixes second issue mentioned in #1476: END cannot be a smaller number than variant start, according to VCF 4.4 specifications, even though this is what happens in the output of breakends from the SV caller Illumina Manta.

As this is a popular SV caller, we will correctly parse the Manta breakend variant (even if out of VCF spec).

Changelog

• Delete END and parse the variant end again (this way, variant end is the same as start)
• Store value of END as END2
  • If the alternative allele of breakend is similar to [1:106864407[A, the information in the INFO field is ignored
  • Otherwise, if both CHR2 and END2 are defined, they will be used to prepare the breakend information (logic already introduced in Add support for breakend variants from VCF #1399)
• Remove unnecessary code regarding END that is already run in $parser->get_end()

Testing

Run VEP with some breakend (and other) variants, such as:

2 227032111 BND00000186 A [1:106864407[A . LowQual IMPRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.7.8;CHR2=1;END=106864407;PE=2;MAPQ=60;CT=5to5;CIPOS=-231,231;CIEND=-231,231 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/0:0,-19.006,-594:10000:PASS:8:5259:1:1169:101:2:0:0

I added unit tests to check changes.

[nakib103]

Looks Good and work as expected, thanks @nuno-agostinho