Report consequences for each breakend (e112)

[nuno-agostinho]

ENSVAR-5962: Report consequences for each breakend

Changelog

• Parse multiple breakends like multiple alternative alleles
• Move breakend parsing code to ensembl-variation: Report consequences for each breakend ensembl-variation#1040
• Manta breakends (CHR2=8;END2=4654454) are now converted to VCF breakend format (such as [8:4654454[N) before being parsed in ensembl-variation

Fixes #1492

Testing

Run multiple types of variants, such as:

1       713044  DUP     C       <CN=2>  .       .       END=755966
1       7936271 .       N       N[12:58877476[,N[8:56445865[    .      .      .
1       7936271 .       N       <BND>    CHR2=8;END2= 4654454      .      .
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
20     17330   .         T      A       3    q10    NS=3;DP=11;AF=0.017               GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3   0/0:41:3

Check if everything looks fine in different output formats (default output, VCF, JSON, TSV).

[likhitha-surapaneni]

Looks good to me. Thanks @nuno-agostinho