annotate_sv duplicates BCL6-MYC rearrangements

[lkhilton]

This command returns a clear BCL6::MYC event:

sv_data <- get_combined_sv(
          these_sample_ids = "CLC03336",
          oncogenes = "MYC")

  CHROM_A   START_A     END_A CHROM_B   START_B     END_B manta_name       SCORE STRAND_A STRAND_B tumour_sample_id normal_sample_id VAF_tumour    DP gridss_name ANNOTATION_A DIST_TO_ANNOTATION_A ANNOTATION_B
1 3       187477179 187477181 8       128893895 128893897 MantaBND:0:2025…    NA +        -        CLC03336         14-11247N             0.175   383 gridss68fb… BCL6                       -13924 MYC         
2 3       187480498 187480500 8       128893597 128893599 MantaBND:0:2025…    NA -        +        CLC03336         14-11247N             0.315   470 gridss68bf… BCL6                       -17243 MYC  

But if I run annotate_sv on the above I get:

   chrom1    start1      end1 chrom2    start2      end2   name score strand1 strand2 tumour_sample_id   gene partner   fusion
1:      3 187477179 187477181      8 128893895 128893897      .    NA       +       -         CLC03336   BCL6    <NA>  NA-BCL6
2:      3 187480498 187480500      8 128893597 128893599      .    NA       -       +         CLC03336   BCL6    <NA>  NA-BCL6
3:      3 187477179 187477181      8 128893895 128893897      .    NA       +       -         CLC03336    MYC    BCL6 BCL6-MYC
4:      3 187480498 187480500      8 128893597 128893599      .    NA       -       +         CLC03336    MYC    BCL6 BCL6-MYC

This is with the latest GAMBLR.utils just installed today.