Is it a bug in the software or a bug in the concept ?

> rownames(dd)[grep('aAn.1A14-1A43L9', dd.yassai)]
[1] "TRAV14-1 TRAJ43 GCAGCAGCTAACAACAATGCCCCACGA AAANNNAPR"
[2] "TRAV14-1 TRAJ43 GCAGCTAATAACAACAATGCCCCACGA AANNNNAPR"
> V_after_C['TRAV14-1',]
[1] "GCAGCAAGTG"
> J_before_FGxG['TRAJ43',]
[1] "GCAATAACAACAATGCCCCACGA"

aAn.1A14-1A43L9
 A   A   A   N   N   N   A   P   R
GCA GCA GCT AAC AAC AAT GCC CCA CGA
GCA GCA agt g
     gc aaT AAC AAC AAT GCC CCA CGA

aAn.1A14-1A43L9
 A   A   N   N   N   N   A   P   R
GCA GCT AAT AAC AAC AAT GCC CCA CGA
GCA GCa agt g
     gc AAT AAC AAC AAT GCC CCA CGA

This is a collision (different colonotypes giving the same Yassai ID) rather than a bug in the implementation → done.