Is it a bug in the software or a bug in the concept ?
> rownames(dd)[grep('aAn.1A14-1A43L9', dd.yassai)]  "TRAV14-1 TRAJ43 GCAGCAGCTAACAACAATGCCCCACGA AAANNNAPR"  "TRAV14-1 TRAJ43 GCAGCTAATAACAACAATGCCCCACGA AANNNNAPR" > V_after_C['TRAV14-1',]  "GCAGCAAGTG" > J_before_FGxG['TRAJ43',]  "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.