docs: def _refine_j(seq, species):
          '''
          Completes the 3' end of a a truncated sequence with germline nucleotides.
          Input is a MongoDB dict (seq) and the species.
          '''
          jgerm = germlines.get_germline(seq['j_gene']['full'], species)
          aln = global_alignment(seq['vdj_nt'], jgerm)
          append = ''
          for s, g in zip(aln.aligned_query[::-1], aln.aligned_target[::-1]):
              if s != '-':
                  break
              else:
                  append += g
          seq['vdj_nt'] = seq['vdj_nt'] + append[::-1]