docs: def _refine_v(seq, species):
          '''
          Completes the 5' end of a a truncated sequence with germline nucleotides.
          Input is a MongoDB dict (seq) and the species.
          '''
          vgerm = germlines.get_germline(seq['v_gene']['full'], species)
          aln = global_alignment(seq['vdj_nt'], vgerm)
          prepend = ''
          for s, g in zip(aln.aligned_query, aln.aligned_target):
              if s != '-':
                  break
              else:
                  prepend += g
          seq['vdj_nt'] = prepend + seq['vdj_nt']