code: def reftrick(iseq, consdict):
      
  
      altrefs = np.zeros((iseq.shape[1], 4), dtype=np.uint8)
      altrefs[:, 1] = 46
  
      for col in xrange(iseq.shape[1]):
          ## expand colums with ambigs and remove N-
          fcounts = np.zeros(111, dtype=np.int64)
          counts = np.bincount(iseq[:, col])#, minlength=90)
          fcounts[:counts.shape[0]] = counts
          ## set N and - to zero, wish numba supported minlen arg
          fcounts[78] = 0
          fcounts[45] = 0
          ## add ambig counts to true bases
          for aidx in xrange(consdict.shape[0]):
              nbases = fcounts[consdict[aidx, 0]]
              for _ in xrange(nbases):
                  fcounts[consdict[aidx, 1]] += 1
                  fcounts[consdict[aidx, 2]] += 1
              fcounts[consdict[aidx, 0]] = 0
  
          ## now get counts from the modified counts arr
          who = np.argmax(fcounts)
          altrefs[col, 0] = who
          fcounts[who] = 0
  
          ## if an alt allele fill over the "." placeholder
          who = np.argmax(fcounts)
          if who:
              altrefs[col, 1] = who
              fcounts[who] = 0
  
              ## if 3rd or 4th alleles observed then add to arr
              who = np.argmax(fcounts)
              altrefs[col, 2] = who
              fcounts[who] = 0
  
              ## if 3rd or 4th alleles observed then add to arr
              who = np.argmax(fcounts)
              altrefs[col, 3] = who
  
      return altrefs
docs: Returns the most common base at each site in order.