code: def resolve_ambigs(tmpseq):
      
  
      ## the order of rows in GETCONS
      for aidx in xrange(6):
          #np.uint([82, 75, 83, 89, 87, 77]):
          ambig, res1, res2 = GETCONS[aidx]
  
          ## get true wherever tmpseq is ambig
          idx, idy = np.where(tmpseq == ambig)
          halfmask = np.random.choice(np.array([True, False]), idx.shape[0])
  
          for col in xrange(idx.shape[0]):
              if halfmask[col]:
                  tmpseq[idx[col], idy[col]] = res1
              else:
                  tmpseq[idx[col], idy[col]] = res2
      return tmpseq
docs: Randomly resolve ambiguous bases. This is applied to each boot
      replicate so that over reps the random resolutions don't matter.
      Sites are randomly resolved, so best for unlinked SNPs since 
      otherwise linked SNPs are losing their linkage information... 
      though it's not like we're using it anyways.