code: def count_var(nex):
      
      arr = np.array([list(i.split()[-1]) for i in nex])
      miss = np.any(arr=="N", axis=0)
      nomiss = arr[:, ~miss]
      nsnps = np.invert(np.all(nomiss==nomiss[0, :], axis=0)).sum()
      return nomiss.shape[1], nsnps
docs: count number of sites with cov=4, and number of variable sites.