code: def fill_dups_arr(data):
      
      ## build the duplicates array
      duplefiles = glob.glob(os.path.join(data.tmpdir, "duples_*.tmp.npy"))
      duplefiles.sort(key=lambda x: int(x.rsplit("_", 1)[-1][:-8]))
  
      ## enter the duplicates filter into super h5 array
      io5 = h5py.File(data.clust_database, 'r+')
      dfilter = io5["duplicates"]
  
      ## enter all duple arrays into full duplicates array
      init = 0
      for dupf in duplefiles:
          end = int(dupf.rsplit("_", 1)[-1][:-8])
          inarr = np.load(dupf)
          dfilter[init:end] = inarr
          init += end-init
          #os.remove(dupf)
      #del inarr
  
      ## continued progress bar
      LOGGER.info("all duplicates: %s", dfilter[:].sum())
      io5.close()
docs: fills the duplicates array from the multi_muscle_align tmp files