code: def _remove_small_contigs(self, infile, outfile, keep=None):
          '''Writes a new file with small contigs removed.
             Returns lists of all names and names of removed contigs'''
          removed = set()
          all_names = set()
          if keep is None:
              keep = set()
  
          file_reader = pyfastaq.sequences.file_reader(infile)
          fout = pyfastaq.utils.open_file_write(outfile)
  
          for seq in file_reader:
              all_names.add(seq.id)
              if len(seq) >= self.min_contig_length or seq.id in keep:
                  print(seq, file=fout)
              else:
                  removed.add(seq.id)
  
          pyfastaq.utils.close(fout)
          return all_names, removef _remove_small_contigs(self, infile, outfile, keep=None):
          '''Writes a new file with small contigs removed.
             Returns lists of all names and names of removed contigs'''
          removed = set()
          all_names = set()
          if keep is None:
              keep = set()
  
          file_reader = pyfastaq.sequences.file_reader(infile)
          fout = pyfastaq.utils.open_file_write(outfile)
  
          for seq in file_reader:
              all_names.add(seq.id)
              if len(seq) >= self.min_contig_length or seq.id in keep:
                  print(seq, file=fout)
              else:
                  removed.add(seq.id)
  
          pyfastaq.utils.close(fout)
          return all_names, removed
docs: Writes a new file with small contigs removed.
             Returns lists of all names and names of removed contigs