code: public static RandomAccessFastaIndex index(Path file, boolean save) {
          return index(file, save, LongProcessReporter.DefaultLongProcessReporter.INSTANCE);
      }
docs: Index fasta file with automatic step selection or load previously created index
  
  @param file file to index
  @param save whether to save index to {input_file_name}.mifdx file
  @return index