code: def _add_sj_index_commands(fq1, ref_file, gtf_file):
      
      if _has_sj_index(ref_file):
          return ""
      else:
          rlength = fastq.estimate_maximum_read_length(fq1)
          cmd = " --sjdbGTFfile %s " % gtf_file
          cmd += " --sjdbOverhang %s " % str(rlength - 1)
          return cmd
docs: newer versions of STAR can generate splice junction databases on thephfly
      this is preferable since we can tailor it to the read lengths