code: def _estimate_paired_innerdist(fastq_file, pair_file, ref_file, out_base,
                                 out_dir, data):
      
      mean, stdev = _bowtie_for_innerdist("100000", fastq_file, pair_file, ref_file,
                                          out_base, out_dir, data, True)
      if not mean or not stdev:
          mean, stdev = _bowtie_for_innerdist("1", fastq_file, pair_file, ref_file,
                                              out_base, out_dir, data, True)
      # No reads aligning so no data to process, set some default values
      if not mean or not stdev:
          mean, stdev = 200, 50
  
      return mean, stdev
docs: Use Bowtie to estimate the inner distance of paired reads.