code: def count_concordant(self, aligned_bam):
          
          cmd = self.tools.samtools + " view " + aligned_bam + " | "
          cmd += "grep 'YT:Z:CP'" + " | uniq -u | wc -l | sed -E 's/^[[:space:]]+//'"
          
          return subprocess.check_output(cmd, shell=True)
docs: Count only reads that "aligned concordantly exactly 1 time."
  
          :param str aligned_bam: File for which to count mapped reads.