report.py 文件源码

def _set_seq_qual_metrics(self, seq, qual, seq_type, cache):
        cache.seq_types.add(seq_type)
        qvs = tk_fasta.get_qvs(qual)

        num_bases_q30 = np.count_nonzero(qvs >= 30)
        # Don't count no-calls towards Q30 denominator.
        # Assume no-calls get Q <= 2
        num_bases_called = np.count_nonzero(qvs > 2)

        num_bases = len(seq)
        num_bases_n = seq.count('N')

        cache.total_bases[seq_type] += num_bases
        cache.called_bases[seq_type] += num_bases_called
        cache.q30_bases[seq_type] += num_bases_q30
        cache.n_bases[seq_type] += num_bases_n