INNER CODE UNIT · C++

overlap_len

soedinglab/plass · lib/flash/combine_reads.cpp:292

        int overlap_len = read_1->seq_len - i;

        compute_mismatch_stats(read_1->seq + i,
                               read_2->seq,
                               read_1->qual + i,
                               read_2->qual,
                               haveN,
                               &overlap_len,
                               &num_mismatches,
                               &mismatch_qual_total);

        if (overlap_len >= min_overlap) {
            float score_len = (float)min(overlap_len, max_overlap);
            float qual_score = mismatch_qual_total / score_len;
            float mismatch_density = num_mismatches / score_len;

            if (mismatch_density <= best_mismatch_density &&
                (mismatch_density < best_mismatch_density ||

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