INNER CODE UNIT · C++

len

soedinglab/plass · lib/flash/combine_reads.cpp:120

    int len = *len_p;

    if (haveN) {
        for (int i = 0; i < len; i++) {
            if (seq_1[i] == 'N' || seq_2[i] == 'N') {
                num_uncalled++;
            } else {
                if (seq_1[i] != seq_2[i])  {
                    num_mismatches++;
                    mismatch_qual_total += min(qual_1[i], qual_2[i]);
                }
            }
        }
    } else {
        /* This part of the 'if' statement is for optimization purposes
         * only; its behavior is equivalent to the block above, except
         * this block assumes there are no N characters in the input,
         * and therefore no further checks for N's are needed.

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