INNER CODE UNIT · C++
best_mismatch_density
soedinglab/plass · lib/flash/combine_reads.cpp:275
float best_mismatch_density = max_mismatch_density + 1.0f;
float best_qual_score = 0.0f;
int best_position = NO_ALIGNMENT;
bool best_was_outie;
bool doing_outie = false;
int start;
int end;
again:
/* Require at least min_overlap bases overlap, and require that the
* second read is not overlapped such that it is completely contained in
* the first read. */
start = max(0, read_1->seq_len - read_2->seq_len);
end = read_1->seq_len - min_overlap + 1;
for (int i = start; i < end; i++) {
unsigned num_mismatches;
unsigned mismatch_qual_total;
int overlap_len = read_1->seq_len - i;