core/representative.cpp: do not stop representative computation to correctly...

core/representative.cpp: do not stop representative computation to correctly compute average quality

This commit may affect the global execution time.

algo/core/representative.cpp

@@ -111,7 +111,8 @@ void KmerRepresentativeComputer::compute() {
   for (size_t seq = 1; seq <= sequences.size() && seq <= seq_index_longest_run + stability_limit ; seq++) {
     Sequence sequence = rc.getithBest(seq);
 
-    if (sequence.sequence.size() <= length_longest_run) {
+    // Break as soon as the sequences are too small
+    if (sequence.sequence.size() < required.size()) {
       break;
     }
     
@@ -131,6 +132,12 @@ void KmerRepresentativeComputer::compute() {
       sequence_used_for_quality++;
     }
 
+    // When sequences are smaller than length_longest_run,
+    // they are used only for the above quality computation
+    if (sequence.sequence.size() <= length_longest_run) {
+      continue;
+    }
+
     size_t pos_end_required = pos_required + required.length();
 
     vector<Kmer> counts = index->getResults(sequence.sequence);