Make WFAExtender apply full length bonuses even though it doesn't use them internally

src/gbwt_extender.cpp

@@ -2284,7 +2284,14 @@ WFAAlignment WFAExtender::connect(std::string sequence, pos_t from, pos_t to) co
 }
 
 WFAAlignment WFAExtender::suffix(const std::string& sequence, pos_t from) const {
-    return this->connect(sequence, from, pos_t(0, false, 0));
+    WFAAlignment result = this->connect(sequence, from, pos_t(0, false, 0));
+
+    if (!result.edits.empty() && result.length == sequence.length() && (result.edits.back().first == WFAAlignment::match || result.edits.back().first == WFAAlignment::mismatch)) {
+        // The alignment used all of the sequence and has a match/mismatch at the appropriate end
+        result.score += this->aligner->full_length_bonus; 
+    }
+
+    return result;
 }
 
 WFAAlignment WFAExtender::prefix(const std::string& sequence, pos_t to) const {
@@ -2297,6 +2304,10 @@ WFAAlignment WFAExtender::prefix(const std::string& sequence, pos_t to) const {
     WFAAlignment result = this->connect(reverse_complement(sequence), to, pos_t(0, false, 0));
     result.flip(*(this->graph), sequence);
 
+    if (!result.edits.empty() && result.length == sequence.length() && (result.edits.front().first == WFAAlignment::match || result.edits.front().first == WFAAlignment::mismatch)) {
+        result.score += this->aligner->full_length_bonus; 
+    }
+
     return result;
 }
 

src/gbwt_extender.hpp

@@ -412,9 +412,11 @@ class WFAExtender {
      * entire sequence with an acceptable score, returns the highest-scoring
      * partial alignment, which may be empty.
      *
+     * Applies the full-length bonus if the result ends with a match or mismatch.
+     * TODO: Use the full-length bonus to determine the optimal alignment.
+     *
      * NOTE: This creates a suffix of the full alignment by aligning a
      * prefix of the sequence.
-     * TODO: Should we use full-length bonuses?
      */
     WFAAlignment suffix(const std::string& sequence, pos_t from) const;
 
@@ -424,9 +426,11 @@ class WFAExtender {
      * sequence with an acceptable score, returns the highest-scoring partial
      * alignment, which may be empty.
      *
+     * Applies the full-length bonus if the result begins with a match or mismatch.
+     * TODO: Use the full-length bonus to determine the optimal alignment.
+     *
      * NOTE: This creates a prefix of the full alignment by aligning a suffix
      * of the sequence.
-     * TODO: Should we use full-length bonuses?
      */
     WFAAlignment prefix(const std::string& sequence, pos_t to) const;