Remove Alignment::mapq field

Keep mapping quality separate from the alignment itself appears to make more
sense:
- Mapping quality for an alignment is not a property of an alignment per se,
  but is derived from its relationship to other alignments.
- get_alignment returns an Alignment, but leaves mapq uninitialized, that
  is, we must remember to fill it in afterwards, which can easily be
  forgotten.
- Sam::add_pair is passed two mapq values and also two Alignment instances,
  which also contain mapq values. It is unclear for the caller which of the
  values is chosen.
- Adding a mapq parameter to Sam::add makes it mirror Sam::add_pair.

src/aln.cpp

@@ -127,8 +127,7 @@ static inline void align_SE(
     uint8_t mapq = 60.0 * (best_score - second_best_score) / best_score;
 
     if (max_secondary == 0) {
-        best_alignment.mapq = mapq;
-        sam.add(best_alignment, record, read.rc, true, details);
+        sam.add(best_alignment, record, read.rc, mapq, true, details);
         return;
     }
     // Sort alignments by score, highest first
@@ -145,12 +144,7 @@ static inline void align_SE(
             break;
         }
         bool is_primary = i == 0;
-        if (is_primary) {
-            alignment.mapq = mapq;
-        } else {
-            alignment.mapq = 255;
-        }
-        sam.add(alignment, record, read.rc, is_primary, details);
+        sam.add(alignment, record, read.rc, mapq, is_primary, details);
     }
 }
 

src/sam.cpp

@@ -120,6 +120,7 @@ void Sam::add(
     const Alignment& alignment,
     const KSeq& record,
     const std::string& sequence_rc,
+    uint8_t mapq,
     bool is_primary,
     const Details& details
 ) {
@@ -131,8 +132,9 @@ void Sam::add(
     }
     if (!is_primary) {
         flags |= SECONDARY;
+        mapq = 255;
     }
-    add_record(record.name, flags, references.names[alignment.ref_id], alignment.ref_start, alignment.mapq, alignment.cigar, "*", -1, 0, record.seq, sequence_rc, record.qual, alignment.edit_distance, alignment.score, details);
+    add_record(record.name, flags, references.names[alignment.ref_id], alignment.ref_start, mapq, alignment.cigar, "*", -1, 0, record.seq, sequence_rc, record.qual, alignment.edit_distance, alignment.score, details);
 }
 
 // Add one individual record

src/sam.hpp

@@ -15,7 +15,6 @@ struct Alignment {
     int edit_distance;
     int global_ed;
     int score;
-    uint8_t mapq;
     int length;
     bool is_rc;
     bool is_unaligned{false};
@@ -79,7 +78,7 @@ class Sam {
         }
 
     /* Add an alignment */
-    void add(const Alignment& alignment, const klibpp::KSeq& record, const std::string& sequence_rc, bool is_primary, const Details& details);
+    void add(const Alignment& alignment, const klibpp::KSeq& record, const std::string& sequence_rc, uint8_t mapq, bool is_primary, const Details& details);
     void add_pair(const Alignment& alignment1, const Alignment& alignment2, const klibpp::KSeq& record1, const klibpp::KSeq& record2, const std::string& read1_rc, const std::string& read2_rc, uint8_t mapq1, uint8_t mapq2, bool is_proper, bool is_primary, const std::array<Details, 2>& details);
     void add_unmapped(const klibpp::KSeq& record, uint16_t flags = UNMAP);
     void add_unmapped_pair(const klibpp::KSeq& r1, const klibpp::KSeq& r2);

tests/test_sam.cpp

@@ -52,7 +52,6 @@ TEST_CASE("Sam::add") {
     aln.ref_start = 2;
     aln.edit_distance = 3;
     aln.score = 9;
-    aln.mapq = 55;
     aln.cigar = Cigar("2S2=1X3=3S");
 
     std::string read_rc = reverse_complement(record.seq);
@@ -61,15 +60,15 @@ TEST_CASE("Sam::add") {
     SUBCASE("Cigar =/X") {
         std::string sam_string;
         Sam sam(sam_string, references);
-        sam.add(aln, record, read_rc, is_primary, details);
+        sam.add(aln, record, read_rc, 55, is_primary, details);
         CHECK(sam_string ==
             "readname\t16\tcontig1\t3\t55\t2S2=1X3=3S\t*\t0\t0\tACGTT\tBB#>\tNM:i:3\tAS:i:9\n"
         );
     }
     SUBCASE("Cigar M") {
         std::string sam_string;
         Sam sam(sam_string, references, CigarOps::M);
-        sam.add(aln, record, read_rc, is_primary, details);
+        sam.add(aln, record, read_rc, 55, is_primary, details);
         CHECK(sam_string ==
             "readname\t16\tcontig1\t3\t55\t2S6M3S\t*\t0\t0\tACGTT\tBB#>\tNM:i:3\tAS:i:9\n"
         );