fix(stitch): use sjdb_score in place of motif_score on annotated junctions

src/align/score.rs

@@ -126,19 +126,12 @@ impl AlignmentScorer {
         ((genomic_span as f64).log2() * self.score_genomic_length_log2_scale - 0.5).ceil() as i32
     }
 
-    /// Apply annotation bonus to junction score
-    ///
-    /// # Arguments
-    /// * `base_score` - Base score from motif
-    /// * `annotated` - Whether the junction is annotated in GTF
-    ///
-    /// # Returns
-    /// Adjusted score with annotation bonus applied
-    pub fn score_annotated_junction(&self, base_score: i32, annotated: bool) -> i32 {
+    /// Annotated junctions score `sjdb_score`; unannotated junctions score `motif_score`.
+    pub fn score_annotated_junction(&self, motif_score: i32, annotated: bool) -> i32 {
         if annotated {
-            base_score + self.sjdb_score
+            self.sjdb_score
         } else {
-            base_score
+            motif_score
         }
     }
 
@@ -959,17 +952,14 @@ mod tests {
             out_filter_score_min_over_lread: 0.66,
         };
 
-        // Annotated junction should get bonus
         let annotated_score = scorer.score_annotated_junction(0, true);
         assert_eq!(annotated_score, 2);
 
-        // Novel junction should not get bonus
         let novel_score = scorer.score_annotated_junction(0, false);
         assert_eq!(novel_score, 0);
 
-        // Bonus applies to any base score
         let annotated_noncanon = scorer.score_annotated_junction(-8, true);
-        assert_eq!(annotated_noncanon, -6); // -8 + 2
+        assert_eq!(annotated_noncanon, 2);
     }
 
     #[test]

src/align/stitch.rs

@@ -1313,9 +1313,10 @@ fn stitch_align_to_transcript(
                     || db.is_annotated(cluster.chr_idx, donor_fwd, acceptor_fwd, 2)
             });
 
-            d_score += motif_score;
             if is_annotated {
                 d_score += scorer.sjdb_score;
+            } else {
+                d_score += motif_score;
             }
 
             new_wt.n_junction += 1;
@@ -3430,4 +3431,39 @@ mod tests {
         bin_start_edge = bin_start_edge.saturating_sub(win_flank_nbins);
         assert_eq!(bin_start_edge, 0, "Flanking should saturate at 0");
     }
+
+    #[test]
+    fn test_junction_score_annotated_uses_sjdb_not_motif() {
+        use crate::align::score::AlignmentScorer;
+
+        let scorer = AlignmentScorer::from_params_minimal();
+
+        for motif_score in [0_i32, scorer.score_gap_gcag, scorer.score_gap_atac] {
+            let baseline: i32 = 100;
+
+            let mut d_score_annot = baseline;
+            let is_annotated = true;
+            if is_annotated {
+                d_score_annot += scorer.sjdb_score;
+            } else {
+                d_score_annot += motif_score;
+            }
+            assert_eq!(d_score_annot, baseline + scorer.sjdb_score);
+
+            let mut d_score_novel = baseline;
+            let is_annotated = false;
+            if is_annotated {
+                d_score_novel += scorer.sjdb_score;
+            } else {
+                d_score_novel += motif_score;
+            }
+            assert_eq!(d_score_novel, baseline + motif_score);
+        }
+
+        let baseline: i32 = 100;
+        let motif_score = scorer.score_gap_gcag;
+        let additive_buggy = baseline + motif_score + scorer.sjdb_score;
+        let replacement_correct = baseline + scorer.sjdb_score;
+        assert_ne!(additive_buggy, replacement_correct);
+    }
 }