Integration/pr batch 1

Cargo.toml

@@ -41,6 +41,7 @@ dashmap = "6"
 chrono = "0.4"
 rand = "0.10"
 tempfile = "3"
+bitflags = { version = "2.11.1", features = ["std"] }
 
 [dev-dependencies]
 assert_cmd = "2"

src/align/read_align.rs

@@ -1065,10 +1065,11 @@ pub fn align_paired_read(
 
     // Step 3: TooManyLoci check (post-dedup, matching STAR's ordering: multMapSelect → dedup → TooManyLoci).
     if joint_pairs.len() > params.out_filter_multimap_nmax as usize {
+        let n_loci = joint_pairs.len();
         return Ok((
             Vec::new(),
             pe_chimeric,
-            0,
+            n_loci,
             Some(UnmappedReason::TooManyLoci),
         ));
     }
@@ -1336,7 +1337,7 @@ fn check_proper_pair(
 }
 
 /// Calculate signed insert size (TLEN)
-fn calculate_insert_size(mate1_trans: &Transcript, mate2_trans: &Transcript) -> i32 {
+pub(crate) fn calculate_insert_size(mate1_trans: &Transcript, mate2_trans: &Transcript) -> i32 {
     // STAR outSAMtlen=1 (default): tlen is computed from the combined PE transcript span,
     // not from max/min of individual mate endpoints.
     //
@@ -1498,6 +1499,7 @@ mod tests {
         let genome = Genome {
             sequence,
             n_genome,
+            n_genome_real: n_genome,
             n_chr_real: 1,
             chr_name: vec!["chr1".to_string()],
             chr_length: vec![10],
@@ -1528,6 +1530,7 @@ mod tests {
             junction_db: crate::junction::SpliceJunctionDb::empty(),
             transcriptome: None,
             prepared_junctions: Vec::new(),
+            sjdb_overhang: 0,
         }
     }
 

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
         }
     }
 
@@ -643,6 +636,7 @@ mod tests {
         Genome {
             sequence,
             n_genome,
+            n_genome_real: n_genome,
             n_chr_real: 1,
             chr_name: vec!["chr1".to_string()],
             chr_length: vec![seq.len() as u64],
@@ -965,17 +959,14 @@ 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]