chore: clippy borrow and infallible functions (#60)

Author: flying-sheep

src/align/read_align.rs

@@ -311,7 +311,7 @@ pub fn align_read(
             junction_db,
             params.align_transcripts_per_window_nmax,
             debug_name,
-        )?;
+        );
         if debug_read {
             eprintln!(
                 "[DEBUG {}] Cluster[{}]: {} transcripts from DP",
@@ -814,7 +814,7 @@ pub fn align_paired_read(
             params.align_transcripts_per_window_nmax,
             params.align_mates_gap_max.into(),
             debug_name,
-        )?;
+        );
 
         for wt in &wts {
             let split_result =

src/align/score.rs

@@ -206,7 +206,7 @@ impl AlignmentScorer {
                         genome_pos
                     };
                     let motif = self.detect_splice_motif(donor, len, genome);
-                    let score = self.score_splice_junction(&motif);
+                    let score = self.score_splice_junction(motif);
                     (
                         score,
                         GapType::SpliceJunction {
@@ -235,7 +235,7 @@ impl AlignmentScorer {
                                 rc_donor
                             };
                             let motif = self.detect_splice_motif(donor, del_len, genome);
-                            let score = self.score_splice_junction(&motif);
+                            let score = self.score_splice_junction(motif);
                             (
                                 score,
                                 GapType::SpliceJunction {
@@ -389,7 +389,7 @@ impl AlignmentScorer {
                     donor_sa
                 };
                 let motif = self.detect_splice_motif(donor_fwd, del as u32, genome);
-                let motif_score = self.score_splice_junction(&motif);
+                let motif_score = self.score_splice_junction(motif);
                 let score2 = score1 + motif_score;
 
                 if score2 > max_score2 {
@@ -493,7 +493,7 @@ impl AlignmentScorer {
                     donor_sa
                 };
                 best_motif = self.detect_splice_motif(donor_fwd, del as u32, genome);
-                best_motif_score = self.score_splice_junction(&best_motif);
+                best_motif_score = self.score_splice_junction(best_motif);
             }
         }
 
@@ -518,7 +518,7 @@ impl AlignmentScorer {
     }
 
     /// Score a splice junction based on motif
-    pub(crate) fn score_splice_junction(&self, motif: &SpliceMotif) -> i32 {
+    pub(crate) fn score_splice_junction(&self, motif: SpliceMotif) -> i32 {
         match motif {
             SpliceMotif::GtAg | SpliceMotif::CtAc => self.score_gap,
             SpliceMotif::GcAg | SpliceMotif::CtGc => self.score_gap_gcag,
@@ -695,7 +695,7 @@ mod tests {
         let motif = scorer.detect_splice_motif(2, 12, &genome);
         assert_eq!(motif, SpliceMotif::GtAg);
 
-        let score = scorer.score_splice_junction(&motif);
+        let score = scorer.score_splice_junction(motif);
         assert_eq!(score, 0); // Canonical
     }
 
@@ -738,7 +738,7 @@ mod tests {
         let motif = scorer.detect_splice_motif(2, 12, &genome);
         assert_eq!(motif, SpliceMotif::GcAg);
 
-        let score = scorer.score_splice_junction(&motif);
+        let score = scorer.score_splice_junction(motif);
         assert_eq!(score, -4);
     }
 
@@ -781,7 +781,7 @@ mod tests {
         let motif = scorer.detect_splice_motif(2, 12, &genome);
         assert_eq!(motif, SpliceMotif::AtAc);
 
-        let score = scorer.score_splice_junction(&motif);
+        let score = scorer.score_splice_junction(motif);
         assert_eq!(score, -8);
     }
 
@@ -822,7 +822,7 @@ mod tests {
         let motif = scorer.detect_splice_motif(2, 12, &genome);
         assert_eq!(motif, SpliceMotif::NonCanonical);
 
-        let score = scorer.score_splice_junction(&motif);
+        let score = scorer.score_splice_junction(motif);
         assert_eq!(score, -8);
     }
 
@@ -1017,7 +1017,7 @@ mod tests {
         let motif = scorer.detect_splice_motif(2, 12, &genome_ctac);
         assert_eq!(motif, SpliceMotif::CtAc);
         // Should score same as canonical GT-AG
-        assert_eq!(scorer.score_splice_junction(&motif), 0);
+        assert_eq!(scorer.score_splice_junction(motif), 0);
 
         // CT-GC motif: (1,3,2,1) — reverse complement of GC-AG
         let seq_ctgc = vec![
@@ -1030,7 +1030,7 @@ mod tests {
         let genome_ctgc = make_test_genome(&seq_ctgc);
         let motif = scorer.detect_splice_motif(2, 12, &genome_ctgc);
         assert_eq!(motif, SpliceMotif::CtGc);
-        assert_eq!(scorer.score_splice_junction(&motif), -4);
+        assert_eq!(scorer.score_splice_junction(motif), -4);
 
         // GT-AT motif: (2,3,0,3) — reverse complement of AT-AC
         let seq_gtat = vec![
@@ -1043,7 +1043,7 @@ mod tests {
         let genome_gtat = make_test_genome(&seq_gtat);
         let motif = scorer.detect_splice_motif(2, 12, &genome_gtat);
         assert_eq!(motif, SpliceMotif::GtAt);
-        assert_eq!(scorer.score_splice_junction(&motif), -8);
+        assert_eq!(scorer.score_splice_junction(motif), -8);
     }
 
     #[test]

src/align/seed.rs

@@ -69,7 +69,7 @@ impl Seed {
             false,
             debug_name,
             &mut seeds,
-        )?;
+        );
 
         // Cap check between directions (STAR: seedPerReadNmax applies across both)
         if seeds.len() >= params.seed_per_read_nmax {
@@ -87,7 +87,7 @@ impl Seed {
             true,
             debug_name,
             &mut seeds,
-        )?;
+        );
 
         // STAR's storeAligns dedup: same rStart + same Length → skip duplicate.
         // Multiple istart chains can find the same (read_pos, length, direction) seed.
@@ -217,7 +217,7 @@ fn search_direction_sparse(
     is_rc: bool,
     debug_name: &str,
     seeds: &mut Vec<Seed>,
-) -> Result<(), Error> {
+) {
     let read_len = read_seq.len();
 
     // STAR (ReadAlign_mapOneRead.cpp lines 41-42):
@@ -262,7 +262,7 @@ fn search_direction_sparse(
             }
 
             let result =
-                find_seed_at_position(read_seq, pos, index, min_seed_length, false, params)?;
+                find_seed_at_position(read_seq, pos, index, min_seed_length, false, params);
 
             if !debug_name.is_empty() {
                 let dir = if is_rc { "RC" } else { "FWD" };
@@ -292,16 +292,14 @@ fn search_direction_sparse(
                 seeds.push(seed);
 
                 if seeds.len() >= params.seed_per_read_nmax {
-                    return Ok(());
+                    return;
                 }
             }
 
             pos += result.advance; // Always advance by MMP length (matches STAR)
             // Remaining-length check at loop top: stop when < seedMapMin bases remain
         }
     }
-
-    Ok(())
 }
 
 /// Find a seed starting at a specific position in the read.
@@ -317,23 +315,23 @@ fn find_seed_at_position(
     min_seed_length: usize,
     is_reverse: bool,
     params: &Parameters,
-) -> Result<MmpResult, Error> {
+) -> MmpResult {
     if read_pos >= read_seq.len() {
-        return Ok(MmpResult {
+        return MmpResult {
             seed: None,
             advance: 1,
-        });
+        };
     }
 
     // Extract k-mer for SAindex lookup
     let sa_nbases = index.sa_index.nbases as usize;
     let remaining = read_seq.len() - read_pos;
 
     if remaining < min_seed_length {
-        return Ok(MmpResult {
+        return MmpResult {
             seed: None,
             advance: 1,
-        });
+        };
     }
 
     // Build k-mer for SAindex lookup, stopping at first N base
@@ -351,10 +349,10 @@ fn find_seed_at_position(
     }
 
     if actual_len == 0 {
-        return Ok(MmpResult {
+        return MmpResult {
             seed: None,
             advance: 1,
-        }); // First base is N
+        }; // First base is N
     }
 
     // Hierarchical SAindex lookup (STAR's maxMappableLength2strands approach).
@@ -367,17 +365,17 @@ fn find_seed_at_position(
         .hierarchical_lookup(kmer_idx, actual_len as u32, n_sa);
 
     let Some((sa_start, sa_end, matched_level, bounds_tight)) = result else {
-        return Ok(MmpResult {
+        return MmpResult {
             seed: None,
             advance: 1,
-        });
+        };
     };
 
     if sa_start >= sa_end {
-        return Ok(MmpResult {
+        return MmpResult {
             seed: None,
             advance: 1,
-        });
+        };
     }
 
     // STAR short-circuit (maxMappableLength2strands.cpp):
@@ -407,14 +405,14 @@ fn find_seed_at_position(
     // Uses narrowed range (accurate loci count, not overestimated k-mer range)
     let n_loci = narrowed_end - narrowed_start;
     if n_loci > params.seed_multimap_nmax {
-        return Ok(MmpResult {
+        return MmpResult {
             seed: None,
             advance,
-        });
+        };
     }
 
     if match_length >= min_seed_length {
-        Ok(MmpResult {
+        MmpResult {
             seed: Some(Seed {
                 read_pos,
                 length: match_length,
@@ -425,12 +423,12 @@ fn find_seed_at_position(
                 mate_id: 2, // Single-end default
             }),
             advance,
-        })
+        }
     } else {
-        Ok(MmpResult {
+        MmpResult {
             seed: None,
             advance,
-        })
+        }
     }
 }
 
@@ -1023,16 +1021,15 @@ mod tests {
         // Count how many seeds dense would produce (every position that has a match)
         let mut dense_count = 0;
         for read_pos in 0..read.len() {
-            let result = find_seed_at_position(&read, read_pos, &index, 4, false, &params).unwrap();
+            let result = find_seed_at_position(&read, read_pos, &index, 4, false, &params);
             if result.seed.is_some() {
                 dense_count += 1;
             }
         }
         // Also count R→L dense seeds
         let rc_read = reverse_complement_read(&read);
         for rc_pos in 0..rc_read.len() {
-            let result =
-                find_seed_at_position(&rc_read, rc_pos, &index, 4, false, &params).unwrap();
+            let result = find_seed_at_position(&rc_read, rc_pos, &index, 4, false, &params);
             if result.seed.is_some() {
                 dense_count += 1;
             }

src/align/stitch.rs

@@ -2,7 +2,6 @@
 use crate::align::score::AlignmentScorer;
 use crate::align::seed::Seed;
 use crate::align::transcript::{CigarOpExt as _, Transcript};
-use crate::error::Error;
 use crate::index::GenomeIndex;
 use noodles::sam::alignment::record::cigar;
 
@@ -1500,7 +1499,7 @@ pub fn stitch_seeds(
     read_seq: &[u8],
     index: &GenomeIndex,
     scorer: &AlignmentScorer,
-) -> Result<Vec<Transcript>, Error> {
+) -> Vec<Transcript> {
     stitch_seeds_with_jdb(cluster, read_seq, index, scorer, None, 1)
 }
 
@@ -1519,7 +1518,7 @@ pub fn stitch_seeds_with_jdb(
     scorer: &AlignmentScorer,
     junction_db: Option<&crate::junction::SpliceJunctionDb>,
     max_transcripts_per_window: usize,
-) -> Result<Vec<Transcript>, Error> {
+) -> Vec<Transcript> {
     stitch_seeds_with_jdb_debug(
         cluster,
         read_seq,
@@ -2469,7 +2468,7 @@ pub(crate) fn stitch_seeds_with_jdb_debug(
     junction_db: Option<&crate::junction::SpliceJunctionDb>,
     max_transcripts_per_window: usize,
     debug_read_name: &str,
-) -> Result<Vec<Transcript>, Error> {
+) -> Vec<Transcript> {
     let (working_transcripts, stitch_cluster, stitch_is_reverse, stitch_read) = stitch_seeds_core(
         cluster,
         read_seq,
@@ -2479,7 +2478,7 @@ pub(crate) fn stitch_seeds_with_jdb_debug(
         max_transcripts_per_window,
         0,
         debug_read_name,
-    )?;
+    );
 
     // Finalize working transcripts → Transcript (filtering by overhang+repeat check)
     let mut transcripts: Vec<Transcript> = Vec::with_capacity(working_transcripts.len());
@@ -2583,7 +2582,7 @@ pub(crate) fn stitch_seeds_with_jdb_debug(
     });
     transcripts.truncate(max_transcripts_per_window);
 
-    Ok(transcripts)
+    transcripts
 }
 
 /// Shared core: preprocessing + recursive stitcher, returns working transcripts + context.
@@ -2597,7 +2596,7 @@ pub(crate) fn stitch_seeds_core(
     max_transcripts_per_window: usize,
     align_mates_gap_max: u64,
     debug_read_name: &str,
-) -> Result<(Vec<WorkingTranscript>, SeedCluster, bool, Vec<u8>), Error> {
+) -> (Vec<WorkingTranscript>, SeedCluster, bool, Vec<u8>) {
     let debug = !debug_read_name.is_empty();
 
     // Include ALL seeds (anchor and non-anchor) in the stitcher.
@@ -2730,12 +2729,12 @@ pub(crate) fn stitch_seeds_core(
     }
 
     if wa_entries.is_empty() {
-        return Ok((
+        return (
             Vec::new(),
             stitch_cluster,
             stitch_is_reverse,
             stitch_read_owned,
-        ));
+        );
     }
 
     if debug {
@@ -2924,12 +2923,12 @@ pub(crate) fn stitch_seeds_core(
         );
     }
 
-    Ok((
+    (
         working_transcripts,
         stitch_cluster,
         stitch_is_reverse,
         stitch_read_owned,
-    ))
+    )
 }
 
 #[cfg(test)]