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flying-sheep merged 1 commit into from
May 16, 2026
Merged

chore: clippy borrow and infallible functions #60

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4 changes: 2 additions & 2 deletions src/align/read_align.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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 =
Expand Down
24 changes: 12 additions & 12 deletions src/align/score.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -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 {
Expand Down Expand Up @@ -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 {
Expand Down Expand Up @@ -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 {
Expand Down Expand Up @@ -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);
}
}

Expand All @@ -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,
Expand Down Expand Up @@ -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
}

Expand Down Expand Up @@ -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);
}

Expand Down Expand Up @@ -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);
}

Expand Down Expand Up @@ -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);
}

Expand Down Expand Up @@ -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![
Expand All @@ -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![
Expand All @@ -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]
Expand Down
51 changes: 24 additions & 27 deletions src/align/seed.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -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 {
Expand All @@ -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.
Expand Down Expand Up @@ -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):
Expand Down Expand Up @@ -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" };
Expand Down Expand Up @@ -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.
Expand All @@ -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
Expand All @@ -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).
Expand All @@ -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):
Expand Down Expand Up @@ -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,
Expand All @@ -425,12 +423,12 @@ fn find_seed_at_position(
mate_id: 2, // Single-end default
}),
advance,
})
}
} else {
Ok(MmpResult {
MmpResult {
seed: None,
advance,
})
}
}
}

Expand Down Expand Up @@ -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;
}
Expand Down
21 changes: 10 additions & 11 deletions src/align/stitch.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -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;

Expand Down Expand Up @@ -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)
}

Expand All @@ -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,
Expand Down Expand Up @@ -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,
Expand All @@ -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());
Expand Down Expand Up @@ -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.
Expand All @@ -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.
Expand Down Expand Up @@ -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 {
Expand Down Expand Up @@ -2924,12 +2923,12 @@ pub(crate) fn stitch_seeds_core(
);
}

Ok((
(
working_transcripts,
stitch_cluster,
stitch_is_reverse,
stitch_read_owned,
))
)
}

#[cfg(test)]
Expand Down
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