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Merged
flying-sheep merged 1 commit into from
May 15, 2026
Merged

chore: enable pedantic lints #56

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241 changes: 119 additions & 122 deletions src/align/read_align.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -749,7 +749,7 @@ pub fn align_paired_read(
combined_seeds.extend(m2_seeds);
// mate_id: positions 0..len1 → mate1(0); positions len1+1.. → RC(mate2)(1).
for s in &mut combined_seeds {
s.mate_id = if s.read_pos < len1 { 0 } else { 1 };
s.mate_id = u8::from(s.read_pos >= len1);
}

// Cluster combined seeds using the combined read length
Expand Down Expand Up @@ -831,135 +831,132 @@ pub fn align_paired_read(
for wt in &wts {
let split_result =
split_combined_wt(wt, len1, len2, stitch_is_reverse, scorer.align_intron_min);
match split_result {
Some((m1_wt, m2_wt)) => {
let (m1_read_slice, m1_orig_rev, m2_read_slice, m2_orig_rev) =
if stitch_is_reverse {
// stitch_read = [mate2(0..len2) | SPACER | RC(mate1)(len2+1..)]
(
&stitch_read[len2 + 1..], // RC(mate1_seq)
true, // mate1 5' at right in RC
&stitch_read[..len2], // mate2_seq
false, // mate2 5' at left
)
} else {
// stitch_read = [mate1(0..len1) | SPACER | RC(mate2)(len1+1..)]
(
&stitch_read[..len1], // mate1_seq
false, // mate1 5' at left
&stitch_read[len1 + 1..], // RC(mate2_seq)
true, // mate2 5' at right in RC
)
};

// Suppress inner-side extensions for each mate.
// Inner = 3' end: right for forward (orig_is_rev=false), left for reverse.
let Some(mut t1) = finalize_transcript(
&m1_wt,
m1_read_slice,
if let Some((m1_wt, m2_wt)) = split_result {
let (m1_read_slice, m1_orig_rev, m2_read_slice, m2_orig_rev) = if stitch_is_reverse
{
// stitch_read = [mate2(0..len2) | SPACER | RC(mate1)(len2+1..)]
(
&stitch_read[len2 + 1..], // RC(mate1_seq)
true, // mate1 5' at right in RC
&stitch_read[..len2], // mate2_seq
false, // mate2 5' at left
)
} else {
// stitch_read = [mate1(0..len1) | SPACER | RC(mate2)(len1+1..)]
(
&stitch_read[..len1], // mate1_seq
false, // mate1 5' at left
&stitch_read[len1 + 1..], // RC(mate2_seq)
true, // mate2 5' at right in RC
)
};

// Suppress inner-side extensions for each mate.
// Inner = 3' end: right for forward (orig_is_rev=false), left for reverse.
let Some(mut t1) = finalize_transcript(
&m1_wt,
m1_read_slice,
index,
&scorer,
&stitch_cluster,
m1_orig_rev,
m1_orig_rev, // no_left_ext = inner for reverse (orig_is_rev=true)
!m1_orig_rev, // no_right_ext = inner for forward (orig_is_rev=false)
) else {
continue;
};
let Some(mut t2) = finalize_transcript(
&m2_wt,
m2_read_slice,
index,
&scorer,
&stitch_cluster,
m2_orig_rev,
m2_orig_rev, // no_left_ext = inner for reverse (orig_is_rev=true)
!m2_orig_rev, // no_right_ext = inner for forward (orig_is_rev=false)
) else {
continue;
};

if stitch_is_reverse {
t1.is_reverse = true;
t2.is_reverse = false;
} else {
t1.is_reverse = false;
t2.is_reverse = true;
}
t1.read_seq = mate1_seq.to_vec();
t2.read_seq = mate2_seq.to_vec();

if params.chim_segment_min > 0 {
all_m1_transcripts.push(t1.clone());
all_m2_transcripts.push(t2.clone());
}

let combined_span =
t1.genome_end.max(t2.genome_end) - t1.genome_start.min(t2.genome_start);
let combined_wt_score = wt.score + scorer.genomic_length_penalty(combined_span);

if let Some(pair) = try_pair_transcripts(
&t1,
&t2,
len1,
len2,
params,
combined_score_threshold,
combined_wt_score,
) {
joint_pairs.push(pair);
}
} else {
// Single-mate WT: save for half-mapped fallback
let all_m1 = wt.exons.iter().all(|e| e.mate_id == 0);
let all_m2 = wt.exons.iter().all(|e| e.mate_id == 1);
if all_m1 {
let (read_slice, orig_rev) = if stitch_is_reverse {
(&stitch_read[len2 + 1..], true)
} else {
(&stitch_read[..len1], false)
};
if let Some(mut t) = finalize_transcript(
wt,
read_slice,
index,
&scorer,
&stitch_cluster,
m1_orig_rev,
m1_orig_rev, // no_left_ext = inner for reverse (orig_is_rev=true)
!m1_orig_rev, // no_right_ext = inner for forward (orig_is_rev=false)
) else {
continue;
orig_rev,
false,
false,
) {
t.is_reverse = stitch_is_reverse;
t.read_seq = mate1_seq.to_vec();
if params.chim_segment_min > 0 {
all_m1_transcripts.push(t.clone());
}
single_mate1_transcripts.push(t);
}
} else if all_m2 {
let (read_slice, orig_rev) = if stitch_is_reverse {
(&stitch_read[..len2], false)
} else {
(&stitch_read[len1 + 1..], true)
};
let Some(mut t2) = finalize_transcript(
&m2_wt,
m2_read_slice,
if let Some(mut t) = finalize_transcript(
wt,
read_slice,
index,
&scorer,
&stitch_cluster,
m2_orig_rev,
m2_orig_rev, // no_left_ext = inner for reverse (orig_is_rev=true)
!m2_orig_rev, // no_right_ext = inner for forward (orig_is_rev=false)
) else {
continue;
};

if stitch_is_reverse {
t1.is_reverse = true;
t2.is_reverse = false;
} else {
t1.is_reverse = false;
t2.is_reverse = true;
}
t1.read_seq = mate1_seq.to_vec();
t2.read_seq = mate2_seq.to_vec();

if params.chim_segment_min > 0 {
all_m1_transcripts.push(t1.clone());
all_m2_transcripts.push(t2.clone());
}

let combined_span =
t1.genome_end.max(t2.genome_end) - t1.genome_start.min(t2.genome_start);
let combined_wt_score = wt.score + scorer.genomic_length_penalty(combined_span);

if let Some(pair) = try_pair_transcripts(
&t1,
&t2,
len1,
len2,
params,
combined_score_threshold,
combined_wt_score,
orig_rev,
false,
false,
) {
joint_pairs.push(pair);
}
}
None => {
// Single-mate WT: save for half-mapped fallback
let all_m1 = wt.exons.iter().all(|e| e.mate_id == 0);
let all_m2 = wt.exons.iter().all(|e| e.mate_id == 1);
if all_m1 {
let (read_slice, orig_rev) = if stitch_is_reverse {
(&stitch_read[len2 + 1..], true)
} else {
(&stitch_read[..len1], false)
};
if let Some(mut t) = finalize_transcript(
wt,
read_slice,
index,
&scorer,
&stitch_cluster,
orig_rev,
false,
false,
) {
t.is_reverse = stitch_is_reverse;
t.read_seq = mate1_seq.to_vec();
if params.chim_segment_min > 0 {
all_m1_transcripts.push(t.clone());
}
single_mate1_transcripts.push(t);
}
} else if all_m2 {
let (read_slice, orig_rev) = if stitch_is_reverse {
(&stitch_read[..len2], false)
} else {
(&stitch_read[len1 + 1..], true)
};
if let Some(mut t) = finalize_transcript(
wt,
read_slice,
index,
&scorer,
&stitch_cluster,
orig_rev,
false,
false,
) {
t.is_reverse = !stitch_is_reverse;
t.read_seq = mate2_seq.to_vec();
if params.chim_segment_min > 0 {
all_m2_transcripts.push(t.clone());
}
single_mate2_transcripts.push(t);
t.is_reverse = !stitch_is_reverse;
t.read_seq = mate2_seq.to_vec();
if params.chim_segment_min > 0 {
all_m2_transcripts.push(t.clone());
}
single_mate2_transcripts.push(t);
}
}
}
Expand Down Expand Up @@ -2144,7 +2141,7 @@ mod tests {
assert_eq!(items[4], (40, 4));
// Tied prefix contains the original three items in some order.
let mut top: Vec<u32> = items[..3].iter().map(|t| t.1).collect();
top.sort();
top.sort_unstable();
assert_eq!(top, vec![0, 1, 2]);
}

Expand Down
58 changes: 31 additions & 27 deletions src/align/score.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -224,35 +224,39 @@ impl AlignmentScorer {
// Score the net indel portion
(gg, rg) if gg > 0 && rg > 0 => {
let excess = gg - rg;
if excess > 0 {
let del_len = excess as u32;
if del_len >= self.align_intron_min && del_len <= self.align_intron_max {
let rc_donor = genome_pos + rg as u64;
let donor = if is_reverse {
n_genome - rc_donor - del_len as u64
match excess {
1.. => {
let del_len = excess as u32;
if del_len >= self.align_intron_min && del_len <= self.align_intron_max {
let rc_donor = genome_pos + rg as u64;
let donor = if is_reverse {
n_genome - rc_donor - del_len as u64
} else {
rc_donor
};
let motif = self.detect_splice_motif(donor, del_len, genome);
let score = self.score_splice_junction(&motif);
(
score,
GapType::SpliceJunction {
intron_len: del_len,
motif,
},
)
} else {
rc_donor
};
let motif = self.detect_splice_motif(donor, del_len, genome);
let score = self.score_splice_junction(&motif);
(
score,
GapType::SpliceJunction {
intron_len: del_len,
motif,
},
)
} else {
let score = self.score_del_open + self.score_del_base * del_len as i32;
(score, GapType::Deletion(del_len))
let score = self.score_del_open + self.score_del_base * del_len as i32;
(score, GapType::Deletion(del_len))
}
}
..=-1 => {
let ins_len = (-excess) as u32;
let score = self.score_ins_open + self.score_ins_base * ins_len as i32;
(score, GapType::Insertion(ins_len))
}
0 => {
// Equal gaps: no net indel
(0, GapType::Deletion(0))
}
} else if excess < 0 {
let ins_len = (-excess) as u32;
let score = self.score_ins_open + self.score_ins_base * ins_len as i32;
(score, GapType::Insertion(ins_len))
} else {
// Equal gaps: no net indel
(0, GapType::Deletion(0))
}
}
// Other cases (negative gaps, etc.)
Expand Down
15 changes: 6 additions & 9 deletions src/align/seed.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -366,14 +366,11 @@ fn find_seed_at_position(
.sa_index
.hierarchical_lookup(kmer_idx, actual_len as u32, n_sa);

let (sa_start, sa_end, matched_level, bounds_tight) = match result {
Some(r) => r,
None => {
return Ok(MmpResult {
seed: None,
advance: 1,
});
}
let Some((sa_start, sa_end, matched_level, bounds_tight)) = result else {
return Ok(MmpResult {
seed: None,
advance: 1,
});
};

if sa_start >= sa_end {
Expand Down Expand Up @@ -440,7 +437,7 @@ fn find_seed_at_position(
/// Overflow-safe median of two unsigned integers.
/// Equivalent to STAR's medianUint2: a/2 + b/2 + (a%2 + b%2)/2
fn median_uint2(a: usize, b: usize) -> usize {
a / 2 + b / 2 + (a % 2 + b % 2) / 2
a / 2 + b / 2 + usize::midpoint(a % 2, b % 2)
}

/// Compare read to genome at a specific SA position, starting from offset l_start.
Expand Down
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