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refactor: drop Transcript::read_seq, a public field nothing reads #170

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2c67fa6
refactor: drop Transcript::read_seq, which nothing ever reads
BenjaminDEMAILLE Jul 30, 2026
fb26c31
docs(changelog): record the Transcript::read_seq removal
BenjaminDEMAILLE Jul 30, 2026
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -131,3 +131,9 @@ Sections commonly used: Features, Bug fixes, Other changes.
needs random access to the SA in RAM.

Initial release of Rust rewrite of STAR.
### Other changes

- Removed `Transcript::read_seq`, a public field that was filled with a
copy of the read at every finalised alignment and never read. **API
removal.** Output is unchanged.

3 changes: 0 additions & 3 deletions src/align/pe_overlap.rs
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Expand Up @@ -364,7 +364,6 @@ pub fn convert_merged_transcript_to_pe(
n_junction,
junction_motifs: out_junctions[i].iter().map(|(m, _)| *m).collect(),
junction_annotated: out_junctions[i].iter().map(|(_, a)| *a).collect(),
read_seq: mate_seqs[i].to_vec(),
});
}

Expand Down Expand Up @@ -479,7 +478,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: merge.merged.clone(),
};

let scorer = AlignmentScorer::from_params_minimal();
Expand Down Expand Up @@ -552,7 +550,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: merge.merged.clone(),
};

let scorer = AlignmentScorer::from_params_minimal();
Expand Down
18 changes: 0 additions & 18 deletions src/align/read_align.rs
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Expand Up @@ -114,7 +114,6 @@ impl PairedAlignment {
n_junction: m1.n_junction + m2.n_junction,
junction_motifs: Vec::new(),
junction_annotated: Vec::new(),
read_seq: Vec::new(),
}
}
}
Expand Down Expand Up @@ -889,8 +888,6 @@ pub fn align_paired_read(
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());
Expand Down Expand Up @@ -934,7 +931,6 @@ pub fn align_paired_read(
0, // mate1
) {
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());
}
Expand All @@ -958,7 +954,6 @@ pub fn align_paired_read(
1, // mate2
) {
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());
}
Expand Down Expand Up @@ -1641,7 +1636,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![],
};
let pair = PairedAlignment {
mate1_transcript: make_tr(1000, 1100, 0, 100),
Expand Down Expand Up @@ -1803,7 +1797,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![0; 100],
};

let t2 = Transcript {
Expand All @@ -1825,7 +1818,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![0; 100],
};

// Distance = 300bp, within default limit (auto mode = unlimited)
Expand Down Expand Up @@ -1859,7 +1851,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![0; 100],
};

let t2 = Transcript {
Expand All @@ -1881,7 +1872,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![0; 100],
};

// Distance = 400bp, exceeds limit of 100bp
Expand Down Expand Up @@ -1913,7 +1903,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![0; 100],
};

let t2 = Transcript {
Expand All @@ -1935,7 +1924,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![0; 100],
};

let tlen = calculate_insert_size(&t1, &t2);
Expand Down Expand Up @@ -1968,7 +1956,6 @@ mod tests {
n_junction: 2,
junction_motifs: vec![SpliceMotif::GtAg, SpliceMotif::CtAc], // +strand and -strand
junction_annotated: vec![],
read_seq: vec![0; 100],
};

// Create a transcript with consistent strand motifs (all + strand)
Expand All @@ -1991,7 +1978,6 @@ mod tests {
n_junction: 2,
junction_motifs: vec![SpliceMotif::GtAg, SpliceMotif::GcAg], // both + strand
junction_annotated: vec![],
read_seq: vec![0; 100],
};

// Note: STAR's RemoveInconsistentStrands filters transcripts where
Expand Down Expand Up @@ -2070,7 +2056,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![0; 100],
};

let t2 = Transcript {
Expand All @@ -2092,7 +2077,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![0; 100],
};

let tlen = calculate_insert_size(&t1, &t2);
Expand Down Expand Up @@ -2133,7 +2117,6 @@ mod tests {
n_junction: 1,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![0; 100],
};

// Case 1: NonCanonical + unannotated → should be filtered
Expand Down Expand Up @@ -2219,7 +2202,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![0; 100],
};

// Test BothMapped variant
Expand Down
2 changes: 0 additions & 2 deletions src/align/stitch.rs
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Expand Up @@ -2155,7 +2155,6 @@ pub(crate) fn finalize_transcript(
n_junction: wt.n_junction,
junction_motifs: wt.junction_motifs.clone(),
junction_annotated: wt.junction_annotated.clone(),
read_seq: read_seq.to_vec(),
})
}

Expand Down Expand Up @@ -2695,7 +2694,6 @@ pub(crate) fn stitch_seeds_with_jdb_debug(
// Restore original reverse-strand flag and read sequence for SAM output.
if stitch_is_reverse {
transcript.is_reverse = true;
transcript.read_seq = read_seq.to_vec();
}
transcripts.push(transcript);
}
Expand Down
7 changes: 0 additions & 7 deletions src/align/transcript.rs
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Expand Up @@ -29,8 +29,6 @@ pub struct Transcript {
pub junction_motifs: Vec<crate::align::score::SpliceMotif>,
/// Whether each junction is annotated in the GTF (for jM +20 offset)
pub junction_annotated: Vec<bool>,
/// Original read sequence
pub read_seq: Vec<u8>,
}

/// An exon segment in a transcript.
Expand Down Expand Up @@ -182,7 +180,6 @@ mod tests {
n_junction: 1,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![],
};

assert_eq!(transcript.cigar_string(), "50M100N50M");
Expand Down Expand Up @@ -230,7 +227,6 @@ mod tests {
n_junction: 1,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![0; 100],
};

// Query: 45 + 3 + 2 + 50 = 100
Expand Down Expand Up @@ -279,7 +275,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![],
};

let [left, right] = transcript.count_soft_clips();
Expand All @@ -303,7 +298,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![],
};

let [left, right] = transcript.count_soft_clips();
Expand All @@ -327,7 +321,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![],
};

let [left, right] = transcript.count_soft_clips();
Expand Down
3 changes: 0 additions & 3 deletions src/chimeric/detect.rs
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Expand Up @@ -1090,7 +1090,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![0u8; read_len],
}
}

Expand Down Expand Up @@ -1210,7 +1209,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![],
};
assert!(transcript_to_segment(&t).is_err());
}
Expand Down Expand Up @@ -1354,7 +1352,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![0u8; read_len],
}
}

Expand Down
1 change: 0 additions & 1 deletion src/io/bam.rs
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Expand Up @@ -550,7 +550,6 @@ mod tests {
n_junction: 0,
junction_motifs: vec![],
junction_annotated: vec![],
read_seq: vec![],
};

let read_name = "read1";
Expand Down
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