chore: apply cargo fmt

Fixes formatting drift inherited from main. No semantic changes.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: ewels

src/align/stitch.rs

@@ -2407,7 +2407,6 @@ pub(crate) fn stitch_seeds_with_jdb_debug(
     Ok(transcripts)
 }
 
-
 /// Shared core: preprocessing + recursive stitcher, returns working transcripts + context.
 #[allow(clippy::too_many_arguments)]
 fn stitch_seeds_core(
@@ -2750,8 +2749,6 @@ fn stitch_seeds_core(
     ))
 }
 
-
-
 #[cfg(test)]
 mod tests {
     use super::*;

src/lib.rs

@@ -144,7 +144,10 @@ fn align_reads(params: &Parameters) -> anyhow::Result<()> {
     let quant_ctx: Option<std::sync::Arc<crate::quant::QuantContext>> =
         if params.quant_gene_counts() {
             let gtf_path = params.sjdb_gtf_file.as_ref().unwrap();
-            info!("quantMode GeneCounts: building gene annotation from {}", gtf_path.display());
+            info!(
+                "quantMode GeneCounts: building gene annotation from {}",
+                gtf_path.display()
+            );
             let ctx = crate::quant::QuantContext::build(gtf_path, &index.genome)?;
             Some(std::sync::Arc::new(ctx))
         } else {
@@ -223,8 +226,22 @@ fn run_single_pass(
 
             // Route to single-end or paired-end mode
             match params.read_files_in.len() {
-                1 => align_reads_single_end(params, index, &mut writer, &stats, &sj_stats, quant.as_ref()),
-                2 => align_reads_paired_end(params, index, &mut writer, &stats, &sj_stats, quant.as_ref()),
+                1 => align_reads_single_end(
+                    params,
+                    index,
+                    &mut writer,
+                    &stats,
+                    &sj_stats,
+                    quant.as_ref(),
+                ),
+                2 => align_reads_paired_end(
+                    params,
+                    index,
+                    &mut writer,
+                    &stats,
+                    &sj_stats,
+                    quant.as_ref(),
+                ),
                 n => anyhow::bail!("Invalid number of read files: {} (expected 1 or 2)", n),
             }?;
         }
@@ -241,8 +258,22 @@ fn run_single_pass(
 
             // Route to single-end or paired-end mode (same functions as SAM, generic!)
             match params.read_files_in.len() {
-                1 => align_reads_single_end(params, index, &mut writer, &stats, &sj_stats, quant.as_ref()),
-                2 => align_reads_paired_end(params, index, &mut writer, &stats, &sj_stats, quant.as_ref()),
+                1 => align_reads_single_end(
+                    params,
+                    index,
+                    &mut writer,
+                    &stats,
+                    &sj_stats,
+                    quant.as_ref(),
+                ),
+                2 => align_reads_paired_end(
+                    params,
+                    index,
+                    &mut writer,
+                    &stats,
+                    &sj_stats,
+                    quant.as_ref(),
+                ),
                 n => anyhow::bail!("Invalid number of read files: {} (expected 1 or 2)", n),
             }?;
 
@@ -345,8 +376,22 @@ fn run_pass1(
 
     // Align reads (single-end or paired-end); no quant counting in pass 1
     match params.read_files_in.len() {
-        1 => align_reads_single_end(&params_pass1, index, &mut null_writer, &stats, &sj_stats, None)?,
-        2 => align_reads_paired_end(&params_pass1, index, &mut null_writer, &stats, &sj_stats, None)?,
+        1 => align_reads_single_end(
+            &params_pass1,
+            index,
+            &mut null_writer,
+            &stats,
+            &sj_stats,
+            None,
+        )?,
+        2 => align_reads_paired_end(
+            &params_pass1,
+            index,
+            &mut null_writer,
+            &stats,
+            &sj_stats,
+            None,
+        )?,
         n => anyhow::bail!("Invalid number of read files: {} (expected 1 or 2)", n),
     }
 
@@ -572,7 +617,8 @@ fn align_reads_single_end<W: AlignmentWriter>(
 
                 // Gene-level quantification (lock-free atomic counts)
                 if let Some(ref q) = quant {
-                    q.counts.count_se_read(&transcripts, n_for_mapq, &q.gene_ann);
+                    q.counts
+                        .count_se_read(&transcripts, n_for_mapq, &q.gene_ann);
                 }
 
                 // Record junction statistics

src/quant/mod.rs

@@ -234,13 +234,8 @@ impl GeneCounts {
     }
 
     /// Write `ReadsPerGene.out.tab` in STAR's format.
-    pub fn write_output(
-        &self,
-        path: &Path,
-        gene_ann: &GeneAnnotation,
-    ) -> Result<(), Error> {
-        let mut file = std::fs::File::create(path)
-            .map_err(|e| Error::io(e, path))?;
+    pub fn write_output(&self, path: &Path, gene_ann: &GeneAnnotation) -> Result<(), Error> {
+        let mut file = std::fs::File::create(path).map_err(|e| Error::io(e, path))?;
 
         macro_rules! wl {
             ($($arg:tt)*) => {
@@ -350,10 +345,7 @@ impl QuantContext {
         let exons = crate::junction::gtf::parse_gtf(gtf_path)?;
         let gene_ann = GeneAnnotation::from_gtf_exons(&exons, genome);
         let n = gene_ann.n_genes();
-        log::info!(
-            "quantMode GeneCounts: {} genes loaded from GTF",
-            n
-        );
+        log::info!("quantMode GeneCounts: {} genes loaded from GTF", n);
         let counts = GeneCounts::new(n);
         Ok(QuantContext { gene_ann, counts })
     }
@@ -381,7 +373,13 @@ mod tests {
         }
     }
 
-    fn make_gtf_exon(seqname: &str, start: u64, end: u64, strand: char, gene_id: &str) -> GtfRecord {
+    fn make_gtf_exon(
+        seqname: &str,
+        start: u64,
+        end: u64,
+        strand: char,
+        gene_id: &str,
+    ) -> GtfRecord {
         let mut attrs = std::collections::HashMap::new();
         attrs.insert("gene_id".to_string(), gene_id.to_string());
         attrs.insert("transcript_id".to_string(), "T1".to_string());
@@ -401,7 +399,12 @@ mod tests {
             genome_start: gs,
             genome_end: ge,
             is_reverse,
-            exons: vec![Exon { genome_start: gs, genome_end: ge, read_start: 0, read_end: (ge - gs) as usize }],
+            exons: vec![Exon {
+                genome_start: gs,
+                genome_end: ge,
+                read_start: 0,
+                read_end: (ge - gs) as usize,
+            }],
             cigar: vec![],
             score: 100,
             n_mismatch: 0,
@@ -417,7 +420,7 @@ mod tests {
     fn test_gene_annotation_basic() {
         let genome = make_genome();
         let exons = vec![
-            make_gtf_exon("chr1", 101, 200, '+', "G1"),  // 0-based: [100, 200)
+            make_gtf_exon("chr1", 101, 200, '+', "G1"), // 0-based: [100, 200)
             make_gtf_exon("chr1", 301, 400, '+', "G1"),
             make_gtf_exon("chr1", 501, 600, '-', "G2"),
         ];
@@ -426,7 +429,7 @@ mod tests {
         assert_eq!(ann.gene_ids[0], "G1");
         assert_eq!(ann.gene_ids[1], "G2");
         assert!(!ann.gene_is_reverse[0]); // G1 is +
-        assert!(ann.gene_is_reverse[1]);  // G2 is -
+        assert!(ann.gene_is_reverse[1]); // G2 is -
         assert_eq!(ann.chr_exons[0].len(), 3);
     }