style: closures to functions and inline format args

Author: flying-sheep

src/align/read_align.rs

@@ -205,7 +205,7 @@ pub fn align_read(
 
     if seeds.is_empty() {
         if debug_read {
-            eprintln!("[DEBUG {}] No seeds found — unmapped", read_name);
+            eprintln!("[DEBUG {read_name}] No seeds found — unmapped");
         }
         return Ok((Vec::new(), Vec::new(), 0, Some(UnmappedReason::Other)));
     }
@@ -266,7 +266,7 @@ pub fn align_read(
 
     if clusters.is_empty() {
         if debug_read {
-            eprintln!("[DEBUG {}] No clusters — unmapped", read_name);
+            eprintln!("[DEBUG {read_name}] No clusters — unmapped");
         }
         return Ok((Vec::new(), Vec::new(), 0, Some(UnmappedReason::Other)));
     }
@@ -525,11 +525,7 @@ pub fn align_read(
     if pre_filter_count > transcripts.len() {
         let filtered = pre_filter_count - transcripts.len();
         log::debug!(
-            "Read {}: Filtered {}/{} transcripts: {:?}",
-            read_name,
-            filtered,
-            pre_filter_count,
-            filter_reasons
+            "Read {read_name}: Filtered {filtered}/{pre_filter_count} transcripts: {filter_reasons:?}"
         );
     }
 
@@ -2165,8 +2161,7 @@ mod tests {
         }
         assert!(
             firsts.len() >= 2,
-            "expected different seeds to pick different primaries, got {:?}",
-            firsts
+            "expected different seeds to pick different primaries, got {firsts:?}"
         );
     }
 

src/align/seed.rs

@@ -669,7 +669,7 @@ mod tests {
     fn make_test_index(sequence: &str) -> GenomeIndex {
         let mut file = NamedTempFile::new().unwrap();
         writeln!(file, ">chr1").unwrap();
-        writeln!(file, "{}", sequence).unwrap();
+        writeln!(file, "{sequence}").unwrap();
 
         let dir = tempfile::tempdir().unwrap();
 
@@ -888,8 +888,7 @@ mod tests {
         // R→L search should find seeds because RC(read) = AACCTTGG matches genome
         assert!(
             !rc_seeds.is_empty(),
-            "R→L search should find seeds (RC of read matches genome). All seeds: {:?}",
-            seeds
+            "R→L search should find seeds (RC of read matches genome). All seeds: {seeds:?}"
         );
 
         // Verify R→L seeds have valid read positions

src/chimeric/detect.rs

@@ -165,9 +165,9 @@ impl<'a> ChimericDetector<'a> {
             }
 
             let donor_seg = transcript_to_segment(tr_donor)
-                .map_err(|e| Error::Chimeric(format!("soft-clip donor: {}", e)))?;
+                .map_err(|e| Error::Chimeric(format!("soft-clip donor: {e}")))?;
             let acceptor_seg = transcript_to_segment(tr_acceptor)
-                .map_err(|e| Error::Chimeric(format!("soft-clip acceptor: {}", e)))?;
+                .map_err(|e| Error::Chimeric(format!("soft-clip acceptor: {e}")))?;
 
             let (repeat_len_donor, repeat_len_acceptor) = calculate_repeat_length(
                 &index.genome,
@@ -292,7 +292,7 @@ impl<'a> ChimericDetector<'a> {
             };
 
             let new_seg = transcript_to_segment(&clip_tr)
-                .map_err(|e| Error::Chimeric(format!("tier3 segment: {}", e)))?;
+                .map_err(|e| Error::Chimeric(format!("tier3 segment: {e}")))?;
 
             // Donor / acceptor ordered by read position
             let (donor_seg, acceptor_seg): (&ChimericSegment, &ChimericSegment) =
@@ -897,9 +897,9 @@ pub fn detect_chimeric_old(
 
     // Build chimeric segments
     let donor_seg = transcript_to_segment(tr_donor)
-        .map_err(|e| Error::Chimeric(format!("chimeric donor segment: {}", e)))?;
+        .map_err(|e| Error::Chimeric(format!("chimeric donor segment: {e}")))?;
     let acceptor_seg = transcript_to_segment(tr_acceptor)
-        .map_err(|e| Error::Chimeric(format!("chimeric acceptor segment: {}", e)))?;
+        .map_err(|e| Error::Chimeric(format!("chimeric acceptor segment: {e}")))?;
 
     // Minimum segment length check
     if !donor_seg.meets_min_length(params.chim_segment_min)

src/chimeric/output.rs

@@ -84,23 +84,9 @@ impl ChimericJunctionWriter {
         // Write line
         writeln!(
             self.writer,
-            "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}",
-            donor_chr,
-            donor_bp,
-            donor_strand,
-            acceptor_chr,
-            acceptor_bp,
-            acceptor_strand,
-            junction_type,
-            repeat_donor,
-            repeat_acceptor,
-            read_name,
-            donor_start,
-            donor_cigar,
-            acceptor_start,
-            acceptor_cigar,
+            "{donor_chr}\t{donor_bp}\t{donor_strand}\t{acceptor_chr}\t{acceptor_bp}\t{acceptor_strand}\t{junction_type}\t{repeat_donor}\t{repeat_acceptor}\t{read_name}\t{donor_start}\t{donor_cigar}\t{acceptor_start}\t{acceptor_cigar}",
         )
-        .map_err(|e| Error::Chimeric(format!("Failed to write chimeric junction: {}", e)))?;
+        .map_err(|e| Error::Chimeric(format!("Failed to write chimeric junction: {e}")))?;
 
         Ok(())
     }
@@ -109,7 +95,7 @@ impl ChimericJunctionWriter {
     pub fn flush(&mut self) -> Result<(), Error> {
         self.writer
             .flush()
-            .map_err(|e| Error::Chimeric(format!("Failed to flush chimeric junction file: {}", e)))
+            .map_err(|e| Error::Chimeric(format!("Failed to flush chimeric junction file: {e}")))
     }
 }
 
@@ -200,7 +186,7 @@ fn build_segment_record(
     let pos = (seg.genome_start - chr_start + 1) as usize;
     *record.alignment_start_mut() = Some(
         pos.try_into()
-            .map_err(|e| Error::Chimeric(format!("invalid chimeric position {}: {}", pos, e)))?,
+            .map_err(|e| Error::Chimeric(format!("invalid chimeric position {pos}: {e}")))?,
     );
 
     *record.mapping_quality_mut() = MappingQuality::new(mapq);
@@ -549,7 +535,7 @@ mod tests {
         // Donor record's SA tag should point to acceptor
         let sa_tag = Tag::new(b'S', b'A');
         let donor_sa = records[0].data().get(&sa_tag).unwrap();
-        let donor_sa_str = format!("{:?}", donor_sa);
+        let donor_sa_str = format!("{donor_sa:?}");
         // SA tag: chr22,89,-,37M,255,1; (pos = 600-512+1=89, strand=-, nm=1)
         assert!(
             donor_sa_str.contains("chr22"),
@@ -566,7 +552,7 @@ mod tests {
 
         // Acceptor record's SA tag should point to donor
         let acceptor_sa = records[1].data().get(&sa_tag).unwrap();
-        let acceptor_sa_str = format!("{:?}", acceptor_sa);
+        let acceptor_sa_str = format!("{acceptor_sa:?}");
         assert!(
             acceptor_sa_str.contains("chr9"),
             "SA tag must name donor chr"

src/genome/mod.rs

@@ -210,30 +210,30 @@ impl Genome {
         let chr_name_path = dir.join("chrName.txt");
         let mut f = fs::File::create(&chr_name_path).map_err(|e| Error::io(e, &chr_name_path))?;
         for name in &self.chr_name {
-            writeln!(f, "{}", name).map_err(|e| Error::io(e, &chr_name_path))?;
+            writeln!(f, "{name}").map_err(|e| Error::io(e, &chr_name_path))?;
         }
 
         // Write chrLength.txt
         let chr_length_path = dir.join("chrLength.txt");
         let mut f =
             fs::File::create(&chr_length_path).map_err(|e| Error::io(e, &chr_length_path))?;
         for &len in &self.chr_length {
-            writeln!(f, "{}", len).map_err(|e| Error::io(e, &chr_length_path))?;
+            writeln!(f, "{len}").map_err(|e| Error::io(e, &chr_length_path))?;
         }
 
         // Write chrStart.txt (includes the extra n_genome entry)
         let chr_start_path = dir.join("chrStart.txt");
         let mut f = fs::File::create(&chr_start_path).map_err(|e| Error::io(e, &chr_start_path))?;
         for &start in &self.chr_start {
-            writeln!(f, "{}", start).map_err(|e| Error::io(e, &chr_start_path))?;
+            writeln!(f, "{start}").map_err(|e| Error::io(e, &chr_start_path))?;
         }
 
         // Write chrNameLength.txt (tab-separated)
         let chr_name_length_path = dir.join("chrNameLength.txt");
         let mut f = fs::File::create(&chr_name_length_path)
             .map_err(|e| Error::io(e, &chr_name_length_path))?;
         for (name, &len) in self.chr_name.iter().zip(&self.chr_length) {
-            writeln!(f, "{}\t{}", name, len).map_err(|e| Error::io(e, &chr_name_length_path))?;
+            writeln!(f, "{name}\t{len}").map_err(|e| Error::io(e, &chr_name_length_path))?;
         }
 
         // Write genomeParameters.txt — byte-for-byte matching STAR's
@@ -319,7 +319,7 @@ impl Genome {
             .sjdb_gtf_file
             .as_ref()
             .map_or_else(|| "-".to_string(), |p| p.display().to_string());
-        writeln!(f, "sjdbGTFfile\t{}", gtf_str).map_err(|e| Error::io(e, &path))?;
+        writeln!(f, "sjdbGTFfile\t{gtf_str}").map_err(|e| Error::io(e, &path))?;
         writeln!(f, "sjdbGTFchrPrefix\t-").map_err(|e| Error::io(e, &path))?;
         writeln!(f, "sjdbGTFfeatureExon\texon").map_err(|e| Error::io(e, &path))?;
         writeln!(f, "sjdbGTFtagExonParentTranscript\ttranscript_id")

src/index/io.rs

@@ -138,7 +138,7 @@ fn load_genome(genome_dir: &Path, _params: &Parameters) -> Result<Genome, Error>
     let chr_name_path = genome_dir.join("chrName.txt");
     let chr_name_contents =
         std::fs::read_to_string(&chr_name_path).map_err(|e| Error::io(e, &chr_name_path))?;
-    let chr_name: Vec<String> = chr_name_contents.lines().map(|s| s.to_string()).collect();
+    let chr_name: Vec<String> = chr_name_contents.lines().map(ToString::to_string).collect();
 
     let chr_length_path = genome_dir.join("chrLength.txt");
     let chr_length_contents =

src/index/sa_index.rs

@@ -65,10 +65,7 @@ impl SaIndex {
         let num_indices = Self::calculate_num_indices(nbases);
 
         log::info!(
-            "Building SA index: nbases={}, num_indices={}, word_length={}",
-            nbases,
-            num_indices,
-            word_length
+            "Building SA index: nbases={nbases}, num_indices={num_indices}, word_length={word_length}"
         );
 
         // Initialize packed array with "absent" markers
@@ -258,7 +255,7 @@ mod tests {
     fn make_test_index_with_sa(sequence: &str, bin_nbits: u32, sa_nbases: u32) -> (SaIndex, usize) {
         let mut file = NamedTempFile::new().unwrap();
         writeln!(file, ">test").unwrap();
-        writeln!(file, "{}", sequence).unwrap();
+        writeln!(file, "{sequence}").unwrap();
 
         let bin_nbits_str = bin_nbits.to_string();
         let sa_nbases_str = sa_nbases.to_string();
@@ -423,13 +420,11 @@ mod tests {
                 let (new_sa_start, _, matched_level, _) = new_result.unwrap();
                 assert_eq!(
                     new_sa_start, old_sa_pos as usize,
-                    "SA start should match for k-mer {}",
-                    kmer_idx
+                    "SA start should match for k-mer {kmer_idx}"
                 );
                 assert_eq!(
                     matched_level, 2,
-                    "Should match at full level for k-mer {}",
-                    kmer_idx
+                    "Should match at full level for k-mer {kmer_idx}"
                 );
             }
         }

src/index/suffix_array.rs

@@ -60,10 +60,7 @@ impl SuffixArray {
 
         let sa_length = suffixes.len();
         log::info!(
-            "Building suffix array with {} entries (gstrand_bit={}, word_length={})",
-            sa_length,
-            gstrand_bit,
-            word_length
+            "Building suffix array with {sa_length} entries (gstrand_bit={gstrand_bit}, word_length={word_length})"
         );
 
         // Sort suffixes using custom comparator
@@ -218,7 +215,7 @@ mod tests {
     fn make_test_genome(sequence: &str, bin_nbits: u32) -> Genome {
         let mut file = NamedTempFile::new().unwrap();
         writeln!(file, ">test").unwrap();
-        writeln!(file, "{}", sequence).unwrap();
+        writeln!(file, "{sequence}").unwrap();
 
         let bin_nbits_str = bin_nbits.to_string();
         let args = vec![

src/io/bam.rs

@@ -281,7 +281,7 @@ fn write_bam_header_lenient<W: Write>(
     writer.write_i32::<LittleEndian>(n_ref)?;
     for (name, rs) in refs {
         let c_name = CString::new(name.to_vec()).map_err(|e| {
-            Error::Index(format!("reference name contains interior NUL byte: {}", e))
+            Error::Index(format!("reference name contains interior NUL byte: {e}"))
         })?;
         let name_bytes = c_name.as_bytes_with_nul();
         let l_name = u32::try_from(name_bytes.len()).map_err(|_| {

src/io/fastq.rs

@@ -134,7 +134,7 @@ impl FastqReader {
                     .map_err(|e| {
                         Error::from(std::io::Error::new(
                             std::io::ErrorKind::InvalidData,
-                            format!("invalid UTF-8 in read name: {}", e),
+                            format!("invalid UTF-8 in read name: {e}"),
                         ))
                     })?
                     .to_string();
@@ -672,7 +672,7 @@ mod tests {
     fn test_paired_batch_reading() {
         let mut tmpfile1 = NamedTempFile::new().unwrap();
         for i in 1..=5 {
-            writeln!(tmpfile1, "@read{}/1", i).unwrap();
+            writeln!(tmpfile1, "@read{i}/1").unwrap();
             writeln!(tmpfile1, "ACGT").unwrap();
             writeln!(tmpfile1, "+").unwrap();
             writeln!(tmpfile1, "IIII").unwrap();
@@ -681,7 +681,7 @@ mod tests {
 
         let mut tmpfile2 = NamedTempFile::new().unwrap();
         for i in 1..=5 {
-            writeln!(tmpfile2, "@read{}/2", i).unwrap();
+            writeln!(tmpfile2, "@read{i}/2").unwrap();
             writeln!(tmpfile2, "GGCC").unwrap();
             writeln!(tmpfile2, "+").unwrap();
             writeln!(tmpfile2, "JJJJ").unwrap();