fix clippy warnings

Author: ayobi

src/derep.rs

@@ -58,7 +58,7 @@ pub fn derep_and_write_fasta(
     let mut w = fasta::open_writer(out_fasta)?;
     let mut rep_to_members: HashMap<String, Vec<String>> = HashMap::with_capacity(unique);
 
-    for (_key, (rep_id, rep_seq, members)) in &groups {
+    for (rep_id, rep_seq, members) in groups.values() {
         fasta::write_fasta_record(&mut w, rep_id, rep_seq)?;
         rep_to_members.insert(rep_id.clone(), members.clone());
     }

src/fasta.rs

@@ -52,8 +52,8 @@ impl FastaReader {
                     return Ok(None);
                 }
                 let line = self.buf.trim_end();
-                if line.starts_with('>') {
-                    let header = line[1..].trim();
+                if let Some(stripped) = line.strip_prefix('>') {
+                    let header = stripped.trim();
                     let id = header
                         .split_whitespace()
                         .next()
@@ -76,8 +76,8 @@ impl FastaReader {
                 break;
             }
             let line = self.buf.trim_end();
-            if line.starts_with('>') {
-                let header = line[1..].trim();
+            if let Some(stripped) = line.strip_prefix('>') {
+                let header = stripped.trim();
                 let next_id = header
                     .split_whitespace()
                     .next()

src/main.rs

@@ -290,6 +290,7 @@ impl AnchorHitOut {
     }
 }
 
+#[allow(clippy::too_many_arguments)]
 fn write_anchor_tsv_row<W: Write>(
     w: &mut W,
     rid: &str,
@@ -328,6 +329,7 @@ fn write_anchor_tsv_row<W: Write>(
     Ok(())
 }
 
+#[allow(clippy::too_many_arguments)]
 fn write_anchor_jsonl_row<W: Write>(
     w: &mut W,
     rid: &str,

src/report.rs

@@ -88,21 +88,13 @@ pub struct SkipCounter {
 }
 
 impl SkipCounter {
-    pub fn new() -> Self {
-        Self::default()
-    }
-
     pub fn record(&mut self, reason: &SkipReason) {
         *self.counts.entry(reason.code().to_string()).or_insert(0) += 1;
     }
 
     pub fn to_map(&self) -> HashMap<String, usize> {
         self.counts.clone()
     }
-
-    pub fn total(&self) -> usize {
-        self.counts.values().sum()
-    }
 }
 
 // ---------------------------------------------------------------------------

src/select.rs

@@ -122,7 +122,7 @@ fn to_anchor_hits(hits: &[TblHit]) -> Vec<HitIvl> {
 }
 
 /// Sort by score desc, then evalue asc, keep top K
-fn top_k<'a>(mut v: Vec<&'a HitIvl>, k: usize) -> Vec<&'a HitIvl> {
+fn top_k(mut v: Vec<&HitIvl>, k: usize) -> Vec<&HitIvl> {
     v.sort_by(|a, b| {
         b.score
             .partial_cmp(&a.score)
@@ -470,82 +470,6 @@ fn count_anchors(ah: &[HitIvl]) -> AnchorCounts {
     c
 }
 
-/// Public: explain why a read likely failed to yield bounds.
-pub fn diagnose(
-    hits: &[TblHit],
-    region: Region,
-    max_per_anchor: usize,
-    constraints: Constraints,
-) -> String {
-    let ah = to_anchor_hits(hits);
-    if ah.is_empty() {
-        return "no classified anchor hits (none of SSU_end/58S/LSU matched)".to_string();
-    }
-
-    let counts = count_anchors(&ah);
-
-    let missing = {
-        let mut v = Vec::new();
-        let has_ssu = counts.ssu_p + counts.ssu_m > 0;
-        let has_s58s = counts.s58s_p + counts.s58s_m > 0;
-        let has_s58e = counts.s58e_p + counts.s58e_m > 0;
-        let has_lsu = counts.lsu_p + counts.lsu_m > 0;
-
-        if !has_ssu {
-            v.push(anchor_name(Anchor::SsuEnd));
-        }
-        if !has_s58s {
-            v.push(anchor_name(Anchor::S58Start));
-        }
-        if !has_s58e {
-            v.push(anchor_name(Anchor::S58End));
-        }
-        if !has_lsu {
-            v.push(anchor_name(Anchor::LsuStart));
-        }
-        v
-    };
-
-    let counts_str = format!(
-        "counts(+/-): SSU_end {}/{}  58S_start {}/{}  58S_end {}/{}  LSU_start {}/{}",
-        counts.ssu_p,
-        counts.ssu_m,
-        counts.s58s_p,
-        counts.s58s_m,
-        counts.s58e_p,
-        counts.s58e_m,
-        counts.lsu_p,
-        counts.lsu_m
-    );
-
-    if !missing.is_empty() {
-        return format!("missing anchors: {} | {}", missing.join(","), counts_str);
-    }
-
-    // anchors exist; do we have a valid chain under constraints?
-    let chain = compute_chain(hits, max_per_anchor, constraints);
-    if chain.is_none() {
-        return format!(
-            "anchors present but no valid SSU_end→58S_start→58S_end→LSU_start chain under constraints | {}",
-            counts_str
-        );
-    }
-
-    let chain = chain.unwrap();
-    if bounds_from_chain(&chain, region).is_none() {
-        return format!(
-            "chain found, but requested region {:?} bounds invalid (start>end) | {}",
-            region, counts_str
-        );
-    }
-
-    // If we reach here, bounds *should* exist; this typically means downstream trimming failed (seq shorter than bounds).
-    format!(
-        "bounds exist logically but trimming failed (likely bounds exceed sequence length) | {}",
-        counts_str
-    )
-}
-
 /// Structured version of `diagnose` returning a machine-readable `SkipReason`.
 pub fn diagnose_structured(
     hits: &[TblHit],

src/trim.rs

@@ -170,6 +170,7 @@ struct RegionOutput {
 // Skip handling
 // ---------------------------------------------------------------------------
 
+#[allow(clippy::too_many_arguments)]
 fn handle_skip(
     rec: &Record,
     topk_map: &HashMap<String, TopKHits>,

tests/extract_subset_from_tblout.rs

@@ -42,13 +42,13 @@ fn read_fasta_as_map(path: &std::path::Path) -> HashMap<String, String> {
     let mut seq = String::new();
 
     for line in text.lines() {
-        if line.starts_with('>') {
+        if let Some(stripped) = line.strip_prefix('>') {
             if let Some(id) = cur_id.take() {
                 map.insert(id, seq.clone());
             }
             seq.clear();
             // output header is like "READ|region:..." -> store by READ
-            let header = line[1..].split_whitespace().next().unwrap();
+            let header = stripped.split_whitespace().next().unwrap();
             let rid = header.split('|').next().unwrap().to_string();
             cur_id = Some(rid);
         } else {