Fix clippy warnings: add allow(dead_code) for aln_filter module

Author: ekg

src/aln_filter.rs

@@ -9,6 +9,9 @@
 //! - Applies sweepga filtering logic
 //! - Writes filtered .1aln using fastga-rs AlnWriter
 
+// TODO: Remove this once the module is integrated into the main code path
+#![allow(dead_code)]
+
 use anyhow::{Context, Result};
 use onecode::{OneFile, OneSchema};
 use std::path::Path;
@@ -92,7 +95,7 @@ D Z 1 6 STRING
         let schema = OneSchema::from_text(schema_text).context("Failed to create .1aln schema")?;
 
         let mut file = OneFile::open_read(path_str, Some(&schema), Some("aln"), 1)
-            .context(format!("Failed to open .1aln file: {}", path_str))?;
+            .context(format!("Failed to open .1aln file: {path_str}"))?;
 
         // Read GDB skeleton to build contig→scaffold mapping
         let (contigs, scaffolds) = Self::read_gdb_skeleton(&mut file)?;
@@ -290,8 +293,7 @@ D Z 1 6 STRING
             } else {
                 // DEBUG: This shouldn't happen!
                 eprintln!(
-                    "[AlnReader] WARNING: No X, M, or D values for alignment at {}..{}",
-                    query_start, query_end
+                    "[AlnReader] WARNING: No X, M, or D values for alignment at {query_start}..{query_end}"
                 );
                 0.0
             };
@@ -319,7 +321,7 @@ D Z 1 6 STRING
                 let name = self
                     .file
                     .get_sequence_name(query_id)
-                    .unwrap_or_else(|| format!("{}", query_id));
+                    .unwrap_or_else(|| format!("{query_id}"));
                 (query_id, name, query_len, query_start, query_end)
             };
 
@@ -344,7 +346,7 @@ D Z 1 6 STRING
                 let name = self
                     .file
                     .get_sequence_name(target_id)
-                    .unwrap_or_else(|| format!("{}", target_id));
+                    .unwrap_or_else(|| format!("{target_id}"));
                 (target_id, name, target_len, target_start, target_end)
             };
 
@@ -443,9 +445,9 @@ pub fn filter_1aln_file_to_paf<P1: AsRef<Path>, P2: AsRef<Path>>(
         for (i, aln) in alignments.iter().enumerate() {
             let paf_line = aln.to_paf_line();
             if i < 3 {
-                eprintln!("[filter_1aln] Sample PAF line: {}", paf_line);
+                eprintln!("[filter_1aln] Sample PAF line: {paf_line}");
             }
-            writeln!(writer, "{}", paf_line)?;
+            writeln!(writer, "{paf_line}")?;
         }
         writer.flush()?;
     }

src/main.rs

@@ -1098,7 +1098,7 @@ fn align_multiple_fastas(
         if !quiet {
             timing.log(
                 "align",
-                &format!("Using user-specified frequency threshold: {}", f),
+                &format!("Using user-specified frequency threshold: {f}"),
             );
         }
         Some(f)
@@ -1109,8 +1109,7 @@ fn align_multiple_fastas(
             timing.log(
                 "align",
                 &format!(
-                    "Setting frequency threshold to {} (number of genome groups)",
-                    auto_freq
+                    "Setting frequency threshold to {auto_freq} (number of genome groups)"
                 ),
             );
         }
@@ -1123,7 +1122,7 @@ fn align_multiple_fastas(
     if !quiet {
         timing.log(
             "align",
-            &format!("Aligning {} genomes in single FastGA run", num_genomes),
+            &format!("Aligning {num_genomes} genomes in single FastGA run"),
         );
     }
 
@@ -1139,7 +1138,7 @@ fn align_multiple_fastas(
         let alignment_count = std::fs::read_to_string(temp_paf.path())?.lines().count();
         timing.log(
             "align",
-            &format!("FastGA produced {} alignments", alignment_count),
+            &format!("FastGA produced {alignment_count} alignments"),
         );
     }