Run cargo fmt to fix formatting issues

Author: ekg

examples/test_format_equivalence.rs

@@ -87,7 +87,13 @@ fn main() -> Result<()> {
         min_scaffold_identity: 0.0,
     };
 
-    filter_file(temp_1aln.path(), temp_filtered_1aln.path(), &config, false, false)?;
+    filter_file(
+        temp_1aln.path(),
+        temp_filtered_1aln.path(),
+        &config,
+        false,
+        false,
+    )?;
     println!("    ✓ .1aln filtering succeeded");
 
     // Filter PAF → PAF

src/binary_paths.rs

@@ -30,14 +30,11 @@ pub fn get_embedded_binary_path(binary_name: &str) -> Result<PathBuf> {
 
     // Check installed location (for cargo install)
     // Try $CARGO_HOME/lib/sweepga/ or ~/.cargo/lib/sweepga/
-    let cargo_home = env::var("CARGO_HOME")
-        .ok()
-        .map(PathBuf::from)
-        .or_else(|| {
-            env::var("HOME")
-                .ok()
-                .map(|h| PathBuf::from(h).join(".cargo"))
-        });
+    let cargo_home = env::var("CARGO_HOME").ok().map(PathBuf::from).or_else(|| {
+        env::var("HOME")
+            .ok()
+            .map(|h| PathBuf::from(h).join(".cargo"))
+    });
 
     if let Some(cargo_home) = cargo_home {
         let installed_path = cargo_home.join("lib").join("sweepga").join(binary_name);

src/fastga_integration.rs

@@ -164,7 +164,10 @@ impl FastGAIntegration {
     fn ensure_fastga_in_path() -> Result<()> {
         // Try to find FastGA using our binary_paths module
         if let Ok(fastga_path) = crate::binary_paths::get_embedded_binary_path("FastGA") {
-            eprintln!("[FastGA] Found embedded binary at: {}", fastga_path.display());
+            eprintln!(
+                "[FastGA] Found embedded binary at: {}",
+                fastga_path.display()
+            );
             if let Some(fastga_dir) = fastga_path.parent() {
                 // Temporarily add this directory to PATH for fastga-rs to find
                 if let Ok(current_path) = std::env::var("PATH") {

src/main.rs

@@ -1364,7 +1364,10 @@ fn main() -> Result<()> {
                         #[cfg(unix)]
                         {
                             use std::os::unix::fs::PermissionsExt;
-                            println!("  Executable: {}", metadata.permissions().mode() & 0o111 != 0);
+                            println!(
+                                "  Executable: {}",
+                                metadata.permissions().mode() & 0o111 != 0
+                            );
                         }
 
                         let path_str = path.to_string_lossy();
@@ -1529,11 +1532,23 @@ fn main() -> Result<()> {
         // Step 3: Filter .1aln directly using unified_filter (format-preserving)
         use crate::unified_filter::filter_file;
         if let Some(ref output_file) = args.output_file {
-            filter_file(&aln_input_path, output_file, &filter_config, false, args.keep_self)?;
+            filter_file(
+                &aln_input_path,
+                output_file,
+                &filter_config,
+                false,
+                args.keep_self,
+            )?;
         } else {
             // Write to temp file then copy to stdout
             let temp_output = tempfile::NamedTempFile::with_suffix(".1aln")?;
-            filter_file(&aln_input_path, temp_output.path(), &filter_config, false, args.keep_self)?;
+            filter_file(
+                &aln_input_path,
+                temp_output.path(),
+                &filter_config,
+                false,
+                args.keep_self,
+            )?;
 
             // Copy binary to stdout
             use std::io::copy;