fix(output): move pass-1 SJ tab into <prefix>_STARpass1/SJ.out.tab

src/lib.rs

@@ -457,13 +457,9 @@ fn run_two_pass(
     info!("Two-pass mode: Pass 1 - Junction discovery");
     let (sj_stats_pass1, novel_junctions) = run_pass1(index, params)?;
 
-    // Write SJ.pass1.out.tab
-    let pass1_path = params.out_file_name_prefix.join("SJ.pass1.out.tab");
-
-    // Create output directory if it doesn't exist
-    if let Some(parent) = pass1_path.parent() {
-        std::fs::create_dir_all(parent)?;
-    }
+    let pass1_dir = params.out_file_name_prefix.join("_STARpass1");
+    std::fs::create_dir_all(&pass1_dir)?;
+    let pass1_path = pass1_dir.join("SJ.out.tab");
 
     info!("Writing pass 1 junctions to {}", pass1_path.display());
     sj_stats_pass1.write_output(&pass1_path, &index.genome, params)?;

tests/alignment_features.rs

@@ -784,10 +784,15 @@ fn test_two_pass_mode() {
         .assert()
         .success();
 
-    let pass1_path = output_dir.join("SJ.pass1.out.tab");
+    let pass1_path = output_dir.join("_STARpass1").join("SJ.out.tab");
     assert!(
         pass1_path.exists(),
-        "SJ.pass1.out.tab not found — two-pass mode did not write pass-1 junctions"
+        "_STARpass1/SJ.out.tab not found — two-pass mode did not write pass-1 junctions"
+    );
+    let top_level_pass1 = output_dir.join("SJ.pass1.out.tab");
+    assert!(
+        !top_level_pass1.exists(),
+        "SJ.pass1.out.tab should no longer be emitted at the top level"
     );
 
     let sam_path = output_dir.join("Aligned.out.sam");