revert(stats): drop Log.out / Log.progress.out stub writers

The previous commit added writers that mimicked STAR's section-header
structure with placeholder content (a Debug-format params dump + three
timestamps for Log.out, a header + final-timestamp line for
Log.progress.out). That closes the file-existence gap but makes the
output look like STAR-equivalent verbose logging when it isn't —
downstream tools parsing for memory usage, per-chunk progress, or
warnings would silently get nothing.

Drop the stub writers. The SJ.pass1.out.tab → <prefix>_STARpass1/SJ.out.tab
placement fix stays — that's a real path-parity change with no fakery.

Real STAR-equivalent Log.out / Log.progress.out content (per-phase
progress, warnings, memory, periodic updates during long runs) is a
separate engineering effort, not a stub.

Co-Authored-By: Claude <noreply@anthropic.com>

Author: pinin4fjords

src/lib.rs

@@ -258,21 +258,6 @@ fn align_reads(params: &Parameters) -> anyhow::Result<()> {
     stats.write_log_final(&log_path, time_start, time_map_start, time_finish)?;
     info!("Wrote {}", log_path.display());
 
-    let log_out_path = params.out_file_name_prefix.join("Log.out");
-    crate::stats::write_log_out(
-        &log_out_path,
-        &params,
-        time_start,
-        time_map_start,
-        time_finish,
-    )?;
-    info!("Wrote {}", log_out_path.display());
-
-    let log_progress_path = params.out_file_name_prefix.join("Log.progress.out");
-    let total_reads = stats.total_reads.load(std::sync::atomic::Ordering::Relaxed);
-    crate::stats::write_log_progress(&log_progress_path, total_reads, time_map_start, time_finish)?;
-    info!("Wrote {}", log_progress_path.display());
-
     // Write ReadsPerGene.out.tab if quantMode GeneCounts was requested.
     if let Some(ref ctx) = quant_ctx {
         let quant_path = params.out_file_name_prefix.join("ReadsPerGene.out.tab");

src/stats.rs

@@ -5,74 +5,6 @@ use std::sync::atomic::{AtomicU64, Ordering};
 
 use crate::align::transcript::{CigarOp, Transcript};
 use crate::junction::encode_motif;
-use crate::params::Parameters;
-
-/// Shared timestamp format used across Log.final.out / Log.out / Log.progress.out.
-pub const LOG_TIME_FMT: &str = "%b %d %H:%M:%S";
-
-/// Write a minimal STAR-compatible Log.out alongside Log.final.out.
-///
-/// Carries a parameters dump and per-phase timestamps. Intentionally a stub
-/// rather than a full STAR-verbose-log reproduction.
-pub fn write_log_out(
-    path: &Path,
-    params: &Parameters,
-    time_start: chrono::DateTime<chrono::Local>,
-    time_map_start: chrono::DateTime<chrono::Local>,
-    time_finish: chrono::DateTime<chrono::Local>,
-) -> std::io::Result<()> {
-    use std::io::Write;
-
-    let mut f = std::fs::File::create(path)?;
-
-    writeln!(f, "##### Run parameters")?;
-    writeln!(f, "{:#?}", params)?;
-    writeln!(f)?;
-    writeln!(f, "##### Run started")?;
-    writeln!(f, "{}", time_start.format(LOG_TIME_FMT))?;
-    writeln!(f)?;
-    writeln!(f, "##### Mapping started")?;
-    writeln!(f, "{}", time_map_start.format(LOG_TIME_FMT))?;
-    writeln!(f)?;
-    writeln!(f, "##### Mapping finished")?;
-    writeln!(f, "{}", time_finish.format(LOG_TIME_FMT))?;
-
-    Ok(())
-}
-
-/// Write a minimal STAR-compatible Log.progress.out alongside Log.final.out.
-///
-/// A header line plus a single "done" line with the final timestamp and
-/// mapping speed (million reads per hour). Intentionally a stub.
-pub fn write_log_progress(
-    path: &Path,
-    total_reads: u64,
-    time_map_start: chrono::DateTime<chrono::Local>,
-    time_finish: chrono::DateTime<chrono::Local>,
-) -> std::io::Result<()> {
-    use std::io::Write;
-
-    let elapsed_hours = {
-        let elapsed = time_finish - time_map_start;
-        elapsed.num_milliseconds() as f64 / 3_600_000.0
-    };
-    let mapping_speed = if elapsed_hours > 0.0 {
-        total_reads as f64 / elapsed_hours / 1_000_000.0
-    } else {
-        0.0
-    };
-
-    let mut f = std::fs::File::create(path)?;
-    writeln!(f, "# completed\tmapping_speed_M_reads_per_hour")?;
-    writeln!(
-        f,
-        "{}\t{:.2}",
-        time_finish.format(LOG_TIME_FMT),
-        mapping_speed
-    )?;
-
-    Ok(())
-}
 
 /// Reason a read could not be mapped
 #[derive(Debug, Clone, Copy, PartialEq, Eq)]
@@ -1086,69 +1018,4 @@ mod tests {
         stats.record_half_mapped();
         assert_eq!(stats.half_mapped_pairs.load(Ordering::Relaxed), 3);
     }
-
-    #[test]
-    fn test_write_log_out_minimal() {
-        use chrono::TimeZone;
-        use clap::Parser;
-
-        let params = Parameters::parse_from(["rustar-aligner", "--readFilesIn", "reads.fq"]);
-        let t_start = chrono::Local
-            .with_ymd_and_hms(2026, 5, 12, 14, 14, 23)
-            .unwrap();
-        let t_map = chrono::Local
-            .with_ymd_and_hms(2026, 5, 12, 14, 14, 30)
-            .unwrap();
-        let t_finish = chrono::Local
-            .with_ymd_and_hms(2026, 5, 12, 14, 14, 58)
-            .unwrap();
-
-        let dir = tempfile::tempdir().unwrap();
-        let path = dir.path().join("Log.out");
-        write_log_out(&path, &params, t_start, t_map, t_finish).unwrap();
-
-        let content = std::fs::read_to_string(&path).unwrap();
-        assert!(!content.is_empty(), "Log.out should not be empty");
-        assert!(content.contains("##### Run parameters"));
-        assert!(content.contains("##### Run started"));
-        assert!(content.contains("##### Mapping started"));
-        assert!(content.contains("##### Mapping finished"));
-        // Each phase header should be followed by a timestamp shaped like "May 12 14:14:23".
-        assert!(content.contains("May 12 14:14:23"));
-        assert!(content.contains("May 12 14:14:58"));
-        // The parameters dump should mention at least one familiar field.
-        assert!(content.contains("read_files_in"));
-    }
-
-    #[test]
-    fn test_write_log_progress_minimal() {
-        use chrono::TimeZone;
-
-        let t_map = chrono::Local
-            .with_ymd_and_hms(2026, 5, 12, 14, 14, 30)
-            .unwrap();
-        let t_finish = chrono::Local
-            .with_ymd_and_hms(2026, 5, 12, 14, 14, 58)
-            .unwrap();
-
-        let dir = tempfile::tempdir().unwrap();
-        let path = dir.path().join("Log.progress.out");
-        write_log_progress(&path, 10_000, t_map, t_finish).unwrap();
-
-        let content = std::fs::read_to_string(&path).unwrap();
-        let lines: Vec<&str> = content.lines().collect();
-        assert!(lines.len() >= 2, "expected header + data line");
-        assert!(lines[0].starts_with('#'), "first line should be a header");
-        assert!(
-            lines[1].contains("May 12 14:14:58"),
-            "second line should contain the finish timestamp, got: {}",
-            lines[1]
-        );
-        // Mapping speed column should be a number with two decimals.
-        let cols: Vec<&str> = lines[1].split('\t').collect();
-        assert_eq!(cols.len(), 2, "expected 2 tab-separated columns");
-        cols[1]
-            .parse::<f64>()
-            .expect("second column should parse as a float");
-    }
 }

tests/alignment_features.rs

@@ -795,23 +795,6 @@ fn test_two_pass_mode() {
         "SJ.pass1.out.tab should no longer be emitted at the top level"
     );
 
-    let log_out = output_dir.join("Log.out");
-    assert!(log_out.exists(), "Log.out not found");
-    let log_out_content = fs::read_to_string(&log_out).unwrap();
-    assert!(!log_out_content.is_empty(), "Log.out is empty");
-    assert!(
-        log_out_content.contains("##### Run parameters"),
-        "Log.out missing parameters section"
-    );
-
-    let log_progress = output_dir.join("Log.progress.out");
-    assert!(log_progress.exists(), "Log.progress.out not found");
-    let log_progress_content = fs::read_to_string(&log_progress).unwrap();
-    assert!(
-        log_progress_content.lines().count() >= 2,
-        "Log.progress.out should have a header and at least one data line"
-    );
-
     let sam_path = output_dir.join("Aligned.out.sam");
     assert!(sam_path.exists(), "Aligned.out.sam not found");