sshash-lib 0.5.0

//! External sorting for minimizer tuples
//!
//! This module implements RAM-bounded external sorting for large datasets,
//! following the C++ sshash implementation precisely:
//!
//! 1. Each thread has a RAM-bounded buffer
//! 2. When buffer fills → parallel sort + flush to temp binary file
//! 3. After all tuples processed → k-way merge of temp files
//! 4. Merge uses buffered file I/O (not mmap) to avoid resident page bloat
//!
//! ## Memory Management
//!
//! Buffer size per thread = `(ram_limit_gib * GiB) / (2 * sizeof(tuple) * num_threads)`
//!
//! The factor of 2 accounts for temporary memory during parallel sort.
//!
//! After merge, the sorted file is accessed via sequential buffered readers
//! (`FileTuples`) rather than mmap, keeping RSS proportional to the I/O buffer
//! size (~4 MB) instead of the file size (~8-10 GB).

use std::fs::{self, File};
use std::io::{BufReader, BufWriter, Read, Write};
use std::path::{Path, PathBuf};
use std::sync::atomic::{AtomicU64, Ordering};
use std::time::{SystemTime, UNIX_EPOCH};

use memmap2::Mmap;
use rayon::prelude::*;
use tracing::{debug, info};

use super::minimizer_tuples::MinimizerTuple;

/// Size of `MinimizerTupleExternal` in bytes (packed, no padding)
pub const TUPLE_SIZE_BYTES: usize = 18;

/// Bytes per GiB
pub const GIB: usize = 1024 * 1024 * 1024;

/// Default buffer size for sequential tuple readers (4 MB).
const READER_BUF_SIZE: usize = 4 * 1024 * 1024;

/// Packed minimizer tuple for disk I/O (matches C++ `#pragma pack(push, 2)`)
///
/// Layout: minimizer (8) + pos_in_seq (8) + pos_in_kmer (1) + num_kmers_in_super_kmer (1) = 18 bytes
#[repr(C, packed(2))]
#[derive(Debug, Clone, Copy, PartialEq, Eq)]
pub struct MinimizerTupleExternal {
    /// The minimizer hash value
    pub minimizer: u64,
    /// Position in the sequence
    pub pos_in_seq: u64,
    /// Position of the minimizer within the k-mer
    pub pos_in_kmer: u8,
    /// Number of k-mers in the super-k-mer
    pub num_kmers_in_super_kmer: u8,
}

impl MinimizerTupleExternal {
    /// Convert from internal MinimizerTuple
    pub fn from_internal(t: &MinimizerTuple) -> Self {
        Self {
            minimizer: t.minimizer,
            pos_in_seq: t.pos_in_seq,
            pos_in_kmer: t.pos_in_kmer,
            num_kmers_in_super_kmer: t.num_kmers_in_super_kmer,
        }
    }

    /// Convert to internal MinimizerTuple
    pub fn to_internal(&self) -> MinimizerTuple {
        MinimizerTuple {
            minimizer: self.minimizer,
            pos_in_seq: self.pos_in_seq,
            pos_in_kmer: self.pos_in_kmer,
            num_kmers_in_super_kmer: self.num_kmers_in_super_kmer,
        }
    }

    /// Read from bytes (unsafe, assumes correct alignment)
    ///
    /// # Safety
    /// Caller must ensure `bytes` points to a valid `MinimizerTupleExternal`
    #[inline]
    pub unsafe fn from_bytes(bytes: *const u8) -> Self {
        // SAFETY: read_unaligned handles packed/unaligned access
        unsafe { std::ptr::read_unaligned(bytes as *const Self) }
    }

    /// Write to bytes
    pub fn to_bytes(&self) -> [u8; TUPLE_SIZE_BYTES] {
        let mut buf = [0u8; TUPLE_SIZE_BYTES];
        unsafe {
            std::ptr::copy_nonoverlapping(
                self as *const Self as *const u8,
                buf.as_mut_ptr(),
                TUPLE_SIZE_BYTES,
            );
        }
        buf
    }

    /// Read one tuple from a reader. Returns None on EOF.
    fn read_from<R: Read>(reader: &mut R) -> std::io::Result<Option<Self>> {
        let mut buf = [0u8; TUPLE_SIZE_BYTES];
        match reader.read_exact(&mut buf) {
            Ok(()) => Ok(Some(unsafe { Self::from_bytes(buf.as_ptr()) })),
            Err(e) if e.kind() == std::io::ErrorKind::UnexpectedEof => Ok(None),
            Err(e) => Err(e),
        }
    }
}

impl PartialOrd for MinimizerTupleExternal {
    fn partial_cmp(&self, other: &Self) -> Option<std::cmp::Ordering> {
        Some(self.cmp(other))
    }
}

impl Ord for MinimizerTupleExternal {
    fn cmp(&self, other: &Self) -> std::cmp::Ordering {
        // Copy fields to avoid taking references to packed struct fields
        let self_min = self.minimizer;
        let other_min = other.minimizer;
        let self_pos = self.pos_in_seq;
        let other_pos = other.pos_in_seq;

        match self_min.cmp(&other_min) {
            std::cmp::Ordering::Equal => self_pos.cmp(&other_pos),
            ord => ord,
        }
    }
}

/// External sorter for minimizer tuples
///
/// Manages RAM-bounded sorting with temp file spillover and k-way merge.
pub struct ExternalSorter {
    /// Temp directory for intermediate files
    tmp_dir: PathBuf,
    /// Run identifier (timestamp-based for uniqueness)
    run_id: u64,
    /// Atomic counter for temp file IDs
    num_files: AtomicU64,
    /// RAM limit in GiB
    ram_limit_gib: usize,
    /// Number of threads
    num_threads: usize,
    /// Verbose logging
    verbose: bool,
    /// If true, merged file cleanup is owned by FileTuples (don't delete in Drop)
    merged_file_handed_off: std::sync::atomic::AtomicBool,
}

impl ExternalSorter {
    /// Create a new external sorter
    pub fn new(tmp_dir: impl AsRef<Path>, ram_limit_gib: usize, num_threads: usize, verbose: bool) -> std::io::Result<Self> {
        let tmp_dir = tmp_dir.as_ref().to_path_buf();

        // Create temp directory if it doesn't exist
        fs::create_dir_all(&tmp_dir)?;

        // Generate unique run ID from timestamp
        let run_id = SystemTime::now()
            .duration_since(UNIX_EPOCH)
            .unwrap()
            .as_nanos() as u64;

        Ok(Self {
            tmp_dir,
            run_id,
            num_files: AtomicU64::new(0),
            ram_limit_gib,
            num_threads,
            verbose,
            merged_file_handed_off: std::sync::atomic::AtomicBool::new(false),
        })
    }

    /// Calculate buffer size per thread in number of tuples
    ///
    /// Formula: `(ram_limit * GiB) / (2 * sizeof(tuple) * num_threads)`
    /// The factor of 2 accounts for temporary memory during parallel sort.
    pub fn buffer_size_per_thread(&self) -> usize {
        let total_bytes = self.ram_limit_gib * GIB;
        let bytes_per_thread = total_bytes / (2 * self.num_threads.max(1));
        bytes_per_thread / TUPLE_SIZE_BYTES
    }

    /// Get path for a temp file by ID
    fn temp_file_path(&self, id: u64) -> PathBuf {
        self.tmp_dir.join(format!(
            "sshash.tmp.run_{}.minimizers.{}.bin",
            self.run_id, id
        ))
    }

    /// Get path for the final merged file
    fn merged_file_path(&self) -> PathBuf {
        self.tmp_dir.join(format!(
            "sshash.tmp.run_{}.minimizers.bin",
            self.run_id
        ))
    }

    /// Sort a buffer and flush to a temp file
    ///
    /// Returns the file ID. Thread-safe via atomic counter.
    pub fn sort_and_flush(&self, buffer: &mut Vec<MinimizerTupleExternal>) -> std::io::Result<u64> {
        // Parallel sort
        buffer.par_sort_unstable();

        // Get unique file ID
        let file_id = self.num_files.fetch_add(1, Ordering::SeqCst);
        let path = self.temp_file_path(file_id);

        if self.verbose {
            debug!("Flushing {} tuples to {:?}", buffer.len(), path);
        }

        // Write to binary file
        let file = File::create(&path)?;
        let mut writer = BufWriter::with_capacity(1024 * 1024, file);

        for tuple in buffer.iter() {
            writer.write_all(&tuple.to_bytes())?;
        }

        writer.flush()?;
        buffer.clear();

        Ok(file_id)
    }

    /// Number of temp files created
    pub fn num_files(&self) -> u64 {
        self.num_files.load(Ordering::SeqCst)
    }

    /// Merge all temp files into final sorted output
    ///
    /// Returns statistics: (num_minimizers, num_positions, num_super_kmers)
    pub fn merge(&self) -> std::io::Result<MergeResult> {
        let num_files = self.num_files();

        if num_files == 0 {
            return Ok(MergeResult::default());
        }

        if num_files == 1 {
            // Just rename the single file
            let src = self.temp_file_path(0);
            let dst = self.merged_file_path();
            fs::rename(&src, &dst)?;
            return self.scan_merged_file();
        }

        // Multiple files: k-way merge using buffered I/O
        info!("Merging {} temp files...", num_files);

        let mut merger = FileMergingIterator::new(
            (0..num_files).map(|id| self.temp_file_path(id)).collect(),
        )?;

        let merged_path = self.merged_file_path();
        let file = File::create(&merged_path)?;
        let mut writer = BufWriter::with_capacity(4 * 1024 * 1024, file);

        let mut result = MergeResult::default();
        let mut prev_minimizer = u64::MAX;
        let mut prev_pos_in_seq = u64::MAX;

        while merger.has_next() {
            let tuple = merger.current();

            // Track statistics
            if tuple.minimizer != prev_minimizer {
                prev_minimizer = tuple.minimizer;
                result.num_minimizers += 1;
                result.num_positions += 1;
            } else if tuple.pos_in_seq != prev_pos_in_seq {
                result.num_positions += 1;
            }
            prev_pos_in_seq = tuple.pos_in_seq;
            result.num_super_kmers += 1;

            writer.write_all(&tuple.to_bytes())?;
            merger.next();

            if self.verbose && result.num_super_kmers % 100_000_000 == 0 {
                info!("Merged {} tuples...", result.num_super_kmers);
            }
        }

        writer.flush()?;
        drop(merger);

        // Remove temp files
        for id in 0..num_files {
            let _ = fs::remove_file(self.temp_file_path(id));
        }

        info!(
            "Merge complete: {} minimizers, {} positions, {} super-kmers",
            result.num_minimizers, result.num_positions, result.num_super_kmers
        );

        Ok(result)
    }

    /// Scan merged file to compute statistics (for single-file case)
    fn scan_merged_file(&self) -> std::io::Result<MergeResult> {
        let path = self.merged_file_path();
        let file = File::open(&path)?;
        let mut reader = BufReader::with_capacity(READER_BUF_SIZE, file);

        let mut result = MergeResult::default();
        let mut prev_minimizer = u64::MAX;
        let mut prev_pos_in_seq = u64::MAX;

        while let Some(tuple) = MinimizerTupleExternal::read_from(&mut reader)? {
            if tuple.minimizer != prev_minimizer {
                prev_minimizer = tuple.minimizer;
                result.num_minimizers += 1;
                result.num_positions += 1;
            } else if tuple.pos_in_seq != prev_pos_in_seq {
                result.num_positions += 1;
            }
            prev_pos_in_seq = tuple.pos_in_seq;
            result.num_super_kmers += 1;
        }

        Ok(result)
    }

    /// Read merged tuples into memory as internal MinimizerTuples
    ///
    /// Call this after `merge()` to get the final sorted tuples.
    /// For large datasets, prefer [`open_merged_file`] to avoid full materialization.
    pub fn read_merged_tuples(&self) -> std::io::Result<Vec<MinimizerTuple>> {
        let path = self.merged_file_path();
        let file = File::open(&path)?;
        let mmap = unsafe { Mmap::map(&file)? };

        let num_tuples = mmap.len() / TUPLE_SIZE_BYTES;
        let mut tuples = Vec::with_capacity(num_tuples);

        for i in 0..num_tuples {
            let offset = i * TUPLE_SIZE_BYTES;
            let ext = unsafe { MinimizerTupleExternal::from_bytes(mmap.as_ptr().add(offset)) };
            tuples.push(ext.to_internal());
        }

        Ok(tuples)
    }

    /// Open the merged file for sequential buffered access.
    ///
    /// Returns a [`FileTuples`] handle that provides sequential access via
    /// buffered readers. Each scan pass opens a fresh `BufReader`, keeping
    /// RSS proportional to the buffer size (~4 MB) instead of the file size.
    ///
    /// **Important**: The returned `FileTuples` takes ownership of cleanup
    /// responsibility for the merged file.
    pub fn open_merged_file(&self) -> std::io::Result<FileTuples> {
        let path = self.merged_file_path();
        let file_len = fs::metadata(&path)?.len() as usize;
        let num_tuples = file_len / TUPLE_SIZE_BYTES;

        // Mark that cleanup responsibility has been transferred to FileTuples
        self.merged_file_handed_off.store(true, Ordering::SeqCst);

        info!("Opened merged file: {} tuples ({:.2} GB on disk)",
            num_tuples, file_len as f64 / GIB as f64);

        Ok(FileTuples {
            path: path.clone(),
            num_tuples,
        })
    }

    /// Remove the merged file (cleanup)
    pub fn remove_merged_file(&self) -> std::io::Result<()> {
        let path = self.merged_file_path();
        if path.exists() {
            fs::remove_file(path)?;
        }
        Ok(())
    }
}

impl Drop for ExternalSorter {
    fn drop(&mut self) {
        // Clean up any remaining temp files
        for id in 0..self.num_files() {
            let _ = fs::remove_file(self.temp_file_path(id));
        }
        // Only clean up merged file if it wasn't handed off to FileTuples
        if !self.merged_file_handed_off.load(Ordering::SeqCst) {
            let _ = fs::remove_file(self.merged_file_path());
        }
    }
}

// ---------------------------------------------------------------------------
// Sequential buffered tuple access (no mmap)
// ---------------------------------------------------------------------------

/// Handle to the merged external sort file for sequential buffered access.
///
/// Unlike the previous `MmapTuples`, this does NOT mmap the file. Instead,
/// each access pass opens a fresh `BufReader`, reading tuples sequentially
/// with a ~4 MB buffer. This keeps RSS proportional to the buffer size
/// instead of the file size (~8-10 GB for large datasets).
pub struct FileTuples {
    /// Path to the merged file
    path: PathBuf,
    /// Total number of tuples
    num_tuples: usize,
}

impl FileTuples {
    /// Total number of tuples in the merged file.
    #[inline]
    pub fn num_tuples(&self) -> usize {
        self.num_tuples
    }

    /// Path to the underlying merged file (for deriving temp file names).
    #[inline]
    pub fn path(&self) -> &Path {
        &self.path
    }

    /// Create an iterator that yields one [`BucketScan`] per unique minimizer,
    /// scanning the file sequentially via buffered I/O.
    ///
    /// Each call opens a fresh `BufReader` — no state is retained between
    /// passes, and no mmap pages linger in memory.
    pub fn bucket_iter(&self) -> std::io::Result<FileBucketIter> {
        let file = File::open(&self.path)?;
        let reader = BufReader::with_capacity(READER_BUF_SIZE, file);
        Ok(FileBucketIter {
            reader,
            pos: 0,
            num_tuples: self.num_tuples,
            lookahead: None,
        })
    }

    /// Create a sequential tuple reader for forward-only access.
    ///
    /// Returns tuples one at a time via `read_next()`. Used by the
    /// sparse/skew index builder for its sequential pass over all tuples.
    pub fn sequential_reader(&self) -> std::io::Result<SequentialTupleReader> {
        let file = File::open(&self.path)?;
        let reader = BufReader::with_capacity(READER_BUF_SIZE, file);
        Ok(SequentialTupleReader { reader })
    }
}

impl Drop for FileTuples {
    fn drop(&mut self) {
        // Clean up the merged file when done
        let _ = fs::remove_file(&self.path);
    }
}

/// Sequential reader for tuples from the merged file.
///
/// Reads tuples one at a time via `read_next()`. All access is
/// strictly forward — no seeking or random access.
pub struct SequentialTupleReader {
    reader: BufReader<File>,
}

impl SequentialTupleReader {
    /// Read the next tuple, or None on EOF.
    #[inline]
    pub fn read_next(&mut self) -> std::io::Result<Option<MinimizerTupleExternal>> {
        MinimizerTupleExternal::read_from(&mut self.reader)
    }
}

/// Sequential iterator over buckets in the merged file via buffered I/O.
///
/// Each call to `next()` returns a [`BucketScan`] describing one bucket
/// (a contiguous group of tuples sharing the same minimizer value).
/// Owns a `BufReader` — no mmap pages are kept resident.
pub struct FileBucketIter {
    reader: BufReader<File>,
    /// Current tuple position index
    pos: usize,
    /// Total tuples in file
    num_tuples: usize,
    /// Lookahead tuple (the first tuple of the NEXT bucket, read while
    /// scanning the current bucket's boundary)
    lookahead: Option<MinimizerTupleExternal>,
}

impl Iterator for FileBucketIter {
    type Item = BucketScan;

    fn next(&mut self) -> Option<BucketScan> {
        if self.pos >= self.num_tuples {
            return None;
        }

        // Get the first tuple of this bucket — either from lookahead or by reading
        let first = if let Some(la) = self.lookahead.take() {
            la
        } else {
            match MinimizerTupleExternal::read_from(&mut self.reader) {
                Ok(Some(t)) => t,
                _ => return None,
            }
        };

        let start = self.pos;
        let minimizer = first.minimizer;
        let mut cached_size = 1usize;
        let mut prev_pos_in_seq = first.pos_in_seq;
        let mut num_kmers = first.num_kmers_in_super_kmer as u64;
        self.pos += 1;

        // Read tuples until we hit a different minimizer
        while self.pos < self.num_tuples {
            match MinimizerTupleExternal::read_from(&mut self.reader) {
                Ok(Some(t)) => {
                    if t.minimizer != minimizer {
                        // This tuple belongs to the next bucket — save as lookahead
                        self.lookahead = Some(t);
                        break;
                    }
                    if t.pos_in_seq != prev_pos_in_seq {
                        cached_size += 1;
                        prev_pos_in_seq = t.pos_in_seq;
                    }
                    num_kmers += t.num_kmers_in_super_kmer as u64;
                    self.pos += 1;
                }
                _ => break,
            }
        }

        Some(BucketScan {
            minimizer,
            cached_size,
            start_tuple_idx: start as u64,
            num_tuples: (self.pos - start) as u32,
            num_kmers,
        })
    }
}

/// Metadata about a single bucket, gathered during a sequential scan.
#[derive(Debug, Clone, Copy)]
pub struct BucketScan {
    /// The minimizer value for this bucket.
    pub minimizer: u64,
    /// Number of unique super-kmers (distinct `pos_in_seq` values).
    pub cached_size: usize,
    /// Index of the first tuple in the file.
    pub start_tuple_idx: u64,
    /// Number of tuples in this bucket.
    pub num_tuples: u32,
    /// Total k-mers across all tuples in this bucket.
    pub num_kmers: u64,
}

/// Result of merge operation
#[derive(Debug, Default, Clone, Copy)]
pub struct MergeResult {
    /// Number of distinct minimizers
    pub num_minimizers: u64,
    /// Total number of positions
    pub num_positions: u64,
    /// Number of super-k-mers
    pub num_super_kmers: u64,
}

/// K-way merge iterator using buffered file I/O.
///
/// Uses buffered readers instead of mmap to avoid keeping all temp file pages
/// resident in memory. Each file gets a ~1 MB read buffer.
///
/// Memory footprint: ~1 MB per file (buffer) + 18 bytes per file (current tuple).
struct FileMergingIterator {
    /// Buffered readers for each input file
    readers: Vec<BufReader<File>>,
    /// Current tuple from each file (None if exhausted)
    current_tuples: Vec<Option<MinimizerTupleExternal>>,
    /// Current minimum index
    min_idx: usize,
    /// Number of active files
    num_active: usize,
}

impl FileMergingIterator {
    fn new(paths: Vec<PathBuf>) -> std::io::Result<Self> {
        let num_files = paths.len();
        if num_files == 0 {
            return Ok(Self {
                readers: Vec::new(),
                current_tuples: Vec::new(),
                min_idx: 0,
                num_active: 0,
            });
        }

        let mut readers = Vec::with_capacity(num_files);
        let mut current_tuples = Vec::with_capacity(num_files);

        for path in &paths {
            let file = File::open(path)?;
            let mut reader = BufReader::with_capacity(1024 * 1024, file);
            let tuple = MinimizerTupleExternal::read_from(&mut reader)?;
            current_tuples.push(tuple);
            readers.push(reader);
        }

        let num_active = current_tuples.iter().filter(|t| t.is_some()).count();
        let mut merger = Self {
            readers,
            current_tuples,
            min_idx: 0,
            num_active,
        };

        if num_active > 0 {
            merger.compute_min();
        }

        Ok(merger)
    }

    fn has_next(&self) -> bool {
        self.num_active > 0
    }

    fn current(&self) -> MinimizerTupleExternal {
        debug_assert!(self.num_active > 0);
        self.current_tuples[self.min_idx].unwrap()
    }

    fn next(&mut self) {
        if self.num_active == 0 {
            return;
        }

        // Advance the min file
        match MinimizerTupleExternal::read_from(&mut self.readers[self.min_idx]) {
            Ok(tuple) => {
                if tuple.is_none() {
                    self.num_active -= 1;
                }
                self.current_tuples[self.min_idx] = tuple;
            }
            Err(_) => {
                self.current_tuples[self.min_idx] = None;
                self.num_active -= 1;
            }
        }

        if self.num_active > 0 {
            self.compute_min();
        }
    }

    fn compute_min(&mut self) {
        self.min_idx = 0;
        let mut min_tuple: Option<MinimizerTupleExternal> = None;

        for (i, tuple_opt) in self.current_tuples.iter().enumerate() {
            if let Some(tuple) = tuple_opt {
                if min_tuple.is_none() || *tuple < min_tuple.unwrap() {
                    min_tuple = Some(*tuple);
                    self.min_idx = i;
                }
            }
        }
    }
}

#[cfg(test)]
mod tests {
    use super::*;
    use tempfile::TempDir;

    #[test]
    fn test_tuple_external_size() {
        // Verify packed size
        assert_eq!(std::mem::size_of::<MinimizerTupleExternal>(), TUPLE_SIZE_BYTES);
    }

    #[test]
    fn test_tuple_roundtrip() {
        let tuple = MinimizerTupleExternal {
            minimizer: 12345,
            pos_in_seq: 67890,
            pos_in_kmer: 5,
            num_kmers_in_super_kmer: 3,
        };

        let bytes = tuple.to_bytes();
        let recovered = unsafe { MinimizerTupleExternal::from_bytes(bytes.as_ptr()) };

        assert_eq!(tuple, recovered);
    }

    #[test]
    fn test_external_sorter_basic() {
        let tmp_dir = TempDir::new().unwrap();
        let sorter = ExternalSorter::new(tmp_dir.path(), 1, 2, false).unwrap();

        // Buffer size should be reasonable
        let buf_size = sorter.buffer_size_per_thread();
        assert!(buf_size > 0);

        // Test sort_and_flush
        let mut buffer: Vec<MinimizerTupleExternal> = vec![
            MinimizerTupleExternal {
                minimizer: 100,
                pos_in_seq: 10,
                pos_in_kmer: 1,
                num_kmers_in_super_kmer: 2,
            },
            MinimizerTupleExternal {
                minimizer: 50,
                pos_in_seq: 20,
                pos_in_kmer: 3,
                num_kmers_in_super_kmer: 1,
            },
        ];

        sorter.sort_and_flush(&mut buffer).unwrap();
        assert!(buffer.is_empty());
        assert_eq!(sorter.num_files(), 1);
    }

    #[test]
    fn test_external_sorter_merge() {
        let tmp_dir = TempDir::new().unwrap();
        let sorter = ExternalSorter::new(tmp_dir.path(), 1, 2, false).unwrap();

        // Create multiple temp files
        let mut buffer1: Vec<MinimizerTupleExternal> = vec![
            MinimizerTupleExternal { minimizer: 10, pos_in_seq: 1, pos_in_kmer: 0, num_kmers_in_super_kmer: 1 },
            MinimizerTupleExternal { minimizer: 30, pos_in_seq: 3, pos_in_kmer: 0, num_kmers_in_super_kmer: 1 },
        ];
        sorter.sort_and_flush(&mut buffer1).unwrap();

        let mut buffer2: Vec<MinimizerTupleExternal> = vec![
            MinimizerTupleExternal { minimizer: 20, pos_in_seq: 2, pos_in_kmer: 0, num_kmers_in_super_kmer: 1 },
            MinimizerTupleExternal { minimizer: 40, pos_in_seq: 4, pos_in_kmer: 0, num_kmers_in_super_kmer: 1 },
        ];
        sorter.sort_and_flush(&mut buffer2).unwrap();

        assert_eq!(sorter.num_files(), 2);

        // Merge
        let result = sorter.merge().unwrap();
        assert_eq!(result.num_super_kmers, 4);
        assert_eq!(result.num_minimizers, 4);

        // Read merged tuples
        let tuples = sorter.read_merged_tuples().unwrap();
        assert_eq!(tuples.len(), 4);

        // Verify sorted order
        assert_eq!(tuples[0].minimizer, 10);
        assert_eq!(tuples[1].minimizer, 20);
        assert_eq!(tuples[2].minimizer, 30);
        assert_eq!(tuples[3].minimizer, 40);
    }

    #[test]
    fn test_tuple_ordering() {
        let t1 = MinimizerTupleExternal { minimizer: 100, pos_in_seq: 50, pos_in_kmer: 0, num_kmers_in_super_kmer: 1 };
        let t2 = MinimizerTupleExternal { minimizer: 100, pos_in_seq: 60, pos_in_kmer: 0, num_kmers_in_super_kmer: 1 };
        let t3 = MinimizerTupleExternal { minimizer: 200, pos_in_seq: 10, pos_in_kmer: 0, num_kmers_in_super_kmer: 1 };

        assert!(t1 < t2);  // Same minimizer, different pos
        assert!(t1 < t3);  // Different minimizer
        assert!(t2 < t3);  // Different minimizer
    }

    #[test]
    fn test_file_tuples_bucket_iter() {
        let tmp_dir = TempDir::new().unwrap();
        let sorter = ExternalSorter::new(tmp_dir.path(), 1, 2, false).unwrap();

        // Create a sorted file with 2 buckets: minimizer 10 (2 tuples), minimizer 20 (1 tuple)
        let mut buffer: Vec<MinimizerTupleExternal> = vec![
            MinimizerTupleExternal { minimizer: 10, pos_in_seq: 1, pos_in_kmer: 0, num_kmers_in_super_kmer: 3 },
            MinimizerTupleExternal { minimizer: 10, pos_in_seq: 2, pos_in_kmer: 0, num_kmers_in_super_kmer: 2 },
            MinimizerTupleExternal { minimizer: 20, pos_in_seq: 5, pos_in_kmer: 1, num_kmers_in_super_kmer: 4 },
        ];
        sorter.sort_and_flush(&mut buffer).unwrap();
        sorter.merge().unwrap();
        let ft = sorter.open_merged_file().unwrap();

        let buckets: Vec<BucketScan> = ft.bucket_iter().unwrap().collect();
        assert_eq!(buckets.len(), 2);
        assert_eq!(buckets[0].minimizer, 10);
        assert_eq!(buckets[0].cached_size, 2);
        assert_eq!(buckets[0].num_tuples, 2);
        assert_eq!(buckets[0].num_kmers, 5); // 3 + 2
        assert_eq!(buckets[1].minimizer, 20);
        assert_eq!(buckets[1].cached_size, 1);
        assert_eq!(buckets[1].num_tuples, 1);
        assert_eq!(buckets[1].num_kmers, 4);
    }

    #[test]
    fn test_sequential_reader() {
        let tmp_dir = TempDir::new().unwrap();
        let sorter = ExternalSorter::new(tmp_dir.path(), 1, 2, false).unwrap();

        let mut buffer: Vec<MinimizerTupleExternal> = vec![
            MinimizerTupleExternal { minimizer: 5, pos_in_seq: 10, pos_in_kmer: 0, num_kmers_in_super_kmer: 1 },
            MinimizerTupleExternal { minimizer: 15, pos_in_seq: 20, pos_in_kmer: 0, num_kmers_in_super_kmer: 2 },
        ];
        sorter.sort_and_flush(&mut buffer).unwrap();
        sorter.merge().unwrap();
        let ft = sorter.open_merged_file().unwrap();

        let mut reader = ft.sequential_reader().unwrap();
        let t1 = reader.read_next().unwrap().unwrap();
        let t1_min = t1.minimizer; // copy to avoid packed struct ref
        assert_eq!(t1_min, 5);
        let t2 = reader.read_next().unwrap().unwrap();
        let t2_min = t2.minimizer;
        assert_eq!(t2_min, 15);
        assert!(reader.read_next().unwrap().is_none());
    }
}