Implement pack CLI command for matrix packing and layer compaction

Adds the `pack` subcommand to `obikmer2` for persisting presence and count matrices in sparse or dense formats. Introduces the `compact_layer` module in `obikrebuild` to merge multiple partition layers into a single layer in-place via atomic operations. Updates dependencies across `obikdump`, `obikmer2`, and `obikrebuild` to resolve new local crate references. Shifts the architecture from multi-layer accumulation to in-place compaction, removing legacy rebuild modules.

src/Cargo.lock

@@ -1523,12 +1523,14 @@ version = "0.1.0"
 name = "obikdump"
 version = "0.1.0"
 dependencies = [
+ "obicompactvec",
  "obidebruinj",
  "obifastwrite",
  "obikfilter",
  "obikidxcache",
  "obikindex",
  "obikseq",
+ "obisys",
  "rayon",
 ]
 
@@ -1674,6 +1676,7 @@ dependencies = [
  "obikindex",
  "obikindexer",
  "obikmerge",
+ "obikrebuild",
  "obikselect",
  "obikseq",
  "obipipeline",
@@ -1736,14 +1739,12 @@ dependencies = [
 name = "obikrebuild"
 version = "0.1.0"
 dependencies = [
- "obicompactvec",
  "obidebruinj",
  "obikfilter",
+ "obikidxcache",
  "obikindex",
  "obikindexer",
- "obikmerge",
  "obikseq",
- "obiskio",
  "obisys",
  "tracing",
 ]

src/obikdump/Cargo.toml

@@ -10,4 +10,6 @@ obikidxcache  = { path = "../obikidxcache" }
 obikseq       = { path = "../obikseq" }
 obidebruinj   = { path = "../obidebruinj" }
 obifastwrite  = { path = "../obifastwrite" }
+obicompactvec = { path = "../obicompactvec" }
+obisys        = { path = "../obisys" }
 rayon         = "1"

src/obikindex/src/index/kmer_index.rs

@@ -245,14 +245,25 @@ impl KmerIndex {
     /// Reduces per-query file-open overhead from O(n_genomes) to O(1) per partition.
     /// Column files are kept in place; packed files take priority when opening.
     ///
-    /// If `sparse` is set, presence matrices go one step further, from the
+    /// If `sparse` is set, both matrix kinds go one step further, from their
-    /// dense `.pbmx` form into `obicompactvec::PersistentSparseBitMatrix`'s
+    /// dense single-file form into `obicompactvec`'s sparse, deduplicated
-    /// on-disk format (see `DevDocMD/architecture/siblings.md`) — count
+    /// on-disk formats (`PersistentSparseBitMatrix` for presence,
-    /// matrices are unaffected, sparse count matrices aren't implemented
+    /// `PersistentSparseCompactIntMatrix` for counts) — smaller and faster
-    /// (see the sparse-matrix design plan's "Explicitly deferred").
+    /// for single-row access on real, sparse data; column-oriented access
-    /// TODO: To be moved somewhere else
+    /// (`--metric` distance matrices) is much slower on the sparse format.
-    pub(crate) fn pack_matrices(&self, sparse: bool) -> OKIResult<()> {
+    ///
-        use obicompactvec::{pack_bit_matrix, pack_compact_int_matrix, pack_sparse_bit_matrix};
+    /// Public — and not moved out of this crate, despite covering the same
+    /// "maintenance operation on an already-built index" territory as
+    /// `obikrebuild` — because `finalize_indexed` calls it internally as the
+    /// shared tail of every index-building algorithm (`select`/`filter`/
+    /// `merge`), and `obikindex` cannot depend on `obikrebuild` (wrong
+    /// direction). Standalone re-packing (`obikmer2 pack`) calls this same
+    /// method directly.
+    pub fn pack_matrices(&self, sparse: bool) -> OKIResult<()> {
+        use obicompactvec::{
+            pack_bit_matrix, pack_compact_int_matrix, pack_sparse_bit_matrix,
+            pack_sparse_compact_int_matrix,
+        };
 
         let n = self.n_partitions();
         let order: Vec<usize> = (0..n).collect();
@@ -277,9 +288,13 @@ impl KmerIndex {
                         }
                     }
                     if counts_dir.exists() {
+                        if sparse {
+                            pack_sparse_compact_int_matrix(&counts_dir).map_err(OKIError::Io)?;
+                        } else {
                             pack_compact_int_matrix(&counts_dir).map_err(OKIError::Io)?;
                         }
                     }
+                }
                 Ok(())
             },
             |_, _, _| {

src/obikmer2/Cargo.toml

@@ -19,6 +19,7 @@ obikmerge     = { path = "../obikmerge" }
 obikfilter    = { path = "../obikfilter" }
 obikselect    = { path = "../obikselect" }
 obikdump      = { path = "../obikdump" }
+obikrebuild   = { path = "../obikrebuild" }
 obifastwrite  = { path = "../obifastwrite" }
 obiskbuilder  = { path = "../obiskbuilder" }
 clap          = { version = "4", features = ["derive"] }

src/obikmer2/src/cmd/mod.rs

@@ -4,6 +4,7 @@ pub mod estimate;
 pub mod filter;
 pub mod index;
 pub mod merge;
+pub mod pack;
 mod predicate;
 pub mod select;
 pub mod superkmer;

src/obikmer2/src/cmd/pack/mod.rs

@@ -0,0 +1,71 @@
+use std::path::PathBuf;
+
+use clap::Args;
+use obikindex::KmerIndex;
+use obikrebuild::IndexCompact;
+use obisys::{Reporter, Stage, progress_bar};
+use tracing::info;
+
+#[derive(Args)]
+pub struct PackArgs {
+    /// Index directory to pack
+    pub index: PathBuf,
+
+    /// Compact every partition's accumulated layers into one before packing
+    /// — undoes the multi-layer stopgap `merge` leaves behind.
+    #[arg(long, default_value_t = false)]
+    pub compact_layers: bool,
+
+    /// Pack presence and count matrices into the dense on-disk format instead
+    /// of the default sparse, deduplicated one. Dense is faster for
+    /// column-oriented access (`--metric` distance matrices); sparse is
+    /// smaller and faster for single-row access on real, sparse data.
+    #[arg(long, default_value_t = false)]
+    pub dense: bool,
+}
+
+pub fn run(args: PackArgs) {
+    // Modifies the index in place; acquired before opening so a concurrent
+    // writer can't slip in between the open and the pack below.
+    let _lock = obisys::DirLock::acquire(&args.index).unwrap_or_else(|e| {
+        eprintln!("error locking index directory {}: {e}", args.index.display());
+        std::process::exit(1);
+    });
+
+    let idx = KmerIndex::open(&args.index).unwrap_or_else(|e| {
+        eprintln!("error opening index: {e}");
+        std::process::exit(1);
+    });
+
+    let n_genomes = idx.meta().genomes().unwrap_or_else(|e| {
+        eprintln!("error reading index metadata: {e}");
+        std::process::exit(1);
+    }).len();
+    info!(
+        "pack: {} partition(s), {} genome(s)",
+        idx.n_partitions(),
+        n_genomes,
+    );
+
+    let mut rep = Reporter::new();
+
+    if args.compact_layers {
+        let t = Stage::start("compact layers");
+        let pb = progress_bar("compact", idx.n_partitions() as u64, "partitions");
+        idx.compact_layers(|| pb.inc(1)).unwrap_or_else(|e| {
+            eprintln!("compact error: {e}");
+            std::process::exit(1);
+        });
+        pb.finish_and_clear();
+        rep.push(t.stop());
+    }
+
+    let t = Stage::start("pack");
+    idx.pack_matrices(!args.dense).unwrap_or_else(|e| {
+        eprintln!("pack error: {e}");
+        std::process::exit(1);
+    });
+    rep.push(t.stop());
+
+    rep.print();
+}

src/obikmer2/src/main.rs

@@ -27,6 +27,8 @@ enum Commands {
     Dump(cmd::dump::DumpArgs),
     /// Assemble an index's kmers into unitigs and write them as FASTA
     Unitig(cmd::unitig::UnitigArgs),
+    /// Pack an index's matrices into single-file, sparse format by default (--dense to opt out), in place
+    Pack(cmd::pack::PackArgs),
     /// Estimate approximate-evidence false-positive rates for given parameters
     Estimate(cmd::estimate::EstimateArgs),
     /// Read/write genome metadata (CSV) on an already-built index
@@ -50,6 +52,7 @@ fn main() {
         Commands::Select(args) => cmd::select::run(args),
         Commands::Dump(args) => cmd::dump::run(args),
         Commands::Unitig(args) => cmd::unitig::run(args),
+        Commands::Pack(args) => cmd::pack::run(args),
         Commands::Estimate(args) => cmd::estimate::run(args),
         Commands::Annotate(args) => cmd::annotate::run(args),
     }

src/obikrebuild/Cargo.toml

@@ -7,9 +7,7 @@ edition = "2024"
 obikindex     = { path = "../obikindex" }
 obikindexer   = { path = "../obikindexer" }
 obikfilter    = { path = "../obikfilter" }
-obikmerge   = { path = "../obikmerge" }
+obikidxcache  = { path = "../obikidxcache" }
-obicompactvec = { path = "../obicompactvec" }
-obiskio     = { path = "../obiskio" }
 obikseq       = { path = "../obikseq" }
 obidebruinj   = { path = "../obidebruinj" }
 obisys        = { path = "../obisys" }

src/obikrebuild/src/compact_layer.rs

@@ -0,0 +1,113 @@
+//! Compacting a partition's multiple layers into one, in place. The
+//! multi-layer structure is a stopgap that lets `obikmerge` add genomes
+//! without a full rebuild; this collapses that accumulated history back
+//! into a single layer. Distinct from `obikfilter::Filter`: no k-mer is
+//! removed here, and every layer of a partition merges into *one*, rather
+//! than one output layer per source layer. `KmerIndex` is foreign, so this
+//! is an extension trait.
+
+use std::collections::HashMap;
+use std::fs;
+
+use obidebruinj::GraphDeBruijn;
+use obikfilter::FilteredPartitionIter;
+use obikidxcache::index_cache::IndexCache;
+use obikindex::layer::{IndexMode, KmerLayer, TypedLayer};
+use obikindex::{KmerIndex, OKIError, OKIResult};
+use obikindexer::write_graph_as_unitigs;
+use obikseq::CanonicalKmer;
+use obisys::PartitionRunner;
+
+pub trait IndexCompact {
+    /// Compact every partition with more than one layer into a single
+    /// layer, in place. Partitions already at one layer are left untouched.
+    fn compact_layers(&self, on_partition: impl Fn() + Send + Sync) -> OKIResult<()>;
+}
+
+impl IndexCompact for KmerIndex {
+    fn compact_layers(&self, on_partition: impl Fn() + Send + Sync) -> OKIResult<()> {
+        let n_genomes = self.meta().genomes().map_err(OKIError::Io)?.len();
+        let use_counts = self.meta().config.with_counts;
+        let block_bits = self.block_bits();
+        let mode = self.evidence_mode();
+        let n_partitions = self.n_partitions();
+        let order: Vec<usize> = (0..n_partitions).collect();
+
+        PartitionRunner::new().run(
+            &order,
+            |i| compact_partition(self, i, use_counts, n_genomes, block_bits, mode),
+            |_, _, _| on_partition(),
+        )?;
+
+        Ok(())
+    }
+}
+
+/// Merge every layer of partition `i` into a single one, replacing the
+/// existing layers in place. No-op if the partition already has one layer
+/// (or none).
+fn compact_partition(
+    idx: &KmerIndex,
+    i: usize,
+    use_counts: bool,
+    n_genomes: usize,
+    block_bits: u8,
+    mode: &IndexMode,
+) -> OKIResult<()> {
+    let partition = idx.partition(i)?;
+    let n_layers = partition.n_layers();
+    if n_layers <= 1 {
+        return Ok(());
+    }
+
+    // ── Read: every layer's kmers, combined — no filter, nothing removed ──
+    let mut survivors: HashMap<CanonicalKmer, Box<[u32]>> = HashMap::new();
+    {
+        let cache = IndexCache::new(idx, Some(vec![i]));
+        cache.iter_partition_kmers(i, use_counts, n_genomes, &[], |kmer, row| {
+            survivors.insert(kmer, row);
+            true
+        })?;
+    }
+
+    // ── Build the combined layer in a scratch directory ────────────────────
+    let tmp_dir = partition.dir().join("layer_compact_tmp");
+    if tmp_dir.exists() {
+        fs::remove_dir_all(&tmp_dir).map_err(OKIError::Io)?;
+    }
+    fs::create_dir_all(&tmp_dir).map_err(OKIError::Io)?;
+
+    let mut g = GraphDeBruijn::new();
+    for &kmer in survivors.keys() {
+        g.push(kmer);
+    }
+    write_graph_as_unitigs(g, &tmp_dir)?;
+
+    TypedLayer::<()>::build_with_matrix(
+        &tmp_dir,
+        block_bits,
+        mode,
+        !use_counts,
+        n_genomes,
+        |kmer| survivors.get(&kmer).cloned().expect("kmer pushed into the graph must be a survivor"),
+    )?;
+
+    // ── Swap: drop every existing layer, install the combined one as layer 0 ─
+    for l in 0..n_layers {
+        let layer_dir = partition.layer_dir(l)?;
+        fs::remove_dir_all(&layer_dir).map_err(OKIError::Io)?;
+    }
+    let layer0_dir = KmerLayer::new(&partition, 0)
+        .create()
+        .map_err(OKIError::Io)?
+        .dir()
+        .to_path_buf();
+    for entry in fs::read_dir(&tmp_dir).map_err(OKIError::Io)? {
+        let entry = entry.map_err(OKIError::Io)?;
+        let dest = layer0_dir.join(entry.file_name());
+        fs::rename(entry.path(), dest).map_err(OKIError::Io)?;
+    }
+    fs::remove_dir_all(&tmp_dir).map_err(OKIError::Io)?;
+
+    Ok(())
+}

src/obikrebuild/src/lib.rs

@@ -1,12 +1,26 @@
-//! Rebuilding an `obikindex::KmerIndex`: compacting a source index into a
+//! Maintenance/transformation operations on an already-built
-//! new single-layer index while applying k-mer filters (`rebuild`), and
+//! `obikindex::KmerIndex`, not part of the `Index { Partition { Layer } }`
-//! reindexing an existing index's evidence representation in place
+//! data model itself — kept out of `obikindex` so that crate doesn't grow
-//! (`reindex`, `Exact`/`Approx`/`Hybrid`). Both are maintenance/
+//! every algorithm's own dependencies (`obikfilter`, `obikidxcache`,
-//! transformation operations on an already-built index, not part of the
+//! `obikindexer`).
-//! `Index { Partition { Layer } }` data model itself — kept out of
+//!
-//! `obikindex` so that crate doesn't grow every algorithm's own
+//! [`compact_layer`] collapses a partition's accumulated layers (the
-//! dependencies (`obikfilter`, `obikmerge`, `obikindexer`).
+//! stopgap `obikmerge` uses to add genomes without a full rebuild) back
+//! into one, in place. `reindex` (reindexing an existing index's evidence
+//! representation in place — `Exact`/`Approx`/`Hybrid`) is temporarily
+//! disabled: it predates this session's refactor and still reaches
+//! `obikindex` internals (`root_path`/`meta` fields, `index_dir`/
+//! `layer_dir` methods) that are no longer accessible from outside that
+//! crate. Fixing it is separate, future work.
+//!
+//! Removing k-mers (filtering) and repacking matrix files are *not* here:
+//! the former lives in `obikfilter::Filter` (a fresh index at a new
+//! output, not in place); the latter is `obikindex::KmerIndex::
+//! pack_matrices` itself, since `finalize_indexed` — the shared tail of
+//! every index-building algorithm — calls it internally and `obikindex`
+//! cannot depend back on this crate.
 
-mod rebuild;
+mod compact_layer;
-mod rebuild_layer;
+// mod reindex; // disabled — see module doc above.
-mod reindex;
+
+pub use compact_layer::IndexCompact;

src/obikrebuild/src/rebuild.rs

@@ -1,79 +0,0 @@
-use std::path::Path;
-
-use obikindex::IndexBuilder;
-use obikfilter::KmerFilter;
-use obikmerge::MergeMode;
-use obisys::{Reporter, Stage, progress_bar};
-use tracing::info;
-
-use obikindex::{OKIError, OKIResult};
-use obikindex::KmerIndex;
-use obikindex::IndexState;
-use obisys::PartitionRunner;
-
-impl KmerIndex {
-    /// Rebuild `src` into a new compact single-layer index at `output`.
-    ///
-    /// Only k-mers whose per-genome row passes every filter in `filters` are
-    /// written. If `filters` is empty every k-mer is kept (pure compaction).
-    ///
-    /// `mode` controls whether the output stores counts or presence/absence.
-    /// A count source may be rebuilt in presence mode; a presence source
-    /// cannot be rebuilt in count mode.
-    pub fn rebuild<P: AsRef<Path>>(
-        output: P,
-        src: &KmerIndex,
-        filters: &[Box<dyn KmerFilter>],
-        mode: MergeMode,
-        force: bool,
-        rep: &mut Reporter,
-    ) -> OKIResult<Self> {
-        let output = output.as_ref();
-
-        if src.state()? != IndexState::Indexed {
-            return Err(OKIError::NotIndexed(src.root_path.clone()));
-        }
-
-        if mode == MergeMode::Count && !src.meta.config.with_counts {
-            return Err(OKIError::InvalidInput(
-                "cannot rebuild in count mode from a presence-only source index".into(),
-            ));
-        }
-
-        KmerIndex::clear_output_for_create(output, force)?;
-
-        // ── Create output directory + metadata ────────────────────────────────
-        let mut config = src.meta.config.clone();
-        config.with_counts = mode == MergeMode::Count;
-        let genomes = src.genomes()?;
-
-        let n_genomes = genomes.len();
-        let n_partitions = src.n_partitions();
-        let block_bits = config.block_bits;
-
-        // ── Create an empty destination KmerPartition ─────────────────────────
-        let dst_partition = KmerIndex::create_skeleton(output, config, genomes)?;
-
-        info!(
-            "rebuild: {} partition(s), {} genome(s), mode={:?}",
-            n_partitions, n_genomes, mode,
-        );
-
-        let t = Stage::start("rebuild");
-        let pb = progress_bar("rebuild", n_partitions as u64, "partitions");
-
-        let order: Vec<usize> = (0..n_partitions).collect();
-        let runner = PartitionRunner::new();
-        runner.run(
-            &order,
-            |i| dst_partition.rebuild_partition(src, i, filters, mode, n_genomes, block_bits),
-            |_, _, _| { pb.inc(1); },
-        ).map_err(OKIError::Partition)?;
-
-        pb.finish_and_clear();
-
-        rep.push(t.stop());
-
-        KmerIndex::finalize_indexed(output, rep, false)
-    }
-}

src/obikrebuild/src/rebuild_layer.rs

@@ -1,270 +0,0 @@
-use std::path::Path;
-
-use obicompactvec::{
-    FilterMask, PersistentBitMatrixBuilder, PersistentBitVecBuilder,
-    PersistentCompactIntMatrixBuilder, PersistentCompactIntVecBuilder, eval_filter_mask,
-};
-use obidebruinj::GraphDeBruijn;
-use obikseq::CanonicalKmer;
-use obikindex::layer::meta::PartitionMeta;
-use obikindex::layer::{IndexMode, MphfLayer};
-use obikindex::layer::utils::layer_dir;
-use obiskio::UnitigFileReader;
-use obikindex::{OKIError, OKIResult};
-
-use obikindex::load_meta;
-use obikfilter::KmerFilter;
-use obikindexer::materialize_layer;
-use obikmerge::{MergeMode, SrcLayerData};
-use obikindex::KmerIndex;
-
-// ── Builders — pair matrix builder + column builders for one mode ─────────────
-
-enum Builders {
-    Presence(PersistentBitMatrixBuilder, Vec<PersistentBitVecBuilder>),
-    Count(
-        PersistentCompactIntMatrixBuilder,
-        Vec<PersistentCompactIntVecBuilder>,
-    ),
-}
-
-impl Builders {
-    fn new(mode: MergeMode, n: usize, dir: &Path, n_genomes: usize) -> OKIResult<Self> {
-        match mode {
-            MergeMode::Presence => {
-                let mut mat = PersistentBitMatrixBuilder::new(n, dir).map_err(OKIError::Io)?;
-                let mut cols = Vec::with_capacity(n_genomes);
-                for _ in 0..n_genomes {
-                    cols.push(mat.add_col().map_err(OKIError::Io)?);
-                }
-                Ok(Builders::Presence(mat, cols))
-            }
-            MergeMode::Count => {
-                let mut mat =
-                    PersistentCompactIntMatrixBuilder::new(n, dir).map_err(OKIError::Io)?;
-                let mut cols = Vec::with_capacity(n_genomes);
-                for _ in 0..n_genomes {
-                    cols.push(mat.add_col().map_err(OKIError::Io)?);
-                }
-                Ok(Builders::Count(mat, cols))
-            }
-        }
-    }
-
-    fn set_val(&mut self, col: usize, slot: usize, value: u32) {
-        match self {
-            Builders::Presence(_, cols) => cols[col].set(slot, value > 0),
-            Builders::Count(_, cols) => cols[col].set(slot, value),
-        }
-    }
-
-    fn close(self) -> OKIResult<()> {
-        match self {
-            Builders::Presence(mat, cols) => {
-                for b in cols {
-                    b.close().map_err(OKIError::Io)?;
-                }
-                mat.close().map_err(OKIError::Io)
-            }
-            Builders::Count(mat, cols) => {
-                for b in cols {
-                    b.close().map_err(OKIError::Io)?;
-                }
-                mat.close().map_err(OKIError::Io)
-            }
-        }
-    }
-}
-
-// ── try_compute_combined_mask ─────────────────────────────────────────────────
-
-/// Build a per-slot `TempBitVec` mask from `filters` using column operations
-/// on the source matrix — no per-kmer MPHF lookup or row read needed.
-///
-/// Returns `Some(mask)` when every filter in `filters` can express itself as
-/// a [`FilterMask`] expression.  Returns `None` when any filter requires
-/// row-level inspection (fall back to `passes_all`).
-fn try_compute_combined_mask(
-    filters: &[Box<dyn KmerFilter>],
-    src_data: &SrcLayerData,
-    n_genomes: usize,
-) -> OKIResult<Option<obicompactvec::TempBitVec>> {
-    if filters.is_empty() {
-        return Ok(None);
-    }
-    let mut exprs: Vec<FilterMask> = Vec::with_capacity(filters.len());
-    for f in filters {
-        match f.column_mask_expr(n_genomes) {
-            Some(expr) => exprs.push(expr),
-            None => return Ok(None),
-        }
-    }
-    let combined = FilterMask::And(exprs);
-    let n = src_data.n_slots();
-    let mask = src_data
-        .with_matrix(|mat| eval_filter_mask(&combined, mat, n))
-        .map_err(OKIError::Io)?;
-    Ok(Some(mask))
-}
-
-// ── iter_src_kmers_masked (pass 1) ────────────────────────────────────────────
-
-/// Iterate all passing kmers in `src_index_dir`, yielding only the kmer value.
-///
-/// When all filters can be expressed as column operations, a per-slot mask is
-/// computed once per layer and used for O(1) slot-check per kmer instead of a
-/// full row read.  Falls back to row-level `passes_all` otherwise.
-fn iter_src_kmers_masked(
-    src_index_dir: &Path,
-    mode: MergeMode,
-    n_genomes: usize,
-    filters: &[Box<dyn KmerFilter>],
-    mut cb: impl FnMut(CanonicalKmer),
-) -> OKIResult<()> {
-    let src_meta = load_meta(src_index_dir)?;
-    for l in 0..src_meta.n_layers {
-        let src_layer_dir = layer_dir(src_index_dir, l);
-        let unitigs_path = src_layer_dir.join("unitigs.bin");
-        if !unitigs_path.exists() {
-            continue;
-        }
-
-        let src_data = SrcLayerData::open(&src_layer_dir, mode)?;
-        let mask = try_compute_combined_mask(filters, &src_data, n_genomes)?;
-        let reader = UnitigFileReader::open_sequential(&unitigs_path)?;
-
-        for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
-            let slot = src_data.slot(kmer);
-            let passes = match &mask {
-                Some(m) => m.get(slot),
-                None => {
-                    let row = src_data.fill_row_by_slot(slot, n_genomes);
-                    filters.iter().all(|f| f.passes(kmer, &row, n_genomes))
-                }
-            };
-            if passes {
-                cb(kmer);
-            }
-        }
-    }
-    Ok(())
-}
-
-// ── iter_src_layers (pass 2) ──────────────────────────────────────────────────
-
-/// Iterate all passing kmers in `src_index_dir`, yielding `(kmer, row)`.
-///
-/// When the slot mask is available, skips the row read for filtered-out slots.
-fn iter_src_layers(
-    src_index_dir: &Path,
-    mode: MergeMode,
-    n_genomes: usize,
-    filters: &[Box<dyn KmerFilter>],
-    mut cb: impl FnMut(CanonicalKmer, Box<[u32]>),
-) -> OKIResult<()> {
-    let src_meta = load_meta(src_index_dir)?;
-    for l in 0..src_meta.n_layers {
-        let src_layer_dir = layer_dir(src_index_dir, l);
-        let unitigs_path = src_layer_dir.join("unitigs.bin");
-        if !unitigs_path.exists() {
-            continue;
-        }
-
-        let src_data = SrcLayerData::open(&src_layer_dir, mode)?;
-        let mask = try_compute_combined_mask(filters, &src_data, n_genomes)?;
-        let reader = UnitigFileReader::open_sequential(&unitigs_path)?;
-
-        for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
-            let slot = src_data.slot(kmer);
-            if let Some(ref m) = mask {
-                if !m.get(slot) {
-                    continue;
-                }
-                let row = src_data.fill_row_by_slot(slot, n_genomes);
-                cb(kmer, row.into_boxed_slice());
-            } else {
-                let row = src_data.fill_row_by_slot(slot, n_genomes);
-                if filters.iter().all(|f| f.passes(kmer, &row, n_genomes)) {
-                    cb(kmer, row.into_boxed_slice());
-                }
-            }
-        }
-    }
-    Ok(())
-}
-
-// ── KmerPartition::rebuild_partition ─────────────────────────────────────────
-
-impl KmerIndex {
-    /// Rebuild partition `i` from `src` into `self` (an empty destination partition).
-    ///
-    /// Only k-mers whose per-genome row passes all `filters` are written.
-    /// The output is a single-layer index — regardless of how many layers the
-    /// source has.
-    ///
-    /// `n_genomes` is the number of genome columns in the source (and destination).
-    pub fn rebuild_partition(
-        &self,
-        src: &KmerIndex,
-        i: usize,
-        filters: &[Box<dyn KmerFilter>],
-        mode: MergeMode,
-        n_genomes: usize,
-        block_bits: u8,
-    ) -> OKIResult<()> {
-        let src_index_dir = src.index_dir(i);
-        if !src_index_dir.exists() {
-            return Ok(());
-        }
-
-        let src_meta = load_meta(&src_index_dir)?;
-        if src_meta.n_layers == 0 {
-            return Ok(());
-        }
-
-        // ── Pass 1: collect filtered kmers into de Bruijn graph ───────────────
-        let mut g = GraphDeBruijn::new();
-        iter_src_kmers_masked(&src_index_dir, mode, n_genomes, filters, |kmer| {
-            g.push(kmer);
-        })?;
-
-        if g.len() == 0 {
-            return Ok(());
-        }
-
-        // ── Build MPHF in dst layer_0 ─────────────────────────────────────────
-        let dst_index_dir = self.index_dir(i);
-        let dst_layer_dir = self.layer_dir(i, 0);
-
-        let n_new = materialize_layer(g, &dst_layer_dir, block_bits, &IndexMode::Exact)?;
-        let dst_mphf = MphfLayer::open(&dst_layer_dir)?;
-
-        // ── Prepare matrix builders (one column per genome) ───────────────────
-        let data_dir = match mode {
-            MergeMode::Presence => dst_layer_dir.join("presence"),
-            MergeMode::Count => dst_layer_dir.join("counts"),
-        };
-        std::fs::create_dir_all(&data_dir)?;
-        let mut builders = Builders::new(mode, n_new, &data_dir, n_genomes)?;
-
-        // ── Pass 2: fill builders ─────────────────────────────────────────────
-        iter_src_layers(&src_index_dir, mode, n_genomes, filters, |kmer, row| {
-            if let Some(slot) = dst_mphf.find(kmer) {
-                for (col, &value) in row.iter().enumerate() {
-                    builders.set_val(col, slot, value);
-                }
-            }
-        })?;
-
-        // ── Close builders and write metadata ─────────────────────────────────
-        builders.close()?;
-
-        PartitionMeta {
-            n_layers: 1,
-            mode: IndexMode::Exact,
-        }
-        .save(&dst_index_dir)?;
-
-        Ok(())
-    }
-}