src/obicompactvec/src/bitvec.rs

@@ -5,7 +5,7 @@ use std::path::{Path, PathBuf};
 use memmap2::{Mmap, MmapMut};
 
 use crate::reader::PersistentCompactIntVec;
-use crate::views::{BitSliceView, BitSliceIter};
+use crate::views::{BitSliceIter, BitSliceView, IntSliceView};
 
 const MAGIC: [u8; 4] = *b"PBIV";
 
@@ -241,6 +241,72 @@ impl PersistentBitVecBuilder {
         }
     }
 
+    /// OR in bits at slots where `pred(col[slot])` is true.
+    pub fn or_where(&mut self, col: IntSliceView<'_>, pred: impl Fn(u32) -> bool) {
+        assert_eq!(self.n, col.len(), "IntSliceView length mismatch");
+        let n = self.n;
+        let primary = col.primary_bytes();
+        let words = self.data_words_mut();
+        let nw = n_words(n);
+        for wi in 0..nw {
+            let base  = wi * 64;
+            let limit = (base + 64).min(n);
+            let mut mask = 0u64;
+            for bit in 0..(limit - base) {
+                let b = primary[base + bit];
+                if b < 255 && pred(b as u32) { mask |= 1u64 << bit; }
+            }
+            words[wi] |= mask;
+        }
+        for (slot, val) in col.overflow_entries() {
+            if pred(val) { words[slot >> 6] |= 1u64 << (slot & 63); }
+        }
+    }
+
+    /// Clear bits at slots where `pred(col[slot])` is false.
+    pub fn and_where(&mut self, col: IntSliceView<'_>, pred: impl Fn(u32) -> bool) {
+        assert_eq!(self.n, col.len(), "IntSliceView length mismatch");
+        let n = self.n;
+        let primary = col.primary_bytes();
+        let words = self.data_words_mut();
+        let nw = n_words(n);
+        for wi in 0..nw {
+            let base  = wi * 64;
+            let limit = (base + 64).min(n);
+            let mut mask = 0u64;
+            for bit in 0..(limit - base) {
+                let b = primary[base + bit];
+                if b < 255 && !pred(b as u32) { mask |= 1u64 << bit; }
+            }
+            words[wi] &= !mask;
+        }
+        for (slot, val) in col.overflow_entries() {
+            if !pred(val) { words[slot >> 6] &= !(1u64 << (slot & 63)); }
+        }
+    }
+
+    /// Toggle bits at slots where `pred(col[slot])` is true.
+    pub fn xor_where(&mut self, col: IntSliceView<'_>, pred: impl Fn(u32) -> bool) {
+        assert_eq!(self.n, col.len(), "IntSliceView length mismatch");
+        let n = self.n;
+        let primary = col.primary_bytes();
+        let words = self.data_words_mut();
+        let nw = n_words(n);
+        for wi in 0..nw {
+            let base  = wi * 64;
+            let limit = (base + 64).min(n);
+            let mut mask = 0u64;
+            for bit in 0..(limit - base) {
+                let b = primary[base + bit];
+                if b < 255 && pred(b as u32) { mask |= 1u64 << bit; }
+            }
+            words[wi] ^= mask;
+        }
+        for (slot, val) in col.overflow_entries() {
+            if pred(val) { words[slot >> 6] ^= 1u64 << (slot & 63); }
+        }
+    }
+
     pub fn iter(&self) -> BitSliceIter<'_> {
         self.view().iter()
     }

src/obicompactvec/src/colgroup.rs

@@ -70,3 +70,73 @@ pub trait MatrixGroupOps {
         b.freeze()
     }
 }
+
+// ── FilterMask — expression tree for column-based slot filters ────────────────
+
+/// A composable filter expression that can be evaluated against a matrix
+/// using only column operations (no MPHF lookup per kmer).
+///
+/// `threshold` semantics follow [`MatrixGroupOps::partial_group_presence_count`]:
+/// a slot contributes to the count when its value is **≥ threshold**.
+/// To match the row-level filter (`value > t`), callers should pass `t + 1`.
+#[derive(Debug, Clone)]
+pub enum FilterMask {
+    /// Slot passes if count of columns in `indices` with value ≥ `threshold` is ≥ `min_count`.
+    PresenceGeq { indices: Vec<usize>, threshold: u32, min_count: usize },
+    /// Slot passes if count of columns in `indices` with value ≥ `threshold` is ≤ `max_count`.
+    PresenceLeq { indices: Vec<usize>, threshold: u32, max_count: usize },
+    /// Slot passes if sum of values across `indices` columns is ≥ `min_sum`.
+    SumGeq { indices: Vec<usize>, min_sum: u32 },
+    /// Slot passes if sum of values across `indices` columns is ≤ `max_sum`.
+    SumLeq { indices: Vec<usize>, max_sum: u32 },
+    /// Slot passes if it passes all sub-expressions. Empty `And` is always true.
+    And(Vec<FilterMask>),
+}
+
+/// Evaluate a [`FilterMask`] against `mat`, returning a per-slot `TempBitVec`
+/// where bit=1 means the slot passes the filter.
+pub fn eval_filter_mask(expr: &FilterMask, mat: &dyn MatrixGroupOps, n: usize) -> io::Result<TempBitVec> {
+    match expr {
+        FilterMask::PresenceGeq { indices, threshold, min_count } => {
+            let g = ColGroup::new("", indices.clone());
+            let counts = mat.partial_group_presence_count(&g, *threshold)?;
+            let mut b = TempBitVecBuilder::new(n)?;
+            let mc = *min_count as u32;
+            b.or_where(counts.view(), |v| v >= mc);
+            b.freeze()
+        }
+        FilterMask::PresenceLeq { indices, threshold, max_count } => {
+            let g = ColGroup::new("", indices.clone());
+            let counts = mat.partial_group_presence_count(&g, *threshold)?;
+            let mut b = TempBitVecBuilder::new(n)?;
+            let mc = *max_count as u32;
+            b.or_where(counts.view(), |v| v <= mc);
+            b.freeze()
+        }
+        FilterMask::SumGeq { indices, min_sum } => {
+            let g = ColGroup::new("", indices.clone());
+            let sums = mat.partial_group_sum(&g)?;
+            let mut b = TempBitVecBuilder::new(n)?;
+            let ms = *min_sum;
+            b.or_where(sums.view(), |v| v >= ms);
+            b.freeze()
+        }
+        FilterMask::SumLeq { indices, max_sum } => {
+            let g = ColGroup::new("", indices.clone());
+            let sums = mat.partial_group_sum(&g)?;
+            let mut b = TempBitVecBuilder::new(n)?;
+            let ms = *max_sum;
+            b.or_where(sums.view(), |v| v <= ms);
+            b.freeze()
+        }
+        FilterMask::And(parts) => {
+            let mut b = TempBitVecBuilder::new(n)?;
+            b.not(); // initialise à tout-1 (tout passe)
+            for part in parts {
+                let m = eval_filter_mask(part, mat, n)?;
+                b.and(m.view());
+            }
+            b.freeze()
+        }
+    }
+}

src/obicompactvec/src/lib.rs

@@ -15,7 +15,7 @@ pub mod traits;
 pub use bitvec::{BitIter, PersistentBitVec, PersistentBitVecBuilder};
 pub use bitmatrix::{PersistentBitMatrix, PersistentBitMatrixBuilder, pack_bit_matrix};
 pub use builder::PersistentCompactIntVecBuilder;
-pub use colgroup::{ColGroup, MatrixGroupOps};
+pub use colgroup::{ColGroup, FilterMask, MatrixGroupOps, eval_filter_mask};
 pub use intmatrix::{PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder, pack_compact_int_matrix};
 pub use layer_meta::LayerMeta;
 pub use reader::PersistentCompactIntVec;

src/obicompactvec/src/tempbitvec.rs

@@ -73,18 +73,31 @@ impl TempBitVecBuilder {
         self.builder.or(other);
     }
 
-    /// Set self[slot] where pred(col[slot]) is true. Two-pass: primary then overflow.
+    pub(crate) fn and(&mut self, other: BitSliceView<'_>) {
+        self.builder.and(other);
+    }
+
+    pub(crate) fn xor(&mut self, other: BitSliceView<'_>) {
+        self.builder.xor(other);
+    }
+
+    pub(crate) fn not(&mut self) {
+        self.builder.not();
+    }
+
+    pub(crate) fn copy_from(&mut self, src: BitSliceView<'_>) {
+        self.builder.copy_from(src);
+    }
+
     pub fn or_where(&mut self, col: IntSliceView<'_>, pred: impl Fn(u32) -> bool) {
-        for slot in 0..col.len() {
+        self.builder.or_where(col, pred);
-            let b = col.primary_bytes()[slot];
-            if b < 255 && pred(b as u32) {
-                self.builder.set(slot, true);
-            }
-        }
-        for (slot, val) in col.overflow_entries() {
-            if pred(val) {
-                self.builder.set(slot, true);
     }
+
+    pub(crate) fn and_where(&mut self, col: IntSliceView<'_>, pred: impl Fn(u32) -> bool) {
+        self.builder.and_where(col, pred);
     }
+
+    pub(crate) fn xor_where(&mut self, col: IntSliceView<'_>, pred: impl Fn(u32) -> bool) {
+        self.builder.xor_where(col, pred);
     }
 }

src/obikpartitionner/src/filter.rs

@@ -1,9 +1,24 @@
+use obicompactvec::FilterMask;
+
 /// Trait for kmer row filters.
 ///
 /// `row` contains raw per-genome counts (or 0/1 for presence/absence data).
 /// `n_genomes` equals `row.len()`.
 pub trait KmerFilter: Send + Sync {
     fn passes(&self, row: &[u32], n_genomes: usize) -> bool;
+
+    /// Express this filter as a [`FilterMask`] column-operation expression.
+    ///
+    /// Returns `Some(expr)` if the filter can be evaluated solely from matrix
+    /// column aggregates (no per-kmer row scan needed).  Returns `None` if the
+    /// filter requires row-level inspection.
+    ///
+    /// `threshold` semantics in the returned mask use `>= threshold`, matching
+    /// [`obicompactvec::MatrixGroupOps`].  Implementations must add 1 to any
+    /// row-level threshold that uses strict `>` comparison.
+    fn column_mask_expr(&self, _n_genomes: usize) -> Option<FilterMask> {
+        None
+    }
 }
 
 /// True when `row` passes every filter in `filters`.
@@ -29,6 +44,16 @@ impl KmerFilter for MinGenomeFraction {
         let p = present_count(row, self.threshold);
         p as f64 / n_genomes as f64 >= self.frac
     }
+
+    fn column_mask_expr(&self, n_genomes: usize) -> Option<FilterMask> {
+        let t = self.threshold.checked_add(1)?;
+        let min_count = (self.frac * n_genomes as f64).ceil() as usize;
+        Some(FilterMask::PresenceGeq {
+            indices: (0..n_genomes).collect(),
+            threshold: t,
+            min_count,
+        })
+    }
 }
 
 /// At most `frac` fraction of genomes contain this kmer (count > `threshold`).
@@ -42,6 +67,16 @@ impl KmerFilter for MaxGenomeFraction {
         let p = present_count(row, self.threshold);
         p as f64 / n_genomes as f64 <= self.frac
     }
+
+    fn column_mask_expr(&self, n_genomes: usize) -> Option<FilterMask> {
+        let t = self.threshold.checked_add(1)?;
+        let max_count = (self.frac * n_genomes as f64).floor() as usize;
+        Some(FilterMask::PresenceLeq {
+            indices: (0..n_genomes).collect(),
+            threshold: t,
+            max_count,
+        })
+    }
 }
 
 /// At least `count` genomes contain this kmer (count > `threshold`).
@@ -54,6 +89,15 @@ impl KmerFilter for MinGenomeCount {
     fn passes(&self, row: &[u32], _n_genomes: usize) -> bool {
         present_count(row, self.threshold) >= self.count
     }
+
+    fn column_mask_expr(&self, n_genomes: usize) -> Option<FilterMask> {
+        let t = self.threshold.checked_add(1)?;
+        Some(FilterMask::PresenceGeq {
+            indices: (0..n_genomes).collect(),
+            threshold: t,
+            min_count: self.count,
+        })
+    }
 }
 
 /// At most `count` genomes contain this kmer (count > `threshold`).
@@ -66,6 +110,15 @@ impl KmerFilter for MaxGenomeCount {
     fn passes(&self, row: &[u32], _n_genomes: usize) -> bool {
         present_count(row, self.threshold) <= self.count
     }
+
+    fn column_mask_expr(&self, n_genomes: usize) -> Option<FilterMask> {
+        let t = self.threshold.checked_add(1)?;
+        Some(FilterMask::PresenceLeq {
+            indices: (0..n_genomes).collect(),
+            threshold: t,
+            max_count: self.count,
+        })
+    }
 }
 
 // ── Total-count filters (count indexes only) ───────────────────────────────────
@@ -79,6 +132,13 @@ impl KmerFilter for MinTotalCount {
     fn passes(&self, row: &[u32], _n_genomes: usize) -> bool {
         row.iter().sum::<u32>() >= self.total
     }
+
+    fn column_mask_expr(&self, n_genomes: usize) -> Option<FilterMask> {
+        Some(FilterMask::SumGeq {
+            indices: (0..n_genomes).collect(),
+            min_sum: self.total,
+        })
+    }
 }
 
 /// Sum of counts across all genomes <= `total`.
@@ -90,6 +150,13 @@ impl KmerFilter for MaxTotalCount {
     fn passes(&self, row: &[u32], _n_genomes: usize) -> bool {
         row.iter().sum::<u32>() <= self.total
     }
+
+    fn column_mask_expr(&self, n_genomes: usize) -> Option<FilterMask> {
+        Some(FilterMask::SumLeq {
+            indices: (0..n_genomes).collect(),
+            max_sum: self.total,
+        })
+    }
 }
 
 // ── Group-based quorum filter ─────────────────────────────────────────────────
@@ -113,6 +180,37 @@ pub struct GroupQuorumFilter {
     pub max_outgroup_frac:  f64,
 }
 
+impl GroupQuorumFilter {
+    // Build PresenceGeq/PresenceLeq constraints for one group (ingroup or outgroup).
+    fn group_mask_parts(
+        indices: &[usize],
+        threshold: u32,
+        min_count: usize,
+        max_count: usize,
+        min_frac: f64,
+        max_frac: f64,
+        parts: &mut Vec<FilterMask>,
+    ) {
+        let n = indices.len();
+        let geq = min_count.max((min_frac * n as f64).ceil() as usize);
+        if geq > 0 {
+            parts.push(FilterMask::PresenceGeq {
+                indices: indices.to_vec(),
+                threshold,
+                min_count: geq,
+            });
+        }
+        let leq = max_count.min((max_frac * n as f64).floor() as usize);
+        if leq < n {
+            parts.push(FilterMask::PresenceLeq {
+                indices: indices.to_vec(),
+                threshold,
+                max_count: leq,
+            });
+        }
+    }
+}
+
 impl KmerFilter for GroupQuorumFilter {
     fn passes(&self, row: &[u32], _n_genomes: usize) -> bool {
         if !self.ingroup_idx.is_empty() {
@@ -139,4 +237,26 @@ impl KmerFilter for GroupQuorumFilter {
         }
         true
     }
+
+    fn column_mask_expr(&self, _n_genomes: usize) -> Option<FilterMask> {
+        let t = self.threshold.checked_add(1)?;
+        let mut parts: Vec<FilterMask> = Vec::new();
+        if !self.ingroup_idx.is_empty() {
+            Self::group_mask_parts(
+                &self.ingroup_idx, t,
+                self.min_count, self.max_count,
+                self.min_frac, self.max_frac,
+                &mut parts,
+            );
+        }
+        if !self.outgroup_idx.is_empty() {
+            Self::group_mask_parts(
+                &self.outgroup_idx, t,
+                self.min_outgroup_count, self.max_outgroup_count,
+                self.min_outgroup_frac, self.max_outgroup_frac,
+                &mut parts,
+            );
+        }
+        Some(FilterMask::And(parts))
+    }
 }

src/obikpartitionner/src/merge_layer.rs

@@ -10,6 +10,7 @@ use obipipeline::{
 };
 
 use obicompactvec::{
+    MatrixGroupOps,
     PersistentBitMatrix, PersistentBitMatrixBuilder, PersistentBitVecBuilder,
     PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder, PersistentCompactIntVecBuilder,
 };
@@ -78,6 +79,41 @@ impl SrcLayerData {
         }
         buf
     }
+
+    pub(crate) fn n_slots(&self) -> usize {
+        match self {
+            SrcLayerData::Presence(_, mat) => mat.n(),
+            SrcLayerData::Count(_, mat) => mat.n(),
+        }
+    }
+
+    /// MPHF lookup: returns the slot index for `kmer` (kmer must be in the domain).
+    #[inline]
+    pub(crate) fn slot(&self, kmer: CanonicalKmer) -> usize {
+        match self {
+            SrcLayerData::Presence(mphf, _) => mphf.index(kmer),
+            SrcLayerData::Count(mphf, _) => mphf.index(kmer),
+        }
+    }
+
+    /// Row lookup by slot index, bypassing the MPHF.
+    #[inline]
+    pub(crate) fn fill_row_by_slot(&self, slot: usize, n_genomes: usize) -> Vec<u32> {
+        let mut buf = vec![0u32; n_genomes];
+        match self {
+            SrcLayerData::Presence(_, mat) => mat.fill_row(slot, &mut buf),
+            SrcLayerData::Count(_, mat) => mat.fill_row(slot, &mut buf),
+        }
+        buf
+    }
+
+    /// Call `f` with a reference to the underlying matrix as `&dyn MatrixGroupOps`.
+    pub(crate) fn with_matrix<R>(&self, f: impl FnOnce(&dyn MatrixGroupOps) -> R) -> R {
+        match self {
+            SrcLayerData::Presence(_, mat) => f(mat),
+            SrcLayerData::Count(_, mat) => f(mat),
+        }
+    }
 }
 
 // ── helpers ───────────────────────────────────────────────────────────────────

src/obikpartitionner/src/rebuild_layer.rs

@@ -1,8 +1,9 @@
 use std::path::Path;
 
 use obicompactvec::{
-    PersistentBitMatrixBuilder, PersistentBitVecBuilder, PersistentCompactIntMatrixBuilder,
+    FilterMask, eval_filter_mask,
-    PersistentCompactIntVecBuilder,
+    PersistentBitMatrixBuilder, PersistentBitVecBuilder,
+    PersistentCompactIntMatrixBuilder, PersistentCompactIntVecBuilder,
 };
 use obidebruinj::GraphDeBruijn;
 use obikseq::CanonicalKmer;
@@ -10,18 +11,135 @@ use obilayeredmap::meta::PartitionMeta;
 use obilayeredmap::{IndexMode, MphfLayer};
 use obiskio::{SKError, SKResult, UnitigFileReader};
 
-use crate::common::{ColBuilder, col_path_bit, col_path_int, load_meta, olm_to_sk, write_matrix_meta};
+use crate::common::{load_meta, olm_to_sk};
-use crate::filter::{KmerFilter, passes_all};
+use crate::filter::KmerFilter;
 use crate::graph_pipeline::materialize_layer;
 use crate::merge_layer::{MergeMode, SrcLayerData};
 use crate::partition::KmerPartition;
 
 const INDEX_SUBDIR: &str = "index";
 
-/// Iterate all kmers in `src_index_dir` that pass `filters`, yielding `(kmer, row)`.
+// ── 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) -> SKResult<Self> {
+        match mode {
+            MergeMode::Presence => {
+                let mut mat = PersistentBitMatrixBuilder::new(n, dir).map_err(SKError::Io)?;
+                let mut cols = Vec::with_capacity(n_genomes);
+                for _ in 0..n_genomes { cols.push(mat.add_col().map_err(SKError::Io)?); }
+                Ok(Builders::Presence(mat, cols))
+            }
+            MergeMode::Count => {
+                let mut mat = PersistentCompactIntMatrixBuilder::new(n, dir).map_err(SKError::Io)?;
+                let mut cols = Vec::with_capacity(n_genomes);
+                for _ in 0..n_genomes { cols.push(mat.add_col().map_err(SKError::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) -> SKResult<()> {
+        match self {
+            Builders::Presence(mat, cols) => {
+                for b in cols { b.close().map_err(SKError::Io)?; }
+                mat.close().map_err(SKError::Io)
+            }
+            Builders::Count(mat, cols) => {
+                for b in cols { b.close().map_err(SKError::Io)?; }
+                mat.close().map_err(SKError::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.
 ///
-/// Uses [`SrcLayerData`] semantics: counts take priority over presence when
+/// Returns `Some(mask)` when every filter in `filters` can express itself as
-/// `mode = Count`; presence (or implicit all-ones) is used for `Presence`.
+/// 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,
+) -> SKResult<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(SKError::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),
+) -> SKResult<()> {
+    let src_meta = load_meta(src_index_dir, "rebuild")?;
+    for l in 0..src_meta.n_layers {
+        let src_layer_dir = src_index_dir.join(format!("layer_{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(&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,
@@ -33,17 +151,23 @@ fn iter_src_layers(
     for l in 0..src_meta.n_layers {
         let src_layer_dir = src_index_dir.join(format!("layer_{l}"));
         let unitigs_path = src_layer_dir.join("unitigs.bin");
-        if !unitigs_path.exists() {
+        if !unitigs_path.exists() { continue; }
-            continue;
-        }
 
-        let reader = UnitigFileReader::open_sequential(&unitigs_path)?;
         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 row = src_data.lookup(kmer, n_genomes);
+            let slot = src_data.slot(kmer);
-            if passes_all(filters, &row, n_genomes) {
+            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(&row, n_genomes)) {
+                    cb(kmer, row.into_boxed_slice());
+                }
             }
         }
     }
@@ -81,7 +205,7 @@ impl KmerPartition {
 
         // ── Pass 1: collect filtered kmers into de Bruijn graph ───────────────
         let mut g = GraphDeBruijn::new();
-        iter_src_layers(&src_index_dir, mode, n_genomes, filters, |kmer, _row| {
+        iter_src_kmers_masked(&src_index_dir, mode, n_genomes, filters, |kmer| {
             g.push(kmer);
         })?;
 
@@ -103,51 +227,19 @@ impl KmerPartition {
             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)?;
-        let mut builders: Vec<ColBuilder> = match mode {
-            MergeMode::Presence => {
-                PersistentBitMatrixBuilder::new(n_new, &data_dir)
-                    .map_err(SKError::Io)?
-                    .close()
-                    .map_err(SKError::Io)?;
-                (0..n_genomes)
-                    .map(|g| -> SKResult<ColBuilder> {
-                        let b = PersistentBitVecBuilder::new(n_new, &col_path_bit(&data_dir, g))?;
-                        Ok(ColBuilder::Bit(b))
-                    })
-                    .collect::<SKResult<_>>()?
-            }
-            MergeMode::Count => {
-                PersistentCompactIntMatrixBuilder::new(n_new, &data_dir)
-                    .map_err(SKError::Io)?
-                    .close()
-                    .map_err(SKError::Io)?;
-                (0..n_genomes)
-                    .map(|g| -> SKResult<ColBuilder> {
-                        let b = PersistentCompactIntVecBuilder::new(
-                            n_new,
-                            &col_path_int(&data_dir, g),
-                        )?;
-                        Ok(ColBuilder::Int(b))
-                    })
-                    .collect::<SKResult<_>>()?
-            }
-        };
 
         // ── 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[col].set_val(slot, value);
+                    builders.set_val(col, slot, value);
                 }
             }
         })?;
 
-        // ── Close builders, write metadata ────────────────────────────────────
+        // ── Close builders and write metadata ─────────────────────────────────
-        for b in builders {
+        builders.close()?;
-            b.close()?;
-        }
-        write_matrix_meta(&data_dir, n_new, n_genomes).map_err(SKError::Io)?;
 
         PartitionMeta {
             n_layers: 1,