diff --git a/src/obicompactvec/Cargo.toml b/src/obicompactvec/Cargo.toml
index dc4527a..ddb1e40 100644
--- a/src/obicompactvec/Cargo.toml
+++ b/src/obicompactvec/Cargo.toml
@@ -4,7 +4,7 @@ version = "0.1.0"
 edition = "2024"
 
 [dependencies]
-memmap2 = "0.9"
+memmap2  = "0.9"
 ndarray  = "0.16"
 rayon    = "1"
 
diff --git a/src/obicompactvec/src/bitmatrix.rs b/src/obicompactvec/src/bitmatrix.rs
index ffa42d5..ead53af 100644
--- a/src/obicompactvec/src/bitmatrix.rs
+++ b/src/obicompactvec/src/bitmatrix.rs
@@ -1,22 +1,29 @@
-use std::{fs, io, path::{Path, PathBuf}};
+use std::fs::{self, File};
+use std::io::{self, Write as _};
+use std::path::{Path, PathBuf};
 
+use memmap2::Mmap;
 use ndarray::{Array1, Array2};
 use rayon::prelude::*;
 
 use crate::bitvec::{PersistentBitVec, PersistentBitVecBuilder};
+use crate::layer_meta::LayerMeta;
 use crate::meta::MatrixMeta;
 
 fn col_path(dir: &Path, col: usize) -> PathBuf {
     dir.join(format!("col_{col:06}.pbiv"))
 }
 
-pub struct PersistentBitMatrix {
+// ── ColumnarBitMatrix ─────────────────────────────────────────────────────────
+
+/// Per-column file layout (original format).
+pub struct ColumnarBitMatrix {
     cols: Vec<PersistentBitVec>,
     n:    usize,
 }
 
-impl PersistentBitMatrix {
-    pub fn open(dir: &Path) -> io::Result<Self> {
+impl ColumnarBitMatrix {
+    pub(crate) fn open(dir: &Path) -> io::Result<Self> {
         let meta = MatrixMeta::load(dir)?;
         let cols = (0..meta.n_cols)
             .map(|c| PersistentBitVec::open(&col_path(dir, c)))
@@ -24,24 +31,21 @@ impl PersistentBitMatrix {
         Ok(Self { cols, n: meta.n })
     }
 
-    pub fn n(&self)      -> usize { self.n }
-    pub fn n_cols(&self) -> usize { self.cols.len() }
-    pub fn col(&self, c: usize) -> &PersistentBitVec { &self.cols[c] }
+    pub(crate) fn n(&self)      -> usize { self.n }
+    pub(crate) fn n_cols(&self) -> usize { self.cols.len() }
+    pub(crate) fn col(&self, c: usize) -> &PersistentBitVec { &self.cols[c] }
 
-    pub fn row(&self, slot: usize) -> Box<[bool]> {
+    pub(crate) fn row(&self, slot: usize) -> Box<[bool]> {
         self.cols.iter().map(|c| c.get(slot)).collect()
     }
 
-    /// Fill `buf[i]` with `col_i[slot]` as 0/1 u32, without allocating.
-    /// `buf` must have length ≥ `self.n_cols()`.
-    pub fn fill_row(&self, slot: usize, buf: &mut [u32]) {
+    pub(crate) fn fill_row(&self, slot: usize, buf: &mut [u32]) {
         for (c, col) in self.cols.iter().enumerate() {
             buf[c] = col.get(slot) as u32;
         }
     }
 
-    /// Returns the number of set bits in each column as `Array1<u64>`.
-    pub fn count_ones(&self) -> Array1<u64> {
+    pub(crate) fn count_ones(&self) -> Array1<u64> {
         let counts: Vec<u64> = (0..self.n_cols())
             .into_par_iter()
             .map(|c| self.col(c).count_ones())
@@ -49,21 +53,15 @@ impl PersistentBitMatrix {
         Array1::from_vec(counts)
     }
 
-    // ── Distance matrices ─────────────────────────────────────────────────────
-
-    pub fn jaccard_dist_matrix(&self) -> Array2<f64> {
+    pub(crate) fn jaccard_dist_matrix(&self) -> Array2<f64> {
         self.pairwise_f64(|i, j| self.col(i).jaccard_dist(self.col(j)))
     }
 
-    pub fn hamming_dist_matrix(&self) -> Array2<u64> {
+    pub(crate) fn hamming_dist_matrix(&self) -> Array2<u64> {
         self.pairwise_u64(|i, j| self.col(i).hamming_dist(self.col(j)))
     }
 
-    // ── Partial matrices (additively decomposable across layers) ──────────────
-
-    /// Returns `(inter[n×n], union[n×n])`.
-    /// Reduce across layers by element-wise addition before computing `1 - inter/union`.
-    pub fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
+    pub(crate) fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
         let n = self.n_cols();
         let results: Vec<(usize, usize, u64, u64)> = upper_pairs(n)
             .into_par_iter()
@@ -72,7 +70,6 @@ impl PersistentBitMatrix {
                 (i, j, inter, union)
             })
             .collect();
-
         let mut inter_m = Array2::zeros((n, n));
         let mut union_m = Array2::zeros((n, n));
         for (i, j, inter, union) in results {
@@ -82,14 +79,10 @@ impl PersistentBitMatrix {
         (inter_m, union_m)
     }
 
-    /// Returns `hamming[n×n]` (number of differing bits per pair).
-    /// Additive across layers — reduce by element-wise addition.
-    pub fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
+    pub(crate) fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
         self.pairwise_u64(|i, j| self.col(i).hamming_dist(self.col(j)))
     }
 
-    // ── Private helpers ───────────────────────────────────────────────────────
-
     fn pairwise_f64(&self, f: impl Fn(usize, usize) -> f64 + Sync) -> Array2<f64> {
         let n = self.n_cols();
         let results: Vec<(usize, usize, f64)> = upper_pairs(n)
@@ -107,17 +100,8 @@ impl PersistentBitMatrix {
             .collect();
         fill_symmetric(n, results.into_iter().map(|(i, j, v)| (i, j, v, v)))
     }
-}
 
-// ── Column append ─────────────────────────────────────────────────────────────
-
-impl PersistentBitMatrix {
-    /// Append a new column to an existing matrix on disk.
-    ///
-    /// Reads `meta.json` to obtain `n` and the current column count, writes
-    /// `col_{n_cols:06}.pbiv` filled by `value_of(slot)`, then increments
-    /// `n_cols` in `meta.json`.
-    pub fn append_column(dir: &Path, value_of: impl Fn(usize) -> bool) -> io::Result<()> {
+    pub(crate) fn append_column(dir: &Path, value_of: impl Fn(usize) -> bool) -> io::Result<()> {
         let mut meta = MatrixMeta::load(dir)?;
         let mut b = PersistentBitVecBuilder::new(meta.n, &col_path(dir, meta.n_cols))?;
         for slot in 0..meta.n {
@@ -129,20 +113,208 @@ impl PersistentBitMatrix {
     }
 }
 
-fn upper_pairs(n: usize) -> Vec<(usize, usize)> {
-    (0..n).flat_map(|i| (i + 1..n).map(move |j| (i, j))).collect()
+// ── PackedBitMatrix ───────────────────────────────────────────────────────────
+
+const PBMX_MAGIC:  [u8; 4] = *b"PBMX";
+const PBMX_HEADER: usize   = 24; // magic(4) + pad(4) + n_rows(8) + n_cols(8)
+const PBIV_HEADER: usize   = 16; // magic(4) + pad(4) + n(8)
+
+/// Single-file packed layout: all columns concatenated behind a header.
+pub struct PackedBitMatrix {
+    mmap:         Mmap,
+    n_rows:       usize,
+    n_cols:       usize,
+    /// Absolute byte offset to the start of each column's bit data
+    /// (= file offset of the PBIV blob + PBIV_HEADER).
+    data_offsets: Vec<usize>,
 }
 
-fn fill_symmetric<T>(n: usize, vals: impl Iterator<Item = (usize, usize, T, T)>) -> Array2<T>
-where
-    T: Clone + Default,
-{
-    let mut m = Array2::from_elem((n, n), T::default());
-    for (i, j, vij, vji) in vals {
-        m[[i, j]] = vij;
-        m[[j, i]] = vji;
+impl PackedBitMatrix {
+    pub(crate) fn open(path: &Path) -> io::Result<Self> {
+        let mmap = unsafe { Mmap::map(&File::open(path)?)? };
+        if mmap.len() < PBMX_HEADER {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "PBMX file too short"));
+        }
+        if &mmap[0..4] != &PBMX_MAGIC {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "bad PBMX magic"));
+        }
+        let n_rows = u64::from_le_bytes(mmap[8..16].try_into().unwrap())  as usize;
+        let n_cols = u64::from_le_bytes(mmap[16..24].try_into().unwrap()) as usize;
+
+        let mut data_offsets = Vec::with_capacity(n_cols);
+        for c in 0..n_cols {
+            let off_pos = PBMX_HEADER + c * 8;
+            let col_file_off = u64::from_le_bytes(mmap[off_pos..off_pos+8].try_into().unwrap()) as usize;
+            data_offsets.push(col_file_off + PBIV_HEADER);
+        }
+
+        Ok(Self { mmap, n_rows, n_cols, data_offsets })
+    }
+
+    #[inline]
+    pub(crate) fn fill_row(&self, slot: usize, buf: &mut [u32]) {
+        for (c, &data_off) in self.data_offsets.iter().enumerate() {
+            buf[c] = ((self.mmap[data_off + (slot >> 3)] >> (slot & 7)) & 1) as u32;
+        }
+    }
+
+    pub(crate) fn row(&self, slot: usize) -> Box<[bool]> {
+        (0..self.n_cols).map(|c| {
+            (self.mmap[self.data_offsets[c] + (slot >> 3)] >> (slot & 7)) & 1 != 0
+        }).collect()
+    }
+}
+
+/// Build `presence/matrix.pbmx` from existing `col_*.pbiv` files.
+pub fn pack_bit_matrix(dir: &Path) -> io::Result<()> {
+    let meta = MatrixMeta::load(dir)?;
+    let n_cols = meta.n_cols;
+
+    let col_files: Vec<Vec<u8>> = (0..n_cols)
+        .map(|c| fs::read(col_path(dir, c)))
+        .collect::<io::Result<_>>()?;
+
+    let header_size = PBMX_HEADER + n_cols * 8;
+    let mut col_offset = header_size;
+    let mut offsets = Vec::with_capacity(n_cols);
+    for data in &col_files {
+        offsets.push(col_offset as u64);
+        col_offset += data.len();
+    }
+
+    let packed_path = dir.join("matrix.pbmx");
+    let mut file = File::create(&packed_path)?;
+    file.write_all(&PBMX_MAGIC)?;
+    file.write_all(&[0u8; 4])?;
+    file.write_all(&(meta.n as u64).to_le_bytes())?;
+    file.write_all(&(n_cols as u64).to_le_bytes())?;
+    for &off in &offsets { file.write_all(&off.to_le_bytes())?; }
+    for data in &col_files { file.write_all(data)?; }
+    Ok(())
+}
+
+// ── PersistentBitMatrix — public enum ────────────────────────────────────────
+
+/// Bit matrix that transparently handles columnar, packed, and implicit formats.
+///
+/// - `Columnar`: per-column `.pbiv` files (original format, used during build)
+/// - `Packed`:   single `matrix.pbmx` file (optimised for query — one `mmap`)
+/// - `Implicit`: no file — all values are 1 (mono-genome presence/absence)
+pub enum PersistentBitMatrix {
+    Columnar(ColumnarBitMatrix),
+    Packed(PackedBitMatrix),
+    Implicit { n_rows: usize, n_cols: usize },
+}
+
+impl PersistentBitMatrix {
+    /// Open from `layer_dir`, auto-detecting the format.
+    ///
+    /// Checks (in order):
+    /// 1. `layer_dir/presence/matrix.pbmx`  → Packed
+    /// 2. `layer_dir/presence/meta.json`    → Columnar
+    /// 3. `layer_dir/layer_meta.json`        → Implicit (new index)
+    /// 4. `layer_dir/unitigs.bin`            → Implicit with warning (old index)
+    pub fn open(layer_dir: &Path) -> io::Result<Self> {
+        let presence_dir = layer_dir.join("presence");
+
+        if presence_dir.join("matrix.pbmx").exists() {
+            return Ok(Self::Packed(PackedBitMatrix::open(&presence_dir.join("matrix.pbmx"))?));
+        }
+
+        if MatrixMeta::load(&presence_dir).is_ok() {
+            return Ok(Self::Columnar(ColumnarBitMatrix::open(&presence_dir)?));
+        }
+
+        // No presence matrix → Implicit; requires layer_meta.json
+        let meta = LayerMeta::load(layer_dir).map_err(|_| io::Error::new(
+            io::ErrorKind::NotFound,
+            format!(
+                "no presence matrix and no layer_meta.json in {} — run 'obikmer upgrade'",
+                layer_dir.display()
+            ),
+        ))?;
+        Ok(Self::Implicit { n_rows: meta.n, n_cols: 1 })
+    }
+
+    pub fn n(&self) -> usize {
+        match self {
+            Self::Columnar(m)            => m.n(),
+            Self::Packed(m)              => m.n_rows,
+            Self::Implicit { n_rows, .. } => *n_rows,
+        }
+    }
+
+    pub fn n_cols(&self) -> usize {
+        match self {
+            Self::Columnar(m)            => m.n_cols(),
+            Self::Packed(m)              => m.n_cols,
+            Self::Implicit { n_cols, .. } => *n_cols,
+        }
+    }
+
+    pub fn col(&self, c: usize) -> &PersistentBitVec {
+        match self {
+            Self::Columnar(m) => m.col(c),
+            _ => panic!("col() only available on Columnar PersistentBitMatrix"),
+        }
+    }
+
+    pub fn row(&self, slot: usize) -> Box<[bool]> {
+        match self {
+            Self::Columnar(m)             => m.row(slot),
+            Self::Packed(m)               => m.row(slot),
+            Self::Implicit { n_cols, .. } => vec![true; *n_cols].into_boxed_slice(),
+        }
+    }
+
+    /// Fill `buf[i]` with `col_i[slot]` as 0/1 u32, without allocating.
+    pub fn fill_row(&self, slot: usize, buf: &mut [u32]) {
+        match self {
+            Self::Columnar(m)             => m.fill_row(slot, buf),
+            Self::Packed(m)               => m.fill_row(slot, buf),
+            Self::Implicit { n_cols, .. } => buf[..*n_cols].fill(1),
+        }
+    }
+
+    pub fn count_ones(&self) -> Array1<u64> {
+        match self {
+            Self::Columnar(m) => m.count_ones(),
+            _ => panic!("count_ones() only available on Columnar PersistentBitMatrix"),
+        }
+    }
+
+    pub fn jaccard_dist_matrix(&self) -> Array2<f64> {
+        match self {
+            Self::Columnar(m) => m.jaccard_dist_matrix(),
+            _ => panic!("jaccard_dist_matrix() only available on Columnar PersistentBitMatrix"),
+        }
+    }
+
+    pub fn hamming_dist_matrix(&self) -> Array2<u64> {
+        match self {
+            Self::Columnar(m) => m.hamming_dist_matrix(),
+            _ => panic!("hamming_dist_matrix() only available on Columnar PersistentBitMatrix"),
+        }
+    }
+
+    pub fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
+        match self {
+            Self::Columnar(m) => m.partial_jaccard_dist_matrix(),
+            _ => panic!("partial_jaccard_dist_matrix() only available on Columnar PersistentBitMatrix"),
+        }
+    }
+
+    pub fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
+        match self {
+            Self::Columnar(m) => m.partial_hamming_dist_matrix(),
+            _ => panic!("partial_hamming_dist_matrix() only available on Columnar PersistentBitMatrix"),
+        }
+    }
+
+    /// Append a new column to an on-disk Columnar matrix.
+    pub fn append_column(dir: &Path, value_of: impl Fn(usize) -> bool) -> io::Result<()> {
+        ColumnarBitMatrix::append_column(dir, value_of)
     }
-    m
 }
 
 // ── Trait impls ───────────────────────────────────────────────────────────────
@@ -162,7 +334,7 @@ impl BitPartials for PersistentBitMatrix {
     }
 }
 
-// ── Builder ───────────────────────────────────────────────────────────────────
+// ── Builder (unchanged — always builds Columnar) ──────────────────────────────
 
 pub struct PersistentBitMatrixBuilder {
     dir:    PathBuf,
@@ -189,3 +361,16 @@ impl PersistentBitMatrixBuilder {
         MatrixMeta { n: self.n, n_cols: self.n_cols }.save(&self.dir)
     }
 }
+
+// ── Helpers ───────────────────────────────────────────────────────────────────
+
+fn upper_pairs(n: usize) -> Vec<(usize, usize)> {
+    (0..n).flat_map(|i| (i + 1..n).map(move |j| (i, j))).collect()
+}
+
+fn fill_symmetric<T>(n: usize, vals: impl Iterator<Item = (usize, usize, T, T)>) -> Array2<T>
+where T: Clone + Default {
+    let mut m = Array2::from_elem((n, n), T::default());
+    for (i, j, vij, vji) in vals { m[[i, j]] = vij; m[[j, i]] = vji; }
+    m
+}
diff --git a/src/obicompactvec/src/intmatrix.rs b/src/obicompactvec/src/intmatrix.rs
index 794d396..5fa1cc4 100644
--- a/src/obicompactvec/src/intmatrix.rs
+++ b/src/obicompactvec/src/intmatrix.rs
@@ -1,9 +1,14 @@
-use std::{fs, io, path::{Path, PathBuf}};
+use std::cmp::Ordering;
+use std::fs::{self, File};
+use std::io::{self, Write as _};
+use std::path::{Path, PathBuf};
 
+use memmap2::Mmap;
 use ndarray::{Array1, Array2};
 use rayon::prelude::*;
 
 use crate::builder::PersistentCompactIntVecBuilder;
+use crate::format::{HEADER_SIZE, INDEX_ENTRY_SIZE, OVERFLOW_ENTRY_SIZE};
 use crate::meta::MatrixMeta;
 use crate::reader::PersistentCompactIntVec;
 
@@ -11,13 +16,15 @@ fn col_path(dir: &Path, col: usize) -> PathBuf {
     dir.join(format!("col_{col:06}.pciv"))
 }
 
-pub struct PersistentCompactIntMatrix {
+// ── ColumnarCompactIntMatrix ──────────────────────────────────────────────────
+
+pub struct ColumnarCompactIntMatrix {
     cols: Vec<PersistentCompactIntVec>,
     n:    usize,
 }
 
-impl PersistentCompactIntMatrix {
-    pub fn open(dir: &Path) -> io::Result<Self> {
+impl ColumnarCompactIntMatrix {
+    pub(crate) fn open(dir: &Path) -> io::Result<Self> {
         let meta = MatrixMeta::load(dir)?;
         let cols = (0..meta.n_cols)
             .map(|c| PersistentCompactIntVec::open(&col_path(dir, c)))
@@ -25,25 +32,29 @@ impl PersistentCompactIntMatrix {
         Ok(Self { cols, n: meta.n })
     }
 
-    pub fn n(&self)      -> usize { self.n }
-    pub fn n_cols(&self) -> usize { self.cols.len() }
-    pub fn col(&self, c: usize) -> &PersistentCompactIntVec { &self.cols[c] }
+    pub(crate) fn n(&self)      -> usize { self.n }
+    pub(crate) fn n_cols(&self) -> usize { self.cols.len() }
+    pub(crate) fn col(&self, c: usize) -> &PersistentCompactIntVec { &self.cols[c] }
 
-    pub fn row(&self, slot: usize) -> Box<[u32]> {
+    pub(crate) fn row(&self, slot: usize) -> Box<[u32]> {
         self.cols.iter().map(|c| c.get(slot)).collect()
     }
 
-    /// Fill `buf[i]` with `col_i[slot]`, without allocating.
-    /// `buf` must have length ≥ `self.n_cols()`.
-    pub fn fill_row(&self, slot: usize, buf: &mut [u32]) {
+    pub(crate) fn fill_row(&self, slot: usize, buf: &mut [u32]) {
         for (c, col) in self.cols.iter().enumerate() {
             buf[c] = col.get(slot);
         }
     }
 
-    // ── Distance matrices ─────────────────────────────────────────────────────
+    pub(crate) fn sum(&self) -> Array1<u64> {
+        let sums: Vec<u64> = (0..self.n_cols())
+            .into_par_iter()
+            .map(|c| self.col(c).sum())
+            .collect();
+        Array1::from_vec(sums)
+    }
 
-    pub fn bray_dist_matrix(&self) -> Array2<f64> {
+    pub(crate) fn bray_dist_matrix(&self) -> Array2<f64> {
         let sum_min  = self.partial_bray_dist_matrix();
         let col_sums = self.sum();
         let n = self.n_cols();
@@ -60,63 +71,19 @@ impl PersistentCompactIntMatrix {
         m
     }
 
-    pub fn relfreq_bray_dist_matrix(&self) -> Array2<f64> {
-        self.pairwise(|i, j| self.col(i).relfreq_bray_dist(self.col(j)))
-    }
-
-    pub fn euclidean_dist_matrix(&self) -> Array2<f64> {
-        self.pairwise(|i, j| self.col(i).euclidean_dist(self.col(j)))
-    }
-
-    pub fn relfreq_euclidean_dist_matrix(&self) -> Array2<f64> {
-        self.pairwise(|i, j| self.col(i).relfreq_euclidean_dist(self.col(j)))
-    }
-
-    pub fn hellinger_dist_matrix(&self) -> Array2<f64> {
-        self.pairwise(|i, j| self.col(i).hellinger_dist(self.col(j)))
-    }
-
-    pub fn jaccard_dist_matrix(&self) -> Array2<f64> {
-        self.pairwise(|i, j| self.col(i).jaccard_dist(self.col(j)))
-    }
-
-    pub fn threshold_jaccard_dist_matrix(&self, threshold: u32) -> Array2<f64> {
-        self.pairwise(|i, j| self.col(i).threshold_jaccard_dist(self.col(j), threshold))
-    }
-
-    /// Returns the sum of each column as `Array1<u64>`.
-    pub fn sum(&self) -> Array1<u64> {
-        let sums: Vec<u64> = (0..self.n_cols())
-            .into_par_iter()
-            .map(|c| self.col(c).sum())
-            .collect();
-        Array1::from_vec(sums)
-    }
-
-    // ── Partial matrices (additively decomposable across layers) ──────────────
-
-    /// Returns `sum_min[n×n]` where `sum_min[i,j]` = Σ_slot min(col_i[slot], col_j[slot]).
-    /// The denominator `col_sums[i] + col_sums[j]` is obtained from `self.sum()`.
-    /// Additive across layers by element-wise addition.
-    pub fn partial_bray_dist_matrix(&self) -> Array2<u64> {
+    pub(crate) fn partial_bray_dist_matrix(&self) -> Array2<u64> {
         self.pairwise_u64(|i, j| self.col(i).partial_bray_dist(self.col(j)))
     }
 
-    /// Returns sum of squared differences `[n×n]`.
-    /// Reduce across layers by element-wise addition, then take `sqrt` for the final distance.
-    pub fn partial_euclidean_dist_matrix(&self) -> Array2<f64> {
+    pub(crate) fn partial_euclidean_dist_matrix(&self) -> Array2<f64> {
         self.pairwise(|i, j| self.col(i).partial_euclidean_dist(self.col(j)))
     }
 
-    /// Returns `(inter[n×n], union[n×n])` for threshold-Jaccard.
-    /// Reduce across layers by element-wise addition before computing `1 - inter/union`.
-    pub fn partial_threshold_jaccard_dist_matrix(
-        &self,
-        threshold: u32,
+    pub(crate) fn partial_threshold_jaccard_dist_matrix(
+        &self, threshold: u32,
     ) -> (Array2<u64>, Array2<u64>) {
         let n = self.n_cols();
         let pairs = upper_pairs(n);
-
         let results: Vec<(usize, usize, u64, u64)> = pairs
             .into_par_iter()
             .map(|(i, j)| {
@@ -125,7 +92,6 @@ impl PersistentCompactIntMatrix {
                 (i, j, inter, union)
             })
             .collect();
-
         let mut inter_m = Array2::zeros((n, n));
         let mut union_m = Array2::zeros((n, n));
         for (i, j, inter, union) in results {
@@ -135,99 +101,299 @@ impl PersistentCompactIntMatrix {
         (inter_m, union_m)
     }
 
-    /// Returns matrix of `Σ_slot min(col_i[slot]/sum_i, col_j[slot]/sum_j)` per pair.
-    /// `col_sums` must be the GLOBAL sums across all layers/partitions.
-    /// Reduce across layers by element-wise addition; final distance = `1 - value`.
-    pub fn partial_relfreq_bray_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
+    pub(crate) fn partial_relfreq_bray_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
         self.pairwise(|i, j| {
-            self.col(i).partial_relfreq_bray_dist(
-                self.col(j),
-                col_sums[i] as f64,
-                col_sums[j] as f64,
-            )
+            self.col(i).partial_relfreq_bray_dist(self.col(j), col_sums[i] as f64, col_sums[j] as f64)
         })
     }
 
-    /// Returns matrix of `Σ_slot (col_i[slot]/sum_i - col_j[slot]/sum_j)²` per pair.
-    /// `col_sums` must be the GLOBAL sums across all layers/partitions.
-    /// Reduce across layers by element-wise addition; final distance = `sqrt(value)`.
-    pub fn partial_relfreq_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
+    pub(crate) fn partial_relfreq_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
         self.pairwise(|i, j| {
-            self.col(i).partial_relfreq_euclidean_dist(
-                self.col(j),
-                col_sums[i] as f64,
-                col_sums[j] as f64,
-            )
+            self.col(i).partial_relfreq_euclidean_dist(self.col(j), col_sums[i] as f64, col_sums[j] as f64)
         })
     }
 
-    /// Returns matrix of `Σ_slot (√(col_i/sum_i) - √(col_j/sum_j))²` per pair.
-    /// `col_sums` must be the GLOBAL sums across all layers/partitions.
-    /// Reduce across layers by element-wise addition; final distance = `sqrt(value) / √2`.
-    pub fn partial_hellinger_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
+    pub(crate) fn partial_hellinger_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
         self.pairwise(|i, j| {
-            self.col(i).partial_hellinger_euclidean_dist(
-                self.col(j),
-                col_sums[i] as f64,
-                col_sums[j] as f64,
-            )
+            self.col(i).partial_hellinger_euclidean_dist(self.col(j), col_sums[i] as f64, col_sums[j] as f64)
         })
     }
 
-    // ── Private helpers ───────────────────────────────────────────────────────
+    pub(crate) fn relfreq_bray_dist_matrix(&self) -> Array2<f64> {
+        self.pairwise(|i, j| self.col(i).relfreq_bray_dist(self.col(j)))
+    }
+
+    pub(crate) fn euclidean_dist_matrix(&self) -> Array2<f64> {
+        self.pairwise(|i, j| self.col(i).euclidean_dist(self.col(j)))
+    }
+
+    pub(crate) fn relfreq_euclidean_dist_matrix(&self) -> Array2<f64> {
+        self.pairwise(|i, j| self.col(i).relfreq_euclidean_dist(self.col(j)))
+    }
+
+    pub(crate) fn hellinger_dist_matrix(&self) -> Array2<f64> {
+        self.pairwise(|i, j| self.col(i).hellinger_dist(self.col(j)))
+    }
+
+    pub(crate) fn jaccard_dist_matrix(&self) -> Array2<f64> {
+        self.pairwise(|i, j| self.col(i).jaccard_dist(self.col(j)))
+    }
+
+    pub(crate) fn threshold_jaccard_dist_matrix(&self, threshold: u32) -> Array2<f64> {
+        self.pairwise(|i, j| self.col(i).threshold_jaccard_dist(self.col(j), threshold))
+    }
+
+    pub(crate) fn append_column(dir: &Path, value_of: impl Fn(usize) -> u32) -> io::Result<()> {
+        let mut meta = MatrixMeta::load(dir)?;
+        let mut b = PersistentCompactIntVecBuilder::new(meta.n, &col_path(dir, meta.n_cols))?;
+        for slot in 0..meta.n { b.set(slot, value_of(slot)); }
+        b.close()?;
+        meta.n_cols += 1;
+        meta.save(dir)
+    }
 
     fn pairwise(&self, f: impl Fn(usize, usize) -> f64 + Sync) -> Array2<f64> {
         let n = self.n_cols();
         let results: Vec<(usize, usize, f64)> = upper_pairs(n)
-            .into_par_iter()
-            .map(|(i, j)| (i, j, f(i, j)))
-            .collect();
+            .into_par_iter().map(|(i, j)| (i, j, f(i, j))).collect();
         fill_symmetric(n, results.into_iter().map(|(i, j, v)| (i, j, v, v)))
     }
 
     fn pairwise_u64(&self, f: impl Fn(usize, usize) -> u64 + Sync) -> Array2<u64> {
         let n = self.n_cols();
         let results: Vec<(usize, usize, u64)> = upper_pairs(n)
-            .into_par_iter()
-            .map(|(i, j)| (i, j, f(i, j)))
-            .collect();
+            .into_par_iter().map(|(i, j)| (i, j, f(i, j))).collect();
         fill_symmetric(n, results.into_iter().map(|(i, j, v)| (i, j, v, v)))
     }
 }
 
-fn upper_pairs(n: usize) -> Vec<(usize, usize)> {
-    (0..n).flat_map(|i| (i + 1..n).map(move |j| (i, j))).collect()
+// ── PackedCompactIntMatrix ────────────────────────────────────────────────────
+
+const PCMX_MAGIC:  [u8; 4] = *b"PCMX";
+const PCMX_HEADER: usize   = 24; // magic(4) + pad(4) + n_rows(8) + n_cols(8)
+
+/// Per-column metadata pre-parsed from the embedded PCIV header.
+struct ColInfo {
+    primary_start: usize,  // absolute mmap offset to primary array
+    data_offset:   usize,  // absolute mmap offset to overflow array
+    n_overflow:    usize,
+    step:          usize,
+    index:         Vec<(usize, usize)>,
 }
 
-fn fill_symmetric<T>(n: usize, vals: impl Iterator<Item = (usize, usize, T, T)>) -> Array2<T>
-where
-    T: Clone + Default,
-{
-    let mut m = Array2::from_elem((n, n), T::default());
-    for (i, j, vij, vji) in vals {
-        m[[i, j]] = vij;
-        m[[j, i]] = vji;
+pub struct PackedCompactIntMatrix {
+    mmap:    Mmap,
+    n_rows:  usize,
+    n_cols:  usize,
+    columns: Vec<ColInfo>,
+}
+
+impl PackedCompactIntMatrix {
+    pub(crate) fn open(path: &Path) -> io::Result<Self> {
+        let mmap = unsafe { Mmap::map(&File::open(path)?)? };
+        if mmap.len() < PCMX_HEADER {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "PCMX file too short"));
+        }
+        if &mmap[0..4] != &PCMX_MAGIC {
+            return Err(io::Error::new(io::ErrorKind::InvalidData, "bad PCMX magic"));
+        }
+        let n_rows = u64::from_le_bytes(mmap[8..16].try_into().unwrap())  as usize;
+        let n_cols = u64::from_le_bytes(mmap[16..24].try_into().unwrap()) as usize;
+
+        let mut columns = Vec::with_capacity(n_cols);
+        for c in 0..n_cols {
+            let off_pos  = PCMX_HEADER + c * 8;
+            let col_base = u64::from_le_bytes(mmap[off_pos..off_pos+8].try_into().unwrap()) as usize;
+            // Parse embedded PCIV header at col_base
+            let n_ov    = u64::from_le_bytes(mmap[col_base+16..col_base+24].try_into().unwrap()) as usize;
+            let n_idx   = u64::from_le_bytes(mmap[col_base+24..col_base+32].try_into().unwrap()) as usize;
+            let step    = u64::from_le_bytes(mmap[col_base+32..col_base+40].try_into().unwrap()) as usize;
+            let n_pciv  = u64::from_le_bytes(mmap[col_base+8..col_base+16].try_into().unwrap())  as usize;
+
+            let primary_start = col_base + HEADER_SIZE;
+            let data_offset   = primary_start + n_pciv;
+            let index_offset  = data_offset + n_ov * OVERFLOW_ENTRY_SIZE;
+
+            let mut index = Vec::with_capacity(n_idx);
+            for i in 0..n_idx {
+                let ioff  = index_offset + i * INDEX_ENTRY_SIZE;
+                let slot  = u64::from_le_bytes(mmap[ioff..ioff+8].try_into().unwrap())   as usize;
+                let pos   = u64::from_le_bytes(mmap[ioff+8..ioff+16].try_into().unwrap()) as usize;
+                index.push((slot, pos));
+            }
+            columns.push(ColInfo { primary_start, data_offset, n_overflow: n_ov, step, index });
+        }
+
+        Ok(Self { mmap, n_rows, n_cols, columns })
+    }
+
+    #[inline]
+    pub(crate) fn get(&self, col: usize, slot: usize) -> u32 {
+        let ci = &self.columns[col];
+        let v = self.mmap[ci.primary_start + slot];
+        if v < 255 { return v as u32; }
+        self.overflow_get(ci, slot)
+    }
+
+    fn overflow_get(&self, ci: &ColInfo, slot: usize) -> u32 {
+        let (pos_start, pos_end) = if ci.step == 0 {
+            (0, ci.n_overflow)
+        } else {
+            let i = ci.index.partition_point(|&(s, _)| s <= slot).saturating_sub(1);
+            let start = ci.index[i].1;
+            let end   = if i + 1 < ci.index.len() { ci.index[i+1].1 } else { ci.n_overflow };
+            (start, end)
+        };
+        let mut lo = pos_start;
+        let mut hi = pos_end;
+        while lo < hi {
+            let mid = lo + (hi - lo) / 2;
+            let off = ci.data_offset + mid * OVERFLOW_ENTRY_SIZE;
+            let stored = u64::from_le_bytes(self.mmap[off..off+8].try_into().unwrap()) as usize;
+            match stored.cmp(&slot) {
+                Ordering::Equal   => return u32::from_le_bytes(self.mmap[off+8..off+12].try_into().unwrap()),
+                Ordering::Less    => lo = mid + 1,
+                Ordering::Greater => hi = mid,
+            }
+        }
+        panic!("slot {slot} marked overflow but not found")
+    }
+
+    pub(crate) fn fill_row(&self, slot: usize, buf: &mut [u32]) {
+        for c in 0..self.n_cols { buf[c] = self.get(c, slot); }
+    }
+
+    pub(crate) fn row(&self, slot: usize) -> Box<[u32]> {
+        (0..self.n_cols).map(|c| self.get(c, slot)).collect()
     }
-    m
 }
 
-// ── Column append ─────────────────────────────────────────────────────────────
+/// Build `counts/matrix.pcmx` from existing `col_*.pciv` files.
+pub fn pack_compact_int_matrix(dir: &Path) -> io::Result<()> {
+    let meta = MatrixMeta::load(dir)?;
+    let n_cols = meta.n_cols;
+
+    let col_files: Vec<Vec<u8>> = (0..n_cols)
+        .map(|c| fs::read(col_path(dir, c)))
+        .collect::<io::Result<_>>()?;
+
+    let header_size = PCMX_HEADER + n_cols * 8;
+    let mut col_offset = header_size;
+    let mut offsets = Vec::with_capacity(n_cols);
+    for data in &col_files {
+        offsets.push(col_offset as u64);
+        col_offset += data.len();
+    }
+
+    let packed_path = dir.join("matrix.pcmx");
+    let mut file = File::create(&packed_path)?;
+    file.write_all(&PCMX_MAGIC)?;
+    file.write_all(&[0u8; 4])?;
+    file.write_all(&(meta.n as u64).to_le_bytes())?;
+    file.write_all(&(n_cols as u64).to_le_bytes())?;
+    for &off in &offsets { file.write_all(&off.to_le_bytes())?; }
+    for data in &col_files { file.write_all(data)?; }
+    Ok(())
+}
+
+// ── PersistentCompactIntMatrix — public enum ──────────────────────────────────
+
+pub enum PersistentCompactIntMatrix {
+    Columnar(ColumnarCompactIntMatrix),
+    Packed(PackedCompactIntMatrix),
+}
 
 impl PersistentCompactIntMatrix {
-    /// Append a new column to an existing matrix on disk.
-    ///
-    /// Reads `meta.json` to obtain `n` and the current column count, writes
-    /// `col_{n_cols:06}.pciv` filled by `value_of(slot)`, then increments
-    /// `n_cols` in `meta.json`.
-    pub fn append_column(dir: &Path, value_of: impl Fn(usize) -> u32) -> io::Result<()> {
-        let mut meta = MatrixMeta::load(dir)?;
-        let mut b = PersistentCompactIntVecBuilder::new(meta.n, &col_path(dir, meta.n_cols))?;
-        for slot in 0..meta.n {
-            b.set(slot, value_of(slot));
+    /// Open from `layer_dir`, auto-detecting Packed or Columnar.
+    pub fn open(layer_dir: &Path) -> io::Result<Self> {
+        let counts_dir = layer_dir.join("counts");
+
+        if counts_dir.join("matrix.pcmx").exists() {
+            return Ok(Self::Packed(PackedCompactIntMatrix::open(&counts_dir.join("matrix.pcmx"))?));
         }
-        b.close()?;
-        meta.n_cols += 1;
-        meta.save(dir)
+
+        if MatrixMeta::load(&counts_dir).is_ok() {
+            return Ok(Self::Columnar(ColumnarCompactIntMatrix::open(&counts_dir)?));
+        }
+
+        Err(io::Error::new(
+            io::ErrorKind::NotFound,
+            format!("no count matrix found in {} — run 'obikmer upgrade'", layer_dir.display()),
+        ))
+    }
+
+    pub fn n(&self) -> usize {
+        match self { Self::Columnar(m) => m.n(), Self::Packed(m) => m.n_rows }
+    }
+
+    pub fn n_cols(&self) -> usize {
+        match self { Self::Columnar(m) => m.n_cols(), Self::Packed(m) => m.n_cols }
+    }
+
+    pub fn col(&self, c: usize) -> &PersistentCompactIntVec {
+        match self {
+            Self::Columnar(m) => m.col(c),
+            _ => panic!("col() only available on Columnar PersistentCompactIntMatrix"),
+        }
+    }
+
+    pub fn row(&self, slot: usize) -> Box<[u32]> {
+        match self { Self::Columnar(m) => m.row(slot), Self::Packed(m) => m.row(slot) }
+    }
+
+    pub fn fill_row(&self, slot: usize, buf: &mut [u32]) {
+        match self { Self::Columnar(m) => m.fill_row(slot, buf), Self::Packed(m) => m.fill_row(slot, buf) }
+    }
+
+    pub fn sum(&self) -> Array1<u64> {
+        match self {
+            Self::Columnar(m) => m.sum(),
+            _ => panic!("sum() only available on Columnar PersistentCompactIntMatrix"),
+        }
+    }
+
+    pub fn bray_dist_matrix(&self) -> Array2<f64> {
+        match self { Self::Columnar(m) => m.bray_dist_matrix(), _ => panic!("Columnar only") }
+    }
+    pub fn relfreq_bray_dist_matrix(&self) -> Array2<f64> {
+        match self { Self::Columnar(m) => m.relfreq_bray_dist_matrix(), _ => panic!("Columnar only") }
+    }
+    pub fn euclidean_dist_matrix(&self) -> Array2<f64> {
+        match self { Self::Columnar(m) => m.euclidean_dist_matrix(), _ => panic!("Columnar only") }
+    }
+    pub fn relfreq_euclidean_dist_matrix(&self) -> Array2<f64> {
+        match self { Self::Columnar(m) => m.relfreq_euclidean_dist_matrix(), _ => panic!("Columnar only") }
+    }
+    pub fn hellinger_dist_matrix(&self) -> Array2<f64> {
+        match self { Self::Columnar(m) => m.hellinger_dist_matrix(), _ => panic!("Columnar only") }
+    }
+    pub fn jaccard_dist_matrix(&self) -> Array2<f64> {
+        match self { Self::Columnar(m) => m.jaccard_dist_matrix(), _ => panic!("Columnar only") }
+    }
+    pub fn threshold_jaccard_dist_matrix(&self, threshold: u32) -> Array2<f64> {
+        match self { Self::Columnar(m) => m.threshold_jaccard_dist_matrix(threshold), _ => panic!("Columnar only") }
+    }
+    pub fn partial_bray_dist_matrix(&self) -> Array2<u64> {
+        match self { Self::Columnar(m) => m.partial_bray_dist_matrix(), _ => panic!("Columnar only") }
+    }
+    pub fn partial_euclidean_dist_matrix(&self) -> Array2<f64> {
+        match self { Self::Columnar(m) => m.partial_euclidean_dist_matrix(), _ => panic!("Columnar only") }
+    }
+    pub fn partial_threshold_jaccard_dist_matrix(&self, threshold: u32) -> (Array2<u64>, Array2<u64>) {
+        match self { Self::Columnar(m) => m.partial_threshold_jaccard_dist_matrix(threshold), _ => panic!("Columnar only") }
+    }
+    pub fn partial_relfreq_bray_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
+        match self { Self::Columnar(m) => m.partial_relfreq_bray_dist_matrix(col_sums), _ => panic!("Columnar only") }
+    }
+    pub fn partial_relfreq_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
+        match self { Self::Columnar(m) => m.partial_relfreq_euclidean_dist_matrix(col_sums), _ => panic!("Columnar only") }
+    }
+    pub fn partial_hellinger_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
+        match self { Self::Columnar(m) => m.partial_hellinger_euclidean_dist_matrix(col_sums), _ => panic!("Columnar only") }
+    }
+
+    pub fn append_column(dir: &Path, value_of: impl Fn(usize) -> u32) -> io::Result<()> {
+        ColumnarCompactIntMatrix::append_column(dir, value_of)
     }
 }
 
@@ -240,24 +406,12 @@ impl ColumnWeights for PersistentCompactIntMatrix {
 }
 
 impl CountPartials for PersistentCompactIntMatrix {
-    fn partial_bray(&self) -> Array2<u64> {
-        self.partial_bray_dist_matrix()
-    }
-    fn partial_euclidean(&self) -> Array2<f64> {
-        self.partial_euclidean_dist_matrix()
-    }
-    fn partial_threshold_jaccard(&self, threshold: u32) -> (Array2<u64>, Array2<u64>) {
-        self.partial_threshold_jaccard_dist_matrix(threshold)
-    }
-    fn partial_relfreq_bray(&self, global: &Array1<u64>) -> Array2<f64> {
-        self.partial_relfreq_bray_dist_matrix(global)
-    }
-    fn partial_relfreq_euclidean(&self, global: &Array1<u64>) -> Array2<f64> {
-        self.partial_relfreq_euclidean_dist_matrix(global)
-    }
-    fn partial_hellinger(&self, global: &Array1<u64>) -> Array2<f64> {
-        self.partial_hellinger_euclidean_dist_matrix(global)
-    }
+    fn partial_bray(&self) -> Array2<u64>                        { self.partial_bray_dist_matrix() }
+    fn partial_euclidean(&self) -> Array2<f64>                   { self.partial_euclidean_dist_matrix() }
+    fn partial_threshold_jaccard(&self, t: u32) -> (Array2<u64>, Array2<u64>) { self.partial_threshold_jaccard_dist_matrix(t) }
+    fn partial_relfreq_bray(&self, g: &Array1<u64>) -> Array2<f64>     { self.partial_relfreq_bray_dist_matrix(g) }
+    fn partial_relfreq_euclidean(&self, g: &Array1<u64>) -> Array2<f64> { self.partial_relfreq_euclidean_dist_matrix(g) }
+    fn partial_hellinger(&self, g: &Array1<u64>) -> Array2<f64>         { self.partial_hellinger_euclidean_dist_matrix(g) }
 }
 
 // ── Builder ───────────────────────────────────────────────────────────────────
@@ -287,3 +441,16 @@ impl PersistentCompactIntMatrixBuilder {
         MatrixMeta { n: self.n, n_cols: self.n_cols }.save(&self.dir)
     }
 }
+
+// ── Helpers ───────────────────────────────────────────────────────────────────
+
+fn upper_pairs(n: usize) -> Vec<(usize, usize)> {
+    (0..n).flat_map(|i| (i + 1..n).map(move |j| (i, j))).collect()
+}
+
+fn fill_symmetric<T>(n: usize, vals: impl Iterator<Item = (usize, usize, T, T)>) -> Array2<T>
+where T: Clone + Default {
+    let mut m = Array2::from_elem((n, n), T::default());
+    for (i, j, vij, vji) in vals { m[[i, j]] = vij; m[[j, i]] = vji; }
+    m
+}
diff --git a/src/obicompactvec/src/layer_meta.rs b/src/obicompactvec/src/layer_meta.rs
new file mode 100644
index 0000000..65dc5bc
--- /dev/null
+++ b/src/obicompactvec/src/layer_meta.rs
@@ -0,0 +1,33 @@
+use std::{fs, io, path::Path};
+
+/// Lightweight metadata stored at the layer level (`layer_meta.json`).
+///
+/// Written by `obilayeredmap::MphfLayer::build` alongside `mphf.bin`.
+/// Read by `PersistentBitMatrix::open` to determine `n_rows` for the
+/// implicit (mono-genome presence/absence) case.
+pub struct LayerMeta {
+    pub n: usize,
+}
+
+impl LayerMeta {
+    pub const FILENAME: &'static str = "layer_meta.json";
+
+    pub fn save(layer_dir: &Path, n: usize) -> io::Result<()> {
+        fs::write(layer_dir.join(Self::FILENAME), format!("{{\"n\":{n}}}\n"))
+    }
+
+    pub fn load(layer_dir: &Path) -> io::Result<Self> {
+        let s = fs::read_to_string(layer_dir.join(Self::FILENAME))?;
+        Self::parse(&s)
+            .ok_or_else(|| io::Error::new(io::ErrorKind::InvalidData, "bad layer_meta.json"))
+    }
+
+    fn parse(s: &str) -> Option<Self> {
+        let key = "\"n\":";
+        let pos = s.find(key)? + key.len();
+        let rest = s[pos..].trim_start();
+        let end = rest.find(|c: char| !c.is_ascii_digit()).unwrap_or(rest.len());
+        let n = rest[..end].parse().ok()?;
+        Some(Self { n })
+    }
+}
diff --git a/src/obicompactvec/src/lib.rs b/src/obicompactvec/src/lib.rs
index 270956f..8a1e5bb 100644
--- a/src/obicompactvec/src/lib.rs
+++ b/src/obicompactvec/src/lib.rs
@@ -3,14 +3,16 @@ mod bitmatrix;
 mod builder;
 mod format;
 mod intmatrix;
+mod layer_meta;
 mod meta;
 mod reader;
 pub mod traits;
 
 pub use bitvec::{BitIter, PersistentBitVec, PersistentBitVecBuilder};
-pub use bitmatrix::{PersistentBitMatrix, PersistentBitMatrixBuilder};
+pub use bitmatrix::{PersistentBitMatrix, PersistentBitMatrixBuilder, pack_bit_matrix};
 pub use builder::PersistentCompactIntVecBuilder;
-pub use intmatrix::{PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder};
+pub use intmatrix::{PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder, pack_compact_int_matrix};
+pub use layer_meta::LayerMeta;
 pub use reader::PersistentCompactIntVec;
 pub use traits::{BitPartials, ColumnWeights, CountPartials};
 
diff --git a/src/obicompactvec/src/tests/bitmatrix.rs b/src/obicompactvec/src/tests/bitmatrix.rs
index f5845d6..d825d85 100644
--- a/src/obicompactvec/src/tests/bitmatrix.rs
+++ b/src/obicompactvec/src/tests/bitmatrix.rs
@@ -5,7 +5,8 @@ use crate::{PersistentBitMatrix, PersistentBitMatrixBuilder};
 fn make_matrix(cols: &[&[bool]]) -> (tempfile::TempDir, PersistentBitMatrix) {
     let n = cols.first().map_or(0, |c| c.len());
     let dir = tempdir().unwrap();
-    let mut b = PersistentBitMatrixBuilder::new(n, dir.path()).unwrap();
+    let presence = dir.path().join("presence");
+    let mut b = PersistentBitMatrixBuilder::new(n, &presence).unwrap();
     for &col in cols {
         let mut cb = b.add_col().unwrap();
         for (slot, &v) in col.iter().enumerate() {
@@ -21,7 +22,8 @@ fn make_matrix(cols: &[&[bool]]) -> (tempfile::TempDir, PersistentBitMatrix) {
 #[test]
 fn single_col_roundtrip() {
     let dir = tempdir().unwrap();
-    let mut b = PersistentBitMatrixBuilder::new(4, dir.path()).unwrap();
+    let presence = dir.path().join("presence");
+    let mut b = PersistentBitMatrixBuilder::new(4, &presence).unwrap();
     let mut col = b.add_col().unwrap();
     col.set(0, true);
     col.set(1, false);
@@ -42,7 +44,8 @@ fn single_col_roundtrip() {
 #[test]
 fn two_cols_roundtrip() {
     let dir = tempdir().unwrap();
-    let mut b = PersistentBitMatrixBuilder::new(3, dir.path()).unwrap();
+    let presence = dir.path().join("presence");
+    let mut b = PersistentBitMatrixBuilder::new(3, &presence).unwrap();
     let mut col0 = b.add_col().unwrap();
     col0.set(0, true); col0.set(1, false); col0.set(2, true);
     col0.close().unwrap();
@@ -61,7 +64,8 @@ fn two_cols_roundtrip() {
 #[test]
 fn col_accessor() {
     let dir = tempdir().unwrap();
-    let mut b = PersistentBitMatrixBuilder::new(3, dir.path()).unwrap();
+    let presence = dir.path().join("presence");
+    let mut b = PersistentBitMatrixBuilder::new(3, &presence).unwrap();
     let mut col = b.add_col().unwrap();
     col.set(0, true); col.set(1, false); col.set(2, true);
     col.close().unwrap();
@@ -76,7 +80,8 @@ fn col_accessor() {
 #[test]
 fn zero_cols_roundtrip() {
     let dir = tempdir().unwrap();
-    let b = PersistentBitMatrixBuilder::new(8, dir.path()).unwrap();
+    let presence = dir.path().join("presence");
+    let b = PersistentBitMatrixBuilder::new(8, &presence).unwrap();
     b.close().unwrap();
 
     let m = PersistentBitMatrix::open(dir.path()).unwrap();
@@ -89,9 +94,9 @@ fn zero_cols_roundtrip() {
 #[test]
 fn count_ones_per_column() {
     let (_d, m) = make_matrix(&[
-        &[true,  false, true,  true],   // 3 ones
-        &[false, false, false, false],  // 0 ones
-        &[true,  true,  true,  false],  // 3 ones
+        &[true,  false, true,  true],
+        &[false, false, false, false],
+        &[true,  true,  true,  false],
     ]);
     let c = m.count_ones();
     assert_eq!(c[0], 3);
diff --git a/src/obicompactvec/src/tests/intmatrix.rs b/src/obicompactvec/src/tests/intmatrix.rs
index 2b9d45e..b9e1841 100644
--- a/src/obicompactvec/src/tests/intmatrix.rs
+++ b/src/obicompactvec/src/tests/intmatrix.rs
@@ -5,7 +5,7 @@ use crate::{PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder};
 fn make_matrix(cols: &[&[u32]]) -> (tempfile::TempDir, PersistentCompactIntMatrix) {
     let n = cols.first().map_or(0, |c| c.len());
     let dir = tempdir().unwrap();
-    let mut b = PersistentCompactIntMatrixBuilder::new(n, dir.path()).unwrap();
+    let mut b = PersistentCompactIntMatrixBuilder::new(n, &dir.path().join("counts")).unwrap();
     for &col in cols {
         let mut cb = b.add_col().unwrap();
         for (slot, &v) in col.iter().enumerate() {
@@ -21,7 +21,7 @@ fn make_matrix(cols: &[&[u32]]) -> (tempfile::TempDir, PersistentCompactIntMatri
 #[test]
 fn single_col_roundtrip() {
     let dir = tempdir().unwrap();
-    let mut b = PersistentCompactIntMatrixBuilder::new(4, dir.path()).unwrap();
+    let mut b = PersistentCompactIntMatrixBuilder::new(4, &dir.path().join("counts")).unwrap();
     let mut col = b.add_col().unwrap();
     col.set(0, 10);
     col.set(1, 200);
@@ -42,7 +42,7 @@ fn single_col_roundtrip() {
 #[test]
 fn two_cols_roundtrip() {
     let dir = tempdir().unwrap();
-    let mut b = PersistentCompactIntMatrixBuilder::new(3, dir.path()).unwrap();
+    let mut b = PersistentCompactIntMatrixBuilder::new(3, &dir.path().join("counts")).unwrap();
     let mut col0 = b.add_col().unwrap();
     col0.set(0, 1); col0.set(1, 2); col0.set(2, 3);
     col0.close().unwrap();
@@ -61,7 +61,7 @@ fn two_cols_roundtrip() {
 #[test]
 fn col_accessor() {
     let dir = tempdir().unwrap();
-    let mut b = PersistentCompactIntMatrixBuilder::new(2, dir.path()).unwrap();
+    let mut b = PersistentCompactIntMatrixBuilder::new(2, &dir.path().join("counts")).unwrap();
     let mut col0 = b.add_col().unwrap();
     col0.set(0, 5); col0.set(1, 7);
     col0.close().unwrap();
@@ -75,7 +75,7 @@ fn col_accessor() {
 #[test]
 fn zero_cols_roundtrip() {
     let dir = tempdir().unwrap();
-    let b = PersistentCompactIntMatrixBuilder::new(10, dir.path()).unwrap();
+    let b = PersistentCompactIntMatrixBuilder::new(10, &dir.path().join("counts")).unwrap();
     b.close().unwrap();
 
     let m = PersistentCompactIntMatrix::open(dir.path()).unwrap();
diff --git a/src/obikindex/src/index.rs b/src/obikindex/src/index.rs
index 8e207a8..6583968 100644
--- a/src/obikindex/src/index.rs
+++ b/src/obikindex/src/index.rs
@@ -6,6 +6,7 @@ use std::sync::{Arc, Mutex};
 
 use indicatif::{ProgressBar, ProgressStyle};
 use obikpartitionner::{KmerPartition, KmerSpectrum};
+use obilayeredmap;
 use obisys::{Reporter, Stage};
 use rayon::prelude::*;
 use tracing::info;
@@ -199,6 +200,87 @@ impl KmerIndex {
             .join(format!("layer_{layer}"))
             .join("unitigs.bin")
     }
+
+    /// Pack all partition matrices into single-file format (presence → .pbmx, counts → .pcmx).
+    ///
+    /// 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.
+    pub fn pack_matrices(&self) -> OKIResult<()> {
+        use obicompactvec::{pack_bit_matrix, pack_compact_int_matrix};
+        use obilayeredmap::meta::PartitionMeta;
+
+        let n = self.n_partitions();
+        let errors: Vec<_> = (0..n)
+            .into_par_iter()
+            .filter_map(|i| {
+                let index_dir = self.partition.part_dir(i).join("index");
+                if !index_dir.exists() { return None; }
+                let meta = match PartitionMeta::load(&index_dir) {
+                    Ok(m) => m,
+                    Err(e) => return Some(OKIError::Io(std::io::Error::new(std::io::ErrorKind::Other, e.to_string()))),
+                };
+                for l in 0..meta.n_layers {
+                    let layer_dir = index_dir.join(format!("layer_{l}"));
+                    let presence_dir = layer_dir.join("presence");
+                    let counts_dir   = layer_dir.join("counts");
+                    if presence_dir.exists() {
+                        if let Err(e) = pack_bit_matrix(&presence_dir) {
+                            return Some(OKIError::Io(e));
+                        }
+                    }
+                    if counts_dir.exists() {
+                        if let Err(e) = pack_compact_int_matrix(&counts_dir) {
+                            return Some(OKIError::Io(e));
+                        }
+                    }
+                }
+                None
+            })
+            .collect();
+
+        if let Some(e) = errors.into_iter().next() { return Err(e); }
+        Ok(())
+    }
+
+    /// Write a `layer_meta.json` in any layer directory that is missing one.
+    ///
+    /// Old indexes were built before this file was required.  The number of
+    /// kmers is recovered from `unitigs.bin`, which is always present.
+    pub fn upgrade_layer_meta(&self) -> OKIResult<()> {
+        use obicompactvec::LayerMeta;
+        use obiskio::UnitigFileReader;
+        use obilayeredmap::meta::PartitionMeta;
+
+        let n = self.n_partitions();
+        let errors: Vec<_> = (0..n)
+            .into_par_iter()
+            .filter_map(|i| {
+                let index_dir = self.partition.part_dir(i).join("index");
+                if !index_dir.exists() { return None; }
+                let meta = match PartitionMeta::load(&index_dir) {
+                    Ok(m) => m,
+                    Err(e) => return Some(OKIError::Io(std::io::Error::new(std::io::ErrorKind::Other, e.to_string()))),
+                };
+                for l in 0..meta.n_layers {
+                    let layer_dir = index_dir.join(format!("layer_{l}"));
+                    let meta_path = layer_dir.join(LayerMeta::FILENAME);
+                    if meta_path.exists() { continue; }
+                    let unitigs_path = layer_dir.join("unitigs.bin");
+                    let n_kmers = match UnitigFileReader::open_sequential(&unitigs_path) {
+                        Ok(r)  => r.n_kmers(),
+                        Err(e) => return Some(OKIError::Partition(e)),
+                    };
+                    if let Err(e) = LayerMeta::save(&layer_dir, n_kmers) {
+                        return Some(OKIError::Io(e));
+                    }
+                }
+                None
+            })
+            .collect();
+
+        if let Some(e) = errors.into_iter().next() { return Err(e); }
+        Ok(())
+    }
 }
 
 fn label_from_path(path: &Path) -> String {
diff --git a/src/obikindex/src/merge.rs b/src/obikindex/src/merge.rs
index 39b4395..dc129d8 100644
--- a/src/obikindex/src/merge.rs
+++ b/src/obikindex/src/merge.rs
@@ -196,6 +196,16 @@ impl KmerIndex {
             rep.push(t.stop());
         }
 
+        // ── Pack matrices after merge ─────────────────────────────────────────
+        {
+            let t = Stage::start("pack");
+            let pb = spinner("pack — consolidating column files …");
+            let dst2 = KmerIndex::open(output)?;
+            dst2.pack_matrices()?;
+            pb.finish_and_clear();
+            rep.push(t.stop());
+        }
+
         // Re-open to get the updated state.
         KmerIndex::open(output)
     }
diff --git a/src/obikmer/src/cmd/mod.rs b/src/obikmer/src/cmd/mod.rs
index 2fc940a..569b543 100644
--- a/src/obikmer/src/cmd/mod.rs
+++ b/src/obikmer/src/cmd/mod.rs
@@ -1,4 +1,5 @@
 pub mod annotate;
+pub mod pack;
 pub mod utils;
 pub mod distance;
 pub mod dump;
diff --git a/src/obikmer/src/cmd/pack.rs b/src/obikmer/src/cmd/pack.rs
new file mode 100644
index 0000000..f3c0d3d
--- /dev/null
+++ b/src/obikmer/src/cmd/pack.rs
@@ -0,0 +1,36 @@
+use std::path::PathBuf;
+
+use clap::Args;
+use obikindex::KmerIndex;
+use obisys::{Reporter, Stage};
+use tracing::info;
+
+#[derive(Args)]
+pub struct PackArgs {
+    /// Index directory to pack
+    pub index: PathBuf,
+}
+
+pub fn run(args: PackArgs) {
+    let idx = KmerIndex::open(&args.index).unwrap_or_else(|e| {
+        eprintln!("error opening index: {e}");
+        std::process::exit(1);
+    });
+
+    info!(
+        "pack: {} partition(s), {} genome(s)",
+        idx.n_partitions(),
+        idx.meta().genomes.len(),
+    );
+
+    let mut rep = Reporter::new();
+    let t = Stage::start("pack");
+
+    idx.pack_matrices().unwrap_or_else(|e| {
+        eprintln!("pack error: {e}");
+        std::process::exit(1);
+    });
+
+    rep.push(t.stop());
+    rep.print();
+}
diff --git a/src/obikmer/src/cmd/utils.rs b/src/obikmer/src/cmd/utils.rs
index 0e7ec20..3bbaf4f 100644
--- a/src/obikmer/src/cmd/utils.rs
+++ b/src/obikmer/src/cmd/utils.rs
@@ -2,6 +2,7 @@ use std::path::PathBuf;
 
 use clap::Args;
 use obikindex::{validate_label, KmerIndex};
+use obikseq::set_k;
 use tracing::info;
 
 #[derive(Args)]
@@ -12,6 +13,10 @@ pub struct UtilsArgs {
     /// Set a new genome label: NEW_LABEL=OLD_LABEL
     #[arg(long, value_name = "NEW=OLD")]
     pub new_label: Option<String>,
+
+    /// Add missing layer_meta.json files to each layer (required after upgrading from old indexes)
+    #[arg(long)]
+    pub upgrade_index: bool,
 }
 
 pub fn run(args: UtilsArgs) {
@@ -22,12 +27,30 @@ pub fn run(args: UtilsArgs) {
         run_rename(&args.index, spec);
     }
 
+    if args.upgrade_index {
+        any = true;
+        run_upgrade_index(&args.index);
+    }
+
     if !any {
-        eprintln!("utils: no operation specified. Available options: --new-label NEW=OLD");
+        eprintln!("utils: no operation specified. Available options: --new-label NEW=OLD, --upgrade-index");
         std::process::exit(1);
     }
 }
 
+fn run_upgrade_index(index_path: &PathBuf) {
+    let idx = KmerIndex::open(index_path).unwrap_or_else(|e| {
+        eprintln!("error opening index: {e}");
+        std::process::exit(1);
+    });
+    set_k(idx.kmer_size());
+    idx.upgrade_layer_meta().unwrap_or_else(|e| {
+        eprintln!("upgrade error: {e}");
+        std::process::exit(1);
+    });
+    info!("upgrade-index: layer_meta.json written to all layers that were missing it");
+}
+
 fn run_rename(index_path: &PathBuf, spec: &str) {
     let (old_label, new_label) = parse_rename_spec(spec);
 
diff --git a/src/obikmer/src/main.rs b/src/obikmer/src/main.rs
index a872e46..47ff4c7 100644
--- a/src/obikmer/src/main.rs
+++ b/src/obikmer/src/main.rs
@@ -38,6 +38,8 @@ enum Commands {
     Reindex(cmd::reindex::ReindexArgs),
     /// Miscellaneous index utilities (--rename, …)
     Utils(cmd::utils::UtilsArgs),
+    /// Pack matrix column files into single-file format to reduce query I/O
+    Pack(cmd::pack::PackArgs),
 }
 
 fn main() {
@@ -71,6 +73,7 @@ fn main() {
         Commands::Estimate(args)  => cmd::estimate::run(args),
         Commands::Reindex(args)   => cmd::reindex::run(args),
         Commands::Utils(args)     => cmd::utils::run(args),
+        Commands::Pack(args)      => cmd::pack::run(args),
     }
 
     #[cfg(feature = "profiling")]
diff --git a/src/obikpartitionner/src/distance.rs b/src/obikpartitionner/src/distance.rs
index b5e6914..f25a45f 100644
--- a/src/obikpartitionner/src/distance.rs
+++ b/src/obikpartitionner/src/distance.rs
@@ -22,8 +22,9 @@ impl KmerPartition {
         }
         let matrices = (0..probe_n_layers(&index_dir))
             .filter_map(|l| {
-                let dir = index_dir.join(format!("layer_{l}")).join("counts");
-                dir.exists().then(|| PersistentCompactIntMatrix::open(&dir).map_err(SKError::Io))
+                let layer_dir = index_dir.join(format!("layer_{l}"));
+                layer_dir.join("counts").exists()
+                    .then(|| PersistentCompactIntMatrix::open(&layer_dir).map_err(SKError::Io))
             })
             .collect::<SKResult<Vec<_>>>()?;
         Ok(LayeredStore::new(matrices))
@@ -38,8 +39,9 @@ impl KmerPartition {
         }
         let matrices = (0..probe_n_layers(&index_dir))
             .filter_map(|l| {
-                let dir = index_dir.join(format!("layer_{l}")).join("presence");
-                dir.exists().then(|| PersistentBitMatrix::open(&dir).map_err(SKError::Io))
+                let layer_dir = index_dir.join(format!("layer_{l}"));
+                layer_dir.join("presence").exists()
+                    .then(|| PersistentBitMatrix::open(&layer_dir).map_err(SKError::Io))
             })
             .collect::<SKResult<Vec<_>>>()?;
         Ok(LayeredStore::new(matrices))
diff --git a/src/obikpartitionner/src/dump_layer.rs b/src/obikpartitionner/src/dump_layer.rs
index 4f060e9..77c7cd3 100644
--- a/src/obikpartitionner/src/dump_layer.rs
+++ b/src/obikpartitionner/src/dump_layer.rs
@@ -51,14 +51,14 @@ impl KmerPartition {
             let presence_dir = layer_dir.join("presence");
 
             if use_counts && counts_dir.exists() {
-                let mat = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
+                let mat = PersistentCompactIntMatrix::open(&layer_dir).map_err(SKError::Io)?;
                 for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
                     if let Some(slot) = mphf.find(kmer) {
                         cb(kmer, mat.row(slot));
                     }
                 }
             } else if !use_counts && presence_dir.exists() {
-                let mat = PersistentBitMatrix::open(&presence_dir).map_err(SKError::Io)?;
+                let mat = PersistentBitMatrix::open(&layer_dir).map_err(SKError::Io)?;
                 for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
                     if let Some(slot) = mphf.find(kmer) {
                         let row: Box<[u32]> = mat.row(slot).iter().map(|&b| b as u32).collect();
@@ -108,14 +108,14 @@ impl KmerPartition {
             let presence_dir = layer_dir.join("presence");
 
             if use_counts && counts_dir.exists() {
-                let mat = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
+                let mat = PersistentCompactIntMatrix::open(&layer_dir).map_err(SKError::Io)?;
                 for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
                     if let Some(slot) = mphf.find(kmer) {
                         cb(part, layer, kmer, mat.row(slot));
                     }
                 }
             } else if !use_counts && presence_dir.exists() {
-                let mat = PersistentBitMatrix::open(&presence_dir).map_err(SKError::Io)?;
+                let mat = PersistentBitMatrix::open(&layer_dir).map_err(SKError::Io)?;
                 for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
                     if let Some(slot) = mphf.find(kmer) {
                         let row: Box<[u32]> = mat.row(slot).iter().map(|&b| b as u32).collect();
diff --git a/src/obikpartitionner/src/merge_layer.rs b/src/obikpartitionner/src/merge_layer.rs
index b8673a2..3af515b 100644
--- a/src/obikpartitionner/src/merge_layer.rs
+++ b/src/obikpartitionner/src/merge_layer.rs
@@ -45,37 +45,35 @@ impl ColBuilder {
 // ── SrcLayerData — opened source matrix for pass-2 lookup ─────────────────────
 
 pub(crate) enum SrcLayerData {
-    /// Pure set-membership layer (no data matrix): every kmer is present in all genomes.
-    SetMembership,
     Presence(MphfOnly, PersistentBitMatrix),
     Count(MphfOnly, PersistentCompactIntMatrix),
 }
 
 impl SrcLayerData {
     pub(crate) fn open(layer_dir: &Path, merge_mode: MergeMode) -> SKResult<Self> {
-        let presence_dir = layer_dir.join("presence");
-        let counts_dir   = layer_dir.join("counts");
+        let counts_dir = layer_dir.join("counts");
         match merge_mode {
             MergeMode::Presence => {
-                if presence_dir.exists() {
+                if counts_dir.exists() && !layer_dir.join("presence").exists() {
                     let mphf = MphfOnly::open(layer_dir).map_err(olm_to_sk)?;
-                    let mat  = PersistentBitMatrix::open(&presence_dir).map_err(SKError::Io)?;
-                    Ok(SrcLayerData::Presence(mphf, mat))
-                } else if counts_dir.exists() {
-                    let mphf = MphfOnly::open(layer_dir).map_err(olm_to_sk)?;
-                    let mat  = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
+                    let mat  = PersistentCompactIntMatrix::open(layer_dir).map_err(SKError::Io)?;
                     Ok(SrcLayerData::Count(mphf, mat))
                 } else {
-                    Ok(SrcLayerData::SetMembership)
+                    // presence dir exists, or neither exists → Implicit handled by open()
+                    let mphf = MphfOnly::open(layer_dir).map_err(olm_to_sk)?;
+                    let mat  = PersistentBitMatrix::open(layer_dir).map_err(SKError::Io)?;
+                    Ok(SrcLayerData::Presence(mphf, mat))
                 }
             }
             MergeMode::Count => {
+                let mphf = MphfOnly::open(layer_dir).map_err(olm_to_sk)?;
                 if counts_dir.exists() {
-                    let mphf = MphfOnly::open(layer_dir).map_err(olm_to_sk)?;
-                    let mat  = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
+                    let mat = PersistentCompactIntMatrix::open(layer_dir).map_err(SKError::Io)?;
                     Ok(SrcLayerData::Count(mphf, mat))
                 } else {
-                    Ok(SrcLayerData::SetMembership)
+                    // No counts → treat as implicit presence (all 1s)
+                    let mat = PersistentBitMatrix::open(layer_dir).map_err(SKError::Io)?;
+                    Ok(SrcLayerData::Presence(mphf, mat))
                 }
             }
         }
@@ -85,15 +83,12 @@ impl SrcLayerData {
     /// The caller guarantees `kmer` is in the source MPHF domain.
     #[inline]
     pub(crate) fn lookup(&self, kmer: CanonicalKmer, n_genomes: usize) -> Vec<u32> {
+        let mut buf = vec![0u32; n_genomes];
         match self {
-            SrcLayerData::SetMembership => vec![1u32; n_genomes],
-            SrcLayerData::Presence(mphf, mat) => {
-                mat.row(mphf.index(kmer)).iter().map(|&b| b as u32).collect()
-            }
-            SrcLayerData::Count(mphf, mat) => {
-                mat.row(mphf.index(kmer)).iter().copied().collect()
-            }
+            SrcLayerData::Presence(mphf, mat) => mat.fill_row(mphf.index(kmer), &mut buf),
+            SrcLayerData::Count(mphf, mat)    => mat.fill_row(mphf.index(kmer), &mut buf),
         }
+        buf
     }
 }
 
diff --git a/src/obikpartitionner/src/query_layer.rs b/src/obikpartitionner/src/query_layer.rs
index 97e09e3..e918ec6 100644
--- a/src/obikpartitionner/src/query_layer.rs
+++ b/src/obikpartitionner/src/query_layer.rs
@@ -20,48 +20,33 @@ fn olm_to_sk(e: OLMError) -> SKError {
 // ── per-layer query handle ────────────────────────────────────────────────────
 
 enum QueryLayer {
-    /// Layer<()> — MPHF-only, no data matrix; all indexed kmers map to 1 per genome.
-    SetOnly(MphfLayer),
     Presence(MphfLayer, PersistentBitMatrix),
     Count(MphfLayer, PersistentCompactIntMatrix),
 }
 
 impl QueryLayer {
     fn open(layer_dir: &Path, with_counts: bool, mode: &IndexMode) -> SKResult<Self> {
+        let mphf        = MphfLayer::open(layer_dir, mode).map_err(olm_to_sk)?;
+        let counts_dir  = layer_dir.join("counts");
         let presence_dir = layer_dir.join("presence");
-        let counts_dir   = layer_dir.join("counts");
 
         if with_counts && counts_dir.exists() {
-            let mphf = MphfLayer::open(layer_dir, mode).map_err(olm_to_sk)?;
-            let mat  = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
+            let mat = PersistentCompactIntMatrix::open(layer_dir).map_err(SKError::Io)?;
             Ok(QueryLayer::Count(mphf, mat))
-        } else if presence_dir.exists() {
-            let mphf = MphfLayer::open(layer_dir, mode).map_err(olm_to_sk)?;
-            let mat  = PersistentBitMatrix::open(&presence_dir).map_err(SKError::Io)?;
+        } else if presence_dir.exists() || !counts_dir.exists() {
+            // presence mode, or no matrix at all → Implicit handled inside open()
+            let mat = PersistentBitMatrix::open(layer_dir).map_err(SKError::Io)?;
             Ok(QueryLayer::Presence(mphf, mat))
-        } else if counts_dir.exists() {
-            // presence query on a count index — return counts as-is
-            let mphf = MphfLayer::open(layer_dir, mode).map_err(olm_to_sk)?;
-            let mat  = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
-            Ok(QueryLayer::Count(mphf, mat))
         } else {
-            let mphf = MphfLayer::open(layer_dir, mode).map_err(olm_to_sk)?;
-            Ok(QueryLayer::SetOnly(mphf))
+            // counts exist but not presence — count layer, no presence requested
+            let mat = PersistentCompactIntMatrix::open(layer_dir).map_err(SKError::Io)?;
+            Ok(QueryLayer::Count(mphf, mat))
         }
     }
 
-    /// Write per-genome values into `buf` if `kmer` is indexed in this layer.
-    /// Returns `true` on hit; `buf` is untouched on miss.
+    /// Write per-genome values into `buf` if `kmer` is indexed; returns true on hit.
     fn find_into(&self, kmer: CanonicalKmer, n_genomes: usize, buf: &mut [u32]) -> bool {
         match self {
-            QueryLayer::SetOnly(mphf) => {
-                if mphf.find(kmer).is_some() {
-                    buf[..n_genomes].fill(1);
-                    true
-                } else {
-                    false
-                }
-            }
             QueryLayer::Presence(mphf, mat) => {
                 if let Some(slot) = mphf.find(kmer) {
                     mat.fill_row(slot, &mut buf[..n_genomes]);
@@ -87,14 +72,11 @@ impl QueryLayer {
 impl KmerPartition {
     /// Query a single partition, calling `on_hit(sk_idx, kmer_idx, row)` for
     /// every found k-mer without allocating intermediate result vectors.
-    ///
-    /// `row` is a shared scratch buffer valid only for the duration of the call;
-    /// the callback must copy what it needs before returning.
     pub fn query_partition_with<F>(
         &self,
         part_idx: usize,
         superkmers: &[&RoutableSuperKmer],
-        k: usize,
+        _k: usize,
         n_genomes: usize,
         with_counts: bool,
         mut on_hit: F,
@@ -133,13 +115,13 @@ impl KmerPartition {
         Ok(())
     }
 
-    /// Query a single partition for a slice of (already-routed) super-kmers.
+    /// Query a single partition for a slice of super-kmers, returning per-kmer rows.
     /// Prefer [`query_partition_with`] to avoid per-kmer heap allocations.
     pub fn query_partition(
         &self,
         part_idx: usize,
         superkmers: &[&RoutableSuperKmer],
-        k: usize,
+        _k: usize,
         n_genomes: usize,
         with_counts: bool,
     ) -> SKResult<Vec<Vec<Option<Box<[u32]>>>>> {
@@ -152,7 +134,7 @@ impl KmerPartition {
         if !index_dir.exists() {
             return Ok(superkmers
                 .iter()
-                .map(|rsk| vec![None; rsk.seql() - k + 1])
+                .map(|rsk| vec![None; rsk.seql()])
                 .collect());
         }
 
diff --git a/src/obilayeredmap/src/layer.rs b/src/obilayeredmap/src/layer.rs
index 63b99d2..72b38ea 100644
--- a/src/obilayeredmap/src/layer.rs
+++ b/src/obilayeredmap/src/layer.rs
@@ -34,7 +34,7 @@ impl LayerData for () {
 impl LayerData for PersistentCompactIntMatrix {
     type Item = Box<[u32]>;
     fn open(layer_dir: &Path) -> OLMResult<Self> {
-        PersistentCompactIntMatrix::open(&layer_dir.join(COUNTS_DIR)).map_err(OLMError::Io)
+        PersistentCompactIntMatrix::open(layer_dir).map_err(OLMError::Io)
     }
     fn read(&self, slot: usize) -> Box<[u32]> { self.row(slot) }
 }
@@ -42,7 +42,7 @@ impl LayerData for PersistentCompactIntMatrix {
 impl LayerData for PersistentBitMatrix {
     type Item = Box<[bool]>;
     fn open(layer_dir: &Path) -> OLMResult<Self> {
-        PersistentBitMatrix::open(&layer_dir.join(PRESENCE_DIR)).map_err(OLMError::Io)
+        PersistentBitMatrix::open(layer_dir).map_err(OLMError::Io)
     }
     fn read(&self, slot: usize) -> Box<[bool]> { self.row(slot) }
 }
diff --git a/src/obilayeredmap/src/layered_store.rs b/src/obilayeredmap/src/layered_store.rs
index f25855d..433183e 100644
--- a/src/obilayeredmap/src/layered_store.rs
+++ b/src/obilayeredmap/src/layered_store.rs
@@ -107,7 +107,7 @@ mod tests {
     fn make_int_matrix(cols: &[&[u32]]) -> (tempfile::TempDir, PersistentCompactIntMatrix) {
         let n = cols.first().map_or(0, |c| c.len());
         let dir = tempdir().unwrap();
-        let mut b = PersistentCompactIntMatrixBuilder::new(n, dir.path()).unwrap();
+        let mut b = PersistentCompactIntMatrixBuilder::new(n, &dir.path().join("counts")).unwrap();
         for &col in cols {
             let mut cb = b.add_col().unwrap();
             for (slot, &v) in col.iter().enumerate() { cb.set(slot, v); }
@@ -121,7 +121,7 @@ mod tests {
     fn make_bit_matrix(cols: &[&[bool]]) -> (tempfile::TempDir, PersistentBitMatrix) {
         let n = cols.first().map_or(0, |c| c.len());
         let dir = tempdir().unwrap();
-        let mut b = PersistentBitMatrixBuilder::new(n, dir.path()).unwrap();
+        let mut b = PersistentBitMatrixBuilder::new(n, &dir.path().join("presence")).unwrap();
         for &col in cols {
             let mut cb = b.add_col().unwrap();
             for (slot, &v) in col.iter().enumerate() { cb.set(slot, v); }
diff --git a/src/obilayeredmap/src/mphf_layer.rs b/src/obilayeredmap/src/mphf_layer.rs
index a5e30b7..2661123 100644
--- a/src/obilayeredmap/src/mphf_layer.rs
+++ b/src/obilayeredmap/src/mphf_layer.rs
@@ -3,6 +3,7 @@ use std::path::{Path, PathBuf};
 
 use cacheline_ef::{CachelineEf, CachelineEfVec};
 use epserde::prelude::*;
+use obicompactvec::LayerMeta;
 use obikseq::CanonicalKmer;
 use obiskio::{CanonicalKmerIter, UnitigFileReader, UnitigFileWriter, build_unitig_idx};
 use ptr_hash::{PtrHash, PtrHashParams, bucket_fn::CubicEps, hash::Xx64};
@@ -341,6 +342,7 @@ impl MphfLayer {
             }
         }
 
+        LayerMeta::save(dir, n)?;
         Ok(n)
     }
 }