refactor: extract matrix helpers and improve bit iteration ergonomics

Refactor parallel matrix construction by extracting reusable `pairwise_matrix` and `pairwise2_matrix` helpers, and consolidate binary record deserialization into dedicated parsing functions. Add `set` and `iter` methods to `BitSliceMut` and `MemoryBitVec` for ergonomic bit manipulation and iteration. Standardize JSON field extraction via `meta::field`, expose `MemoryBitIter`, and improve test reliability by automatically cleaning up temporary directories.

src/obicompactvec/src/bitmatrix.rs

@@ -56,34 +56,11 @@ impl ColumnarBitMatrix {
     }
 
     pub(crate) fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
-        let n = self.n_cols();
+        pairwise2_matrix(self.n_cols(), |i, j| self.col(i).partial_jaccard_dist(self.col(j)))
-        let results: Vec<(usize, usize, u64, u64)> = upper_pairs(n)
-            .into_par_iter()
-            .map(|(i, j)| {
-                let (inter, union) = self.col(i).partial_jaccard_dist(self.col(j));
-                (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 {
-            inter_m[[i, j]] = inter; inter_m[[j, i]] = inter;
-            union_m[[i, j]] = union; union_m[[j, i]] = union;
-        }
-        (inter_m, union_m)
     }
 
     pub(crate) fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
-        self.pairwise_u64(|i, j| self.col(i).hamming_dist(self.col(j)))
+        pairwise_matrix(self.n_cols(), |i, j| self.col(i).hamming_dist(self.col(j)))
-    }
-
-    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();
-        fill_symmetric(n, results.into_iter().map(|(i, j, v)| (i, j, v, v)))
     }
 
     pub(crate) fn append_column(dir: &Path, value_of: impl Fn(usize) -> bool) -> io::Result<()> {
@@ -228,27 +205,11 @@ impl PackedBitMatrix {
     }
 
     pub(crate) fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
-        let n = self.n_cols;
+        pairwise2_matrix(self.n_cols, |i, j| self.partial_jaccard_col(i, j))
-        let results: Vec<(usize, usize, u64, u64)> = upper_pairs(n)
-            .into_par_iter()
-            .map(|(i, j)| { let (inter, union) = self.partial_jaccard_col(i, j); (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 {
-            inter_m[[i, j]] = inter; inter_m[[j, i]] = inter;
-            union_m[[i, j]] = union; union_m[[j, i]] = union;
-        }
-        (inter_m, union_m)
     }
 
     pub(crate) fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
-        let n = self.n_cols;
+        pairwise_matrix(self.n_cols, |i, j| self.pair_op(i, j, false))
-        let results: Vec<(usize, usize, u64)> = upper_pairs(n)
-            .into_par_iter()
-            .map(|(i, j)| (i, j, self.pair_op(i, j, false)))
-            .collect();
-        fill_symmetric(n, results.into_iter().map(|(i, j, v)| (i, j, v, v)))
     }
 }
 
@@ -488,7 +449,7 @@ impl PersistentBitMatrixBuilder {
     }
 }
 
-// ── Helpers ───────────────────────────────────────────────────────────────────
+// ── Shared matrix helpers (also used by intmatrix.rs) ─────────────────────────
 
 fn upper_pairs(n: usize) -> Vec<(usize, usize)> {
     (0..n).flat_map(|i| (i + 1..n).map(move |j| (i, j))).collect()
@@ -500,3 +461,30 @@ where T: Clone + Default {
     for (i, j, vij, vji) in vals { m[[i, j]] = vij; m[[j, i]] = vji; }
     m
 }
+
+/// Compute a symmetric `n×n` matrix in parallel by evaluating `f(i,j)` for
+/// all upper-triangle pairs. `T: Copy` avoids the `.clone()` needed for the
+/// lower-triangle mirror.
+pub(crate) fn pairwise_matrix<T>(n: usize, f: impl Fn(usize, usize) -> T + Sync) -> Array2<T>
+where T: Copy + Default + Send {
+    let results: Vec<(usize, usize, T)> = upper_pairs(n)
+        .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)))
+}
+
+/// Same as `pairwise_matrix` but `f` returns two values that fill two
+/// symmetric matrices simultaneously (e.g. intersection + union for Jaccard).
+pub(crate) fn pairwise2_matrix<T>(n: usize, f: impl Fn(usize, usize) -> (T, T) + Sync) -> (Array2<T>, Array2<T>)
+where T: Copy + Default + Send {
+    let results: Vec<(usize, usize, T, T)> = upper_pairs(n)
+        .into_par_iter()
+        .map(|(i, j)| { let (a, b) = f(i, j); (i, j, a, b) })
+        .collect();
+    let mut m0 = Array2::from_elem((n, n), T::default());
+    let mut m1 = Array2::from_elem((n, n), T::default());
+    for (i, j, a, b) in results {
+        m0[[i, j]] = a; m0[[j, i]] = a;
+        m1[[i, j]] = b; m1[[j, i]] = b;
+    }
+    (m0, m1)
+}

src/obicompactvec/src/bitvec.rs

@@ -14,7 +14,7 @@ const MAGIC: [u8; 4] = *b"PBIV";
 const HEADER_SIZE: usize = 16;
 
 #[inline]
-fn n_words(n: usize) -> usize {
+pub(crate) fn n_words(n: usize) -> usize {
     n.div_ceil(64)
 }
 
@@ -222,16 +222,6 @@ impl PersistentBitVecBuilder {
         (self.mmap[HEADER_SIZE + (slot >> 3)] >> (slot & 7)) & 1 != 0
     }
 
-    pub fn set(&mut self, slot: usize, value: bool) {
-        let byte = HEADER_SIZE + (slot >> 3);
-        let bit = 1u8 << (slot & 7);
-        if value {
-            self.mmap[byte] |= bit;
-        } else {
-            self.mmap[byte] &= !bit;
-        }
-    }
-
     fn data_words(&self) -> &[u64] {
         let nw = n_words(self.n);
         let ptr = self.mmap[HEADER_SIZE..].as_ptr() as *const u64;

src/obicompactvec/src/builder.rs

@@ -5,7 +5,7 @@ use std::path::{Path, PathBuf};
 
 use memmap2::MmapMut;
 
-use crate::format::{HEADER_SIZE, OVERFLOW_ENTRY_SIZE, finalize_pciv};
+use crate::format::{HEADER_SIZE, finalize_pciv, parse_overflow_entry};
 use crate::reader::PersistentCompactIntVec;
 
 pub struct PersistentCompactIntVecBuilder {
@@ -78,9 +78,7 @@ impl PersistentCompactIntVecBuilder {
 
         let mut overflow = HashMap::with_capacity(n_overflow);
         for i in 0..n_overflow {
-            let off = data_offset + i * OVERFLOW_ENTRY_SIZE;
+            let (slot, value) = parse_overflow_entry(&mmap, data_offset, i);
-            let slot  = u64::from_le_bytes(mmap[off..off + 8].try_into().unwrap()) as usize;
-            let value = u32::from_le_bytes(mmap[off + 8..off + 12].try_into().unwrap());
             overflow.insert(slot, value);
         }
 

src/obicompactvec/src/format.rs

@@ -13,6 +13,24 @@ pub const OVERFLOW_ENTRY_SIZE: usize = 12;
 // Index entry: slot(u64) + pos(u64) = 16 bytes.
 pub const INDEX_ENTRY_SIZE: usize = 16;
 
+/// Parse a single overflow entry `(slot, value)` from a byte slice.
+#[inline]
+pub fn parse_overflow_entry(data: &[u8], base: usize, i: usize) -> (usize, u32) {
+    let off = base + i * OVERFLOW_ENTRY_SIZE;
+    let slot  = u64::from_le_bytes(data[off..off+8].try_into().unwrap()) as usize;
+    let value = u32::from_le_bytes(data[off+8..off+12].try_into().unwrap());
+    (slot, value)
+}
+
+/// Parse a single sparse-index entry `(slot, pos)` from a byte slice.
+#[inline]
+pub fn parse_index_entry(data: &[u8], base: usize, i: usize) -> (usize, usize) {
+    let off = base + i * INDEX_ENTRY_SIZE;
+    let slot = u64::from_le_bytes(data[off..off+8].try_into().unwrap()) as usize;
+    let pos  = u64::from_le_bytes(data[off+8..off+16].try_into().unwrap()) as usize;
+    (slot, pos)
+}
+
 // Sparse index target: ≤ 32 KB in L1 cache (16 B per entry → 2048 entries).
 pub const L1_INDEX_ENTRIES: usize = 2048;
 

src/obicompactvec/src/intmatrix.rs

@@ -8,9 +8,10 @@ use memmap2::Mmap;
 use ndarray::{Array1, Array2};
 use rayon::prelude::*;
 
+use crate::bitmatrix::{pairwise_matrix, pairwise2_matrix};
 use crate::builder::PersistentCompactIntVecBuilder;
 use crate::memoryintvec::MemoryIntVec;
-use crate::format::{HEADER_SIZE, INDEX_ENTRY_SIZE, OVERFLOW_ENTRY_SIZE};
+use crate::format::{HEADER_SIZE, OVERFLOW_ENTRY_SIZE, parse_index_entry, parse_overflow_entry};
 use crate::meta::MatrixMeta;
 use crate::reader::PersistentCompactIntVec;
 
@@ -65,49 +66,35 @@ impl ColumnarCompactIntMatrix {
     }
 
     pub(crate) fn partial_bray_dist_matrix(&self) -> Array2<u64> {
-        self.pairwise_u64(|i, j| self.col(i).partial_bray_dist(self.col(j)))
+        pairwise_matrix(self.n_cols(), |i, j| self.col(i).partial_bray_dist(self.col(j)))
     }
 
     pub(crate) fn partial_euclidean_dist_matrix(&self) -> Array2<f64> {
-        self.pairwise(|i, j| self.col(i).partial_euclidean_dist(self.col(j)))
+        pairwise_matrix(self.n_cols(), |i, j| self.col(i).partial_euclidean_dist(self.col(j)))
     }
 
     pub(crate) fn partial_threshold_jaccard_dist_matrix(
         &self, threshold: u32,
     ) -> (Array2<u64>, Array2<u64>) {
-        let n = self.n_cols();
+        pairwise2_matrix(self.n_cols(), |i, j| {
-        let pairs = upper_pairs(n);
+            self.col(i).partial_threshold_jaccard_dist(self.col(j), threshold)
-        let results: Vec<(usize, usize, u64, u64)> = pairs
-            .into_par_iter()
-            .map(|(i, j)| {
-                let (inter, union) =
-                    self.col(i).partial_threshold_jaccard_dist(self.col(j), threshold);
-                (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 {
-            inter_m[[i, j]] = inter; inter_m[[j, i]] = inter;
-            union_m[[i, j]] = union; union_m[[j, i]] = union;
-        }
-        (inter_m, union_m)
     }
 
     pub(crate) fn partial_relfreq_bray_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
-        self.pairwise(|i, j| {
+        pairwise_matrix(self.n_cols(), |i, j| {
             self.col(i).partial_relfreq_bray_dist(self.col(j), col_sums[i] as f64, col_sums[j] as f64)
         })
     }
 
     pub(crate) fn partial_relfreq_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
-        self.pairwise(|i, j| {
+        pairwise_matrix(self.n_cols(), |i, j| {
             self.col(i).partial_relfreq_euclidean_dist(self.col(j), col_sums[i] as f64, col_sums[j] as f64)
         })
     }
 
     pub(crate) fn partial_hellinger_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
-        self.pairwise(|i, j| {
+        pairwise_matrix(self.n_cols(), |i, j| {
             self.col(i).partial_hellinger_euclidean_dist(self.col(j), col_sums[i] as f64, col_sums[j] as f64)
         })
     }
@@ -121,19 +108,6 @@ impl ColumnarCompactIntMatrix {
         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();
-        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();
-        fill_symmetric(n, results.into_iter().map(|(i, j, v)| (i, j, v, v)))
-    }
 }
 
 // ── PackedCompactIntMatrix ────────────────────────────────────────────────────
@@ -185,10 +159,7 @@ impl PackedCompactIntMatrix {
 
             let mut index = Vec::with_capacity(n_idx);
             for i in 0..n_idx {
-                let ioff  = index_offset + i * INDEX_ENTRY_SIZE;
+                index.push(parse_index_entry(&mmap, index_offset, i));
-                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 });
         }
@@ -196,30 +167,25 @@ impl PackedCompactIntMatrix {
         Ok(Self { mmap, n_rows, n_cols, columns })
     }
 
+    fn col_overflow_map(&self, ci: &ColInfo) -> HashMap<usize, u32> {
+        let mut overflow = HashMap::with_capacity(ci.n_overflow);
+        for i in 0..ci.n_overflow {
+            let (slot, value) = parse_overflow_entry(&self.mmap, ci.data_offset, i);
+            overflow.insert(slot, value);
+        }
+        overflow
+    }
+
     pub(crate) fn col_persist(&self, c: usize, path: &Path) -> io::Result<PersistentCompactIntVecBuilder> {
         let ci = &self.columns[c];
         let primary = &self.mmap[ci.primary_start..ci.primary_start + self.n_rows];
-        let mut overflow = HashMap::with_capacity(ci.n_overflow);
+        PersistentCompactIntVecBuilder::from_raw_primary(primary, self.col_overflow_map(ci), path)
-        for i in 0..ci.n_overflow {
-            let off   = ci.data_offset + i * OVERFLOW_ENTRY_SIZE;
-            let slot  = u64::from_le_bytes(self.mmap[off..off+8].try_into().unwrap()) as usize;
-            let value = u32::from_le_bytes(self.mmap[off+8..off+12].try_into().unwrap());
-            overflow.insert(slot, value);
-        }
-        PersistentCompactIntVecBuilder::from_raw_primary(primary, overflow, path)
     }
 
     pub(crate) fn col_as_memory(&self, c: usize) -> MemoryIntVec {
         let ci = &self.columns[c];
         let primary = self.mmap[ci.primary_start..ci.primary_start + self.n_rows].to_vec();
-        let mut overflow = HashMap::with_capacity(ci.n_overflow);
+        MemoryIntVec::from_primary_and_overflow(primary, self.col_overflow_map(ci))
-        for i in 0..ci.n_overflow {
-            let off   = ci.data_offset + i * OVERFLOW_ENTRY_SIZE;
-            let slot  = u64::from_le_bytes(self.mmap[off..off+8].try_into().unwrap()) as usize;
-            let value = u32::from_le_bytes(self.mmap[off+8..off+12].try_into().unwrap());
-            overflow.insert(slot, value);
-        }
-        MemoryIntVec::from_primary_and_overflow(primary, overflow)
     }
 
     #[inline]
@@ -327,55 +293,28 @@ impl PackedCompactIntMatrix {
 
     // ── Matrix methods ────────────────────────────────────────────────────────
 
-    fn pairwise<T>(&self, f: impl Fn(usize, usize) -> T + Sync) -> Array2<T>
-    where T: Clone + Default + Send {
-        let n = self.n_cols;
-        let results: Vec<(usize, usize, T)> = upper_pairs(n)
-            .into_par_iter().map(|(i, j)| (i, j, f(i, j))).collect();
-        fill_symmetric(n, results.into_iter().map(|(i, j, v)| { let w = v.clone(); (i, j, v, w) }))
-    }
-
-    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();
-        fill_symmetric(n, results.into_iter().map(|(i, j, v)| (i, j, v, v)))
-    }
-
     pub(crate) fn partial_bray_dist_matrix(&self) -> Array2<u64> {
-        self.pairwise_u64(|i, j| self.pair_partial_bray(i, j))
+        pairwise_matrix(self.n_cols, |i, j| self.pair_partial_bray(i, j))
     }
 
-
     pub(crate) fn partial_euclidean_dist_matrix(&self) -> Array2<f64> {
-        self.pairwise(|i, j| self.pair_partial_euclidean(i, j))
+        pairwise_matrix(self.n_cols, |i, j| self.pair_partial_euclidean(i, j))
     }
 
     pub(crate) fn partial_threshold_jaccard_dist_matrix(&self, t: u32) -> (Array2<u64>, Array2<u64>) {
-        let n = self.n_cols;
+        pairwise2_matrix(self.n_cols, |i, j| self.pair_partial_threshold_jaccard(i, j, t))
-        let results: Vec<(usize, usize, u64, u64)> = upper_pairs(n)
-            .into_par_iter()
-            .map(|(i, j)| { let (inter, union) = self.pair_partial_threshold_jaccard(i, j, t); (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 {
-            inter_m[[i, j]] = inter; inter_m[[j, i]] = inter;
-            union_m[[i, j]] = union; union_m[[j, i]] = union;
-        }
-        (inter_m, union_m)
     }
 
     pub(crate) fn partial_relfreq_bray_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
-        self.pairwise(|i, j| self.pair_partial_relfreq_bray(i, j, col_sums[i] as f64, col_sums[j] as f64))
+        pairwise_matrix(self.n_cols, |i, j| self.pair_partial_relfreq_bray(i, j, col_sums[i] as f64, col_sums[j] as f64))
     }
 
     pub(crate) fn partial_relfreq_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
-        self.pairwise(|i, j| self.pair_partial_relfreq_euclidean(i, j, col_sums[i] as f64, col_sums[j] as f64))
+        pairwise_matrix(self.n_cols, |i, j| self.pair_partial_relfreq_euclidean(i, j, col_sums[i] as f64, col_sums[j] as f64))
     }
 
     pub(crate) fn partial_hellinger_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
-        self.pairwise(|i, j| self.pair_partial_hellinger(i, j, col_sums[i] as f64, col_sums[j] as f64))
+        pairwise_matrix(self.n_cols, |i, j| self.pair_partial_hellinger(i, j, col_sums[i] as f64, col_sums[j] as f64))
     }
 
 }
@@ -570,15 +509,3 @@ impl PersistentCompactIntMatrixBuilder {
     }
 }
 
-// ── 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
-}

src/obicompactvec/src/layer_meta.rs

@@ -23,11 +23,6 @@ impl LayerMeta {
     }
 
     fn parse(s: &str) -> Option<Self> {
-        let key = "\"n\":";
+        Some(Self { n: crate::meta::field(s, "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 })
     }
 }

src/obicompactvec/src/lib.rs

@@ -16,7 +16,7 @@ pub use builder::PersistentCompactIntVecBuilder;
 pub use intmatrix::{PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder, pack_compact_int_matrix};
 pub use layer_meta::LayerMeta;
 pub use memoryintvec::MemoryIntVec;
-pub use memoryvec::MemoryBitVec;
+pub use memoryvec::{MemoryBitIter, MemoryBitVec};
 pub use reader::PersistentCompactIntVec;
 pub use traits::{BitPartials, BitSlice, BitSliceMut, BitToInt, ColumnWeights, CountPartials, IntSlice, IntSliceMut, IntToBit};
 

src/obicompactvec/src/memoryvec.rs

@@ -2,12 +2,9 @@ use std::io;
 use std::ops::{BitAnd, BitAndAssign, BitOr, BitOrAssign, BitXor, BitXorAssign, Not};
 use std::path::Path;
 
-use crate::bitvec::PersistentBitVecBuilder;
+use crate::bitvec::{PersistentBitVecBuilder, n_words};
 use crate::traits::{BitSlice, BitSliceMut};
 
-#[inline]
-fn n_words(n: usize) -> usize { n.div_ceil(64) }
-
 // ── MemoryBitVec ──────────────────────────────────────────────────────────────
 
 #[derive(Clone)]
@@ -41,11 +38,6 @@ impl MemoryBitVec {
         (self.words[slot >> 6] >> (slot & 63)) & 1 != 0
     }
 
-    pub fn set(&mut self, slot: usize, value: bool) {
-        let bit = 1u64 << (slot & 63);
-        if value { self.words[slot >> 6] |= bit; } else { self.words[slot >> 6] &= !bit; }
-    }
-
     pub fn count_ones(&self) -> u64 {
         self.words.iter().map(|w| w.count_ones() as u64).sum()
     }
@@ -136,3 +128,41 @@ impl<B: BitSlice> BitOrAssign<&B> for MemoryBitVec {
 impl<B: BitSlice> BitXorAssign<&B> for MemoryBitVec {
     fn bitxor_assign(&mut self, rhs: &B) { self.xor(rhs); }
 }
+
+// ── Iterator ──────────────────────────────────────────────────────────────────
+
+pub struct MemoryBitIter<'a> {
+    words: &'a [u64],
+    slot: usize,
+    n: usize,
+}
+
+impl Iterator for MemoryBitIter<'_> {
+    type Item = bool;
+
+    fn next(&mut self) -> Option<bool> {
+        if self.slot >= self.n { return None; }
+        let v = (self.words[self.slot >> 6] >> (self.slot & 63)) & 1 != 0;
+        self.slot += 1;
+        Some(v)
+    }
+
+    fn size_hint(&self) -> (usize, Option<usize>) {
+        let rem = self.n - self.slot;
+        (rem, Some(rem))
+    }
+}
+
+impl ExactSizeIterator for MemoryBitIter<'_> {}
+
+impl MemoryBitVec {
+    pub fn iter(&self) -> MemoryBitIter<'_> {
+        MemoryBitIter { words: &self.words, slot: 0, n: self.n }
+    }
+}
+
+impl<'a> IntoIterator for &'a MemoryBitVec {
+    type Item = bool;
+    type IntoIter = MemoryBitIter<'a>;
+    fn into_iter(self) -> MemoryBitIter<'a> { self.iter() }
+}

src/obicompactvec/src/meta.rs

@@ -23,7 +23,7 @@ fn parse(s: &str) -> Option<MatrixMeta> {
     Some(MatrixMeta { n: field(s, "n")?, n_cols: field(s, "n_cols")? })
 }
 
-fn field(s: &str, name: &str) -> Option<usize> {
+pub(crate) fn field(s: &str, name: &str) -> Option<usize> {
     let key = format!("\"{}\":", name);
     let pos = s.find(&key)? + key.len();
     let rest = s[pos..].trim_start();

src/obicompactvec/src/reader.rs

@@ -4,7 +4,7 @@ use std::path::{Path, PathBuf};
 
 use memmap2::Mmap;
 
-use crate::format::{HEADER_SIZE, INDEX_ENTRY_SIZE, MAGIC, OVERFLOW_ENTRY_SIZE};
+use crate::format::{HEADER_SIZE, MAGIC, OVERFLOW_ENTRY_SIZE, parse_index_entry};
 
 pub struct PersistentCompactIntVec {
     mmap: Mmap,
@@ -43,10 +43,7 @@ impl PersistentCompactIntVec {
 
         let mut index = Vec::with_capacity(n_index);
         for i in 0..n_index {
-            let off = index_offset + i * INDEX_ENTRY_SIZE;
+            index.push(parse_index_entry(&mmap, index_offset, i));
-            let slot = u64::from_le_bytes(mmap[off..off + 8].try_into().unwrap()) as usize;
-            let pos = u64::from_le_bytes(mmap[off + 8..off + 16].try_into().unwrap()) as usize;
-            index.push((slot, pos));
         }
 
         Ok(Self {

src/obicompactvec/src/tests/bitmatrix.rs

@@ -1,7 +1,7 @@
 use tempfile::tempdir;
 
 use crate::{PersistentBitMatrix, PersistentBitMatrixBuilder};
-use crate::traits::BitPartials;
+use crate::traits::{BitPartials, BitSliceMut};
 
 fn make_matrix(cols: &[&[bool]]) -> (tempfile::TempDir, PersistentBitMatrix) {
     let n = cols.first().map_or(0, |c| c.len());

src/obicompactvec/src/traits.rs

@@ -20,6 +20,11 @@ pub trait BitSlice {
 pub trait BitSliceMut: BitSlice {
     fn words_mut(&mut self) -> &mut [u64];
 
+    fn set(&mut self, slot: usize, value: bool) {
+        let bit = 1u64 << (slot & 63);
+        if value { self.words_mut()[slot >> 6] |= bit; } else { self.words_mut()[slot >> 6] &= !bit; }
+    }
+
     fn copy_from<S: BitSlice>(&mut self, src: &S) -> &mut Self {
         assert_eq!(self.len(), src.len(), "BitSlice length mismatch");
         self.words_mut().copy_from_slice(src.words());
@@ -62,6 +67,7 @@ pub trait IntSlice {
     fn len(&self) -> usize;
     fn get(&self, slot: usize) -> u32;
     fn is_empty(&self) -> bool { self.len() == 0 }
+    fn iter(&self) -> impl Iterator<Item = u32> + '_ { (0..self.len()).map(|i| self.get(i)) }
     fn sum(&self) -> u64 { (0..self.len()).map(|s| self.get(s) as u64).sum() }
     fn count_nonzero(&self) -> u64 { (0..self.len()).filter(|&s| self.get(s) > 0).count() as u64 }
 

src/obikpartitionner/src/common.rs

@@ -3,6 +3,7 @@ use std::io;
 use std::path::{Path, PathBuf};
 
 use obicompactvec::{PersistentBitVecBuilder, PersistentCompactIntVecBuilder};
+use obicompactvec::traits::BitSliceMut;
 use obilayeredmap::meta::PartitionMeta;
 use obilayeredmap::{IndexMode, OLMError};
 use obiskio::{SKError, SKResult};

src/obikpartitionner/src/select_layer.rs

@@ -6,6 +6,7 @@ use obicompactvec::{
     PersistentBitMatrix, PersistentBitMatrixBuilder, PersistentBitVecBuilder,
     PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder, PersistentCompactIntVecBuilder,
 };
+use obicompactvec::traits::BitSliceMut;
 use obilayeredmap::meta::PartitionMeta;
 use obilayeredmap::OLMError;
 use obiskio::{SKError, SKResult};

src/obilayeredmap/src/layer.rs

@@ -6,6 +6,7 @@ use obicompactvec::{
     PersistentBitMatrix, PersistentBitMatrixBuilder,
     PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder,
 };
+use obicompactvec::traits::BitSliceMut;
 use obikseq::CanonicalKmer;
 use obiskio::{UnitigFileReader, UnitigFileWriter};
 

src/obilayeredmap/src/layered_store.rs

@@ -102,6 +102,7 @@ mod tests {
         PersistentBitMatrix, PersistentBitMatrixBuilder,
         PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder,
     };
+    use obicompactvec::traits::BitSliceMut;
     use tempfile::tempdir;
 
     fn make_int_matrix(cols: &[&[u32]]) -> (tempfile::TempDir, PersistentCompactIntMatrix) {