feat: add vectorized column filters and optimize partitioner iteration

Adds `FilterMask` and conditional bitwise methods (`*_where`) to `obicompactvec` for composable column-based slot filtering. Extends `obikpartitionner` with a `MatrixGroupOps` trait and `column_mask_expr` method to express aggregate constraints as vectorized masks. Refactors matrix builder management into a unified `Builders` enum and introduces `try_compute_combined_mask`, enabling O(1) slot checks and skipping unnecessary row reads during partitioning and rebuilding passes.

src/obicompactvec/src/bitvec.rs

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

src/obicompactvec/src/colgroup.rs

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

src/obicompactvec/src/lib.rs

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

src/obicompactvec/src/tempbitvec.rs

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