docmd/implementation/obicompactvec.md

@@ -444,71 +444,64 @@ Defined **once at the index level** from column metadata. Valid in all matrices
 
 ### MatrixGroupOps
 
-Group operations expose only **additive intermediates** backed by temp files. Final predicates are applied at the index level after accumulation.
+Five required primitives + two default methods derived from them. All return temp-file-backed types.
 
 ```rust
 pub trait MatrixGroupOps {
+    // required
     fn partial_group_presence_count(&self, g: &ColGroup, threshold: u32)
         -> io::Result<TempCompactIntVec>;
-
     fn partial_group_sum(&self, g: &ColGroup)
         -> io::Result<TempCompactIntVec>;
-
     fn partial_group_any(&self, g: &ColGroup, threshold: u32)
         -> io::Result<TempBitVec>;
+    fn partial_group_min(&self, g: &ColGroup)
+        -> io::Result<TempCompactIntVec>;
+    fn partial_group_max(&self, g: &ColGroup)
+        -> io::Result<TempCompactIntVec>;
+
+    // defaults derived from partial_group_presence_count
+    fn partial_group_all(&self, g: &ColGroup, threshold: u32)
+        -> io::Result<TempBitVec>;   // slot=1 iff count == g.indices.len()
+    fn partial_group_none(&self, g: &ColGroup, threshold: u32)
+        -> io::Result<TempBitVec>;   // slot=1 iff count == 0
 }
 ```
 
-Implemented for both `PersistentCompactIntMatrix` and `PersistentBitMatrix`. For bit matrices, `partial_group_sum` delegates to `partial_group_presence_count(g, 1)`.
+Implemented for both `PersistentCompactIntMatrix` and `PersistentBitMatrix`.
+
+For **bit matrices**: values are 0/1, so `partial_group_sum` = `partial_group_presence_count(g, 1)`; `partial_group_min` is AND (set first column then mask-with remaining); `partial_group_max` is OR via `partial_group_any` + `inc_present`.
 
 **`partial_group_presence_count` — chunking for large groups:**
 
-When `g.indices.len() < 255`: per-slot counts stay within `u8` range. Use `inc_present_fast` (bit matrix) or `inc_predicate_fast(col_view(c), |v| v >= threshold)` (int matrix) — raw u8 increment, no overflow map written.
+When `g.indices.len() < 255`: per-slot counts stay within `u8` range. Use `inc_present_fast` (bit) or `inc_predicate_fast(col_view(c), |v| v >= threshold)` (int) — raw u8 increment, no overflow entry written.
 
-When `g.indices.len() ≥ 255`: process in chunks of 254 columns (each chunk stays within u8 range), accumulate into a running builder via `.add(chunk_frozen.view())`.
+When `g.indices.len() ≥ 255`: process in chunks of 254 columns, accumulate via `.add(chunk_frozen.view())`.
 
-```
-fast path (< 255 cols):
-  builder = TempCompactIntVecBuilder::new(n)
-  for c in group:
-    builder.inc_predicate_fast(matrix.col_view(c), |v| v >= threshold)
-  builder.freeze()
+**`partial_group_min` (int matrix)**: copy first column via `.add(col_view(first))` (start from 0 ⇒ copy), then `.min(col_view(c))` for remaining.
 
-slow path (≥ 255 cols):
-  result = TempCompactIntVecBuilder::new(n)
-  for chunk in group.chunks(254):
-    chunk_b = TempCompactIntVecBuilder::new(n)
-    for c in chunk:
-      chunk_b.inc_predicate_fast(matrix.col_view(c), |v| v >= threshold)
-    frozen = chunk_b.freeze()
-    result.add(frozen.view())
-  result.freeze()
-```
+**`partial_group_max` (int matrix)**: `.max(col_view(c))` for all columns (start from 0 ⇒ first column acts as copy).
 
-**`partial_group_any`** uses `or_where` on `TempBitVecBuilder`:
+**`partial_group_any`** uses `or_where` on `TempBitVecBuilder` (two-pass: primary bytes then overflow entries).
 
-```
-result = TempBitVecBuilder::new(n)
-for c in group:
-  result.or_where(matrix.col_view(c), |v| v >= threshold)
-result.freeze()
-```
+**`partial_group_all` / `partial_group_none`** (default): call `partial_group_presence_count`, then iterate slots to produce the bit result. O(n) extra pass, not chunked.
 
-**Non-additive predicates** (`group_all`, `group_at_least(k)`) are composed at the index level:
+### add_col_from — matrix builder integration
+
+Both matrix builders accept temp-file results directly:
 
 ```rust
-// "present in >= 2 ingroup columns with count >= 3, absent from all outgroup"
-let presence = layers.map(|l| l.partial_group_presence_count(&ingroup, 3)?).add_all()?;
-let in_mask  = presence.view().geq(2);   // IntSliceView method
+// PersistentBitMatrixBuilder
+fn add_col_from(&mut self, src: &TempBitVec)         -> io::Result<()>
+fn add_col_from_int(&mut self, src: &TempCompactIntVec) -> io::Result<()>  // nonzero → 1
 
-let out_sum  = layers.map(|l| l.partial_group_sum(&outgroup)?).add_all()?;
-let out_mask = out_sum.view().leq(0);
-
-let mut mask_b = TempBitVecBuilder::new(n)?;
-mask_b.copy_from(in_mask);
-mask_b.and(out_mask);
+// PersistentCompactIntMatrixBuilder
+fn add_col_from(&mut self, src: &TempCompactIntVec)  -> io::Result<()>
+fn add_col_from_bit(&mut self, src: &TempBitVec)     -> io::Result<()>  // bit → 0/1 u32
 ```
 
+`add_col_from` copies the temp file to the matrix directory and increments `n_cols`; `close()` writes `meta.json` with the final column count. No separate `write_meta` step needed.
+
 ### mask_with
 
 Direct method on `PersistentCompactIntVecBuilder` (and delegation via `TempCompactIntVecBuilder`). Zeros every slot where the corresponding mask bit is 0. Iterates only zero bits — O(n_zeros), O(1) when mask is all-ones.

src/obicompactvec/src/bitmatrix.rs

@@ -402,6 +402,26 @@ impl PersistentBitMatrixBuilder {
         PersistentBitVecBuilder::new(self.n, &path)
     }
 
+    pub fn add_col_from(&mut self, src: &TempBitVec) -> io::Result<()> {
+        src.make_persistent(&col_path(&self.dir, self.n_cols))?;
+        self.n_cols += 1;
+        Ok(())
+    }
+
+    pub fn add_col_from_int(&mut self, src: &TempCompactIntVec) -> io::Result<()> {
+        let path = col_path(&self.dir, self.n_cols);
+        self.n_cols += 1;
+        let mut b = PersistentBitVecBuilder::new(self.n, &path)?;
+        let view = src.view();
+        for slot in 0..self.n {
+            if view.primary_bytes()[slot] > 0 { b.set(slot, true); }
+        }
+        for (slot, _) in view.overflow_entries() {
+            b.set(slot, true);
+        }
+        b.close()
+    }
+
     pub fn close(self) -> io::Result<()> {
         MatrixMeta { n: self.n, n_cols: self.n_cols }.save(&self.dir)
     }
@@ -446,6 +466,26 @@ impl MatrixGroupOps for PersistentBitMatrix {
         }
         result.freeze()
     }
+
+    fn partial_group_min(&self, g: &ColGroup) -> io::Result<TempCompactIntVec> {
+        // min of 0/1 values = AND: 1 only if ALL columns are 1
+        let n = self.n();
+        let mut result = TempCompactIntVecBuilder::new(n)?;
+        if let Some((&first, rest)) = g.indices.split_first() {
+            result.inc_present_fast(self.col_view(first));
+            for &c in rest { result.mask_with(self.col_view(c)); }
+        }
+        result.freeze()
+    }
+
+    fn partial_group_max(&self, g: &ColGroup) -> io::Result<TempCompactIntVec> {
+        // max of 0/1 values = OR: 1 if any column is 1
+        let any = self.partial_group_any(g, 1)?;
+        let n = any.len();
+        let mut result = TempCompactIntVecBuilder::new(n)?;
+        result.inc_present(any.view());
+        result.freeze()
+    }
 }
 
 // ── Shared matrix helpers (also used by intmatrix.rs) ─────────────────────────

src/obicompactvec/src/colgroup.rs

@@ -1,6 +1,6 @@
 use std::io;
 
-use crate::tempbitvec::TempBitVec;
+use crate::tempbitvec::{TempBitVec, TempBitVecBuilder};
 use crate::tempintvec::TempCompactIntVec;
 
 // ── ColGroup ──────────────────────────────────────────────────────────────────
@@ -23,12 +23,14 @@ impl ColGroup {
 
 // ── MatrixGroupOps ────────────────────────────────────────────────────────────
 
-/// Per-matrix group aggregations that return **additive intermediates**.
+/// Per-matrix group aggregations.
 ///
-/// Results must be composed by the caller (concat across partitions, add across
-/// layers) before applying final predicates (`geq`, `leq`, …).  Non-additive
-/// predicates like `group_all` or `group_at_least(k)` are intentionally absent
-/// — they are derived at the index level from these intermediates.
+/// `partial_group_presence_count`, `partial_group_sum`, `partial_group_any`,
+/// `partial_group_min`, `partial_group_max` are the primitives; each impl must
+/// provide all five.
+///
+/// `partial_group_all` and `partial_group_none` have default implementations
+/// derived from `partial_group_presence_count` and should rarely need overriding.
 pub trait MatrixGroupOps {
     /// Per-slot count of group columns whose value ≥ `threshold`.
     fn partial_group_presence_count(&self, g: &ColGroup, threshold: u32) -> io::Result<TempCompactIntVec>;
@@ -36,6 +38,35 @@ pub trait MatrixGroupOps {
     /// Per-slot sum of values across all group columns.
     fn partial_group_sum(&self, g: &ColGroup) -> io::Result<TempCompactIntVec>;
 
-    /// Per-slot OR: true if any group column has value ≥ `threshold`.
+    /// Per-slot OR: 1 if any group column has value ≥ `threshold`.
     fn partial_group_any(&self, g: &ColGroup, threshold: u32) -> io::Result<TempBitVec>;
+
+    /// Per-slot min value across all group columns (0 if group is empty).
+    fn partial_group_min(&self, g: &ColGroup) -> io::Result<TempCompactIntVec>;
+
+    /// Per-slot max value across all group columns (0 if group is empty).
+    fn partial_group_max(&self, g: &ColGroup) -> io::Result<TempCompactIntVec>;
+
+    /// Per-slot AND: 1 if ALL group columns have value ≥ `threshold`.
+    fn partial_group_all(&self, g: &ColGroup, threshold: u32) -> io::Result<TempBitVec> {
+        let counts = self.partial_group_presence_count(g, threshold)?;
+        let n = counts.len();
+        let n_required = g.indices.len() as u32;
+        let mut b = TempBitVecBuilder::new(n)?;
+        for slot in 0..n {
+            if counts.get(slot) >= n_required { b.set(slot, true); }
+        }
+        b.freeze()
+    }
+
+    /// Per-slot NOR: 1 if NO group column has value ≥ `threshold`.
+    fn partial_group_none(&self, g: &ColGroup, threshold: u32) -> io::Result<TempBitVec> {
+        let counts = self.partial_group_presence_count(g, threshold)?;
+        let n = counts.len();
+        let mut b = TempBitVecBuilder::new(n)?;
+        for slot in 0..n {
+            if counts.get(slot) == 0 { b.set(slot, true); }
+        }
+        b.freeze()
+    }
 }

src/obicompactvec/src/intmatrix.rs

@@ -386,6 +386,21 @@ impl PersistentCompactIntMatrixBuilder {
         self.n_cols += 1;
         PersistentCompactIntVecBuilder::new(self.n, &path)
     }
+
+    pub fn add_col_from(&mut self, src: &TempCompactIntVec) -> io::Result<()> {
+        src.make_persistent(&col_path(&self.dir, self.n_cols))?;
+        self.n_cols += 1;
+        Ok(())
+    }
+
+    pub fn add_col_from_bit(&mut self, src: &TempBitVec) -> io::Result<()> {
+        let path = col_path(&self.dir, self.n_cols);
+        self.n_cols += 1;
+        let mut b = PersistentCompactIntVecBuilder::new(self.n, &path)?;
+        b.inc_present(src.view());
+        b.close()
+    }
+
     pub fn close(self) -> io::Result<()> {
         MatrixMeta { n: self.n, n_cols: self.n_cols }.save(&self.dir)
     }
@@ -431,4 +446,21 @@ impl MatrixGroupOps for PersistentCompactIntMatrix {
         }
         result.freeze()
     }
+
+    fn partial_group_min(&self, g: &ColGroup) -> io::Result<TempCompactIntVec> {
+        let n = self.n();
+        let mut result = TempCompactIntVecBuilder::new(n)?;
+        if let Some((&first, rest)) = g.indices.split_first() {
+            result.add(self.col_view(first));
+            for &c in rest { result.min(self.col_view(c)); }
+        }
+        result.freeze()
+    }
+
+    fn partial_group_max(&self, g: &ColGroup) -> io::Result<TempCompactIntVec> {
+        let n = self.n();
+        let mut result = TempCompactIntVecBuilder::new(n)?;
+        for &c in &g.indices { result.max(self.col_view(c)); }
+        result.freeze()
+    }
 }

src/obikpartitionner/src/select_layer.rs

@@ -3,8 +3,9 @@ use std::io;
 use std::path::{Path, PathBuf};
 
 use obicompactvec::{
-    PersistentBitMatrix, PersistentBitMatrixBuilder, PersistentBitVecBuilder,
-    PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder, PersistentCompactIntVecBuilder,
+    ColGroup, MatrixGroupOps,
+    PersistentBitMatrix, PersistentBitMatrixBuilder,
+    PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder,
 };
 use obilayeredmap::meta::PartitionMeta;
 use obilayeredmap::OLMError;
@@ -40,52 +41,6 @@ pub struct OutputCol {
     pub op:      AggOp,
 }
 
-// ── Aggregation ───────────────────────────────────────────────────────────────
-
-#[inline]
-fn aggregate(op: AggOp, indices: &[usize], src_row: &[u32], threshold: u32) -> u32 {
-    match op {
-        AggOp::Any => {
-            if indices.iter().any(|&i| src_row[i] > threshold) { 1 } else { 0 }
-        }
-        AggOp::All => {
-            if indices.is_empty() { return 0; }
-            if indices.iter().all(|&i| src_row[i] > threshold) { 1 } else { 0 }
-        }
-        AggOp::None => {
-            if indices.iter().all(|&i| src_row[i] <= threshold) { 1 } else { 0 }
-        }
-        AggOp::Sum => {
-            indices.iter().map(|&i| src_row[i]).fold(0u32, |a, b| a.saturating_add(b))
-        }
-        AggOp::Min => indices.iter().map(|&i| src_row[i]).min().unwrap_or(0),
-        AggOp::Max => indices.iter().map(|&i| src_row[i]).max().unwrap_or(0),
-    }
-}
-
-// ── ColBuilder ────────────────────────────────────────────────────────────────
-
-enum ColBuilder {
-    Bit(PersistentBitVecBuilder),
-    Int(PersistentCompactIntVecBuilder),
-}
-
-impl ColBuilder {
-    fn set_val(&mut self, slot: usize, value: u32) {
-        match self {
-            ColBuilder::Bit(b) => b.set(slot, value > 0),
-            ColBuilder::Int(b) => b.set(slot, value),
-        }
-    }
-
-    fn close(self) -> SKResult<()> {
-        match self {
-            ColBuilder::Bit(b) => b.close().map_err(SKError::Io),
-            ColBuilder::Int(b) => b.close().map_err(SKError::Io),
-        }
-    }
-}
-
 // ── Helpers ───────────────────────────────────────────────────────────────────
 
 fn olm_to_sk(e: OLMError) -> SKError {
@@ -95,21 +50,6 @@ fn olm_to_sk(e: OLMError) -> SKError {
     }
 }
 
-fn col_path_bit(dir: &Path, col: usize) -> PathBuf {
-    dir.join(format!("col_{col:06}.pbiv"))
-}
-
-fn col_path_int(dir: &Path, col: usize) -> PathBuf {
-    dir.join(format!("col_{col:06}.pciv"))
-}
-
-fn write_matrix_meta(dir: &Path, n: usize, n_cols: usize) -> io::Result<()> {
-    fs::write(
-        dir.join("meta.json"),
-        format!("{{\"n\":{n},\"n_cols\":{n_cols}}}\n"),
-    )
-}
-
 /// Copy all plain files (not subdirectories) from `src_dir` to `dst_dir`.
 fn copy_layer_files(src_dir: &Path, dst_dir: &Path) -> io::Result<()> {
     for entry in fs::read_dir(src_dir)? {
@@ -125,30 +65,64 @@ fn copy_layer_files(src_dir: &Path, dst_dir: &Path) -> io::Result<()> {
 // ── fill_builders ─────────────────────────────────────────────────────────────
 
 fn fill_builders(
-    builders: &mut [ColBuilder],
     specs: &[OutputCol],
-    n: usize,
-    n_src: usize,
     src_layer_dir: &Path,
     src_is_count: bool,
     threshold: u32,
+    output_presence: bool,
+    mut dst_bit: Option<&mut PersistentBitMatrixBuilder>,
+    mut dst_int: Option<&mut PersistentCompactIntMatrixBuilder>,
 ) -> SKResult<()> {
-    let mut src_buf = vec![0u32; n_src];
-
     if src_is_count {
         let mat = PersistentCompactIntMatrix::open(src_layer_dir).map_err(SKError::Io)?;
-        for slot in 0..n {
-            mat.fill_row(slot, &mut src_buf);
-            for (col, spec) in specs.iter().enumerate() {
-                builders[col].set_val(slot, aggregate(spec.op, &spec.indices, &src_buf, threshold));
+        for spec in specs {
+            let g = ColGroup::new(&spec.label, spec.indices.clone());
+            if output_presence {
+                let b = dst_bit.as_deref_mut().unwrap();
+                match spec.op {
+                    AggOp::Any  => b.add_col_from    (&mat.partial_group_any (&g, threshold).map_err(SKError::Io)?),
+                    AggOp::All  => b.add_col_from    (&mat.partial_group_all (&g, threshold).map_err(SKError::Io)?),
+                    AggOp::None => b.add_col_from    (&mat.partial_group_none(&g, threshold).map_err(SKError::Io)?),
+                    AggOp::Sum  => b.add_col_from_int(&mat.partial_group_sum (&g).map_err(SKError::Io)?),
+                    AggOp::Min  => b.add_col_from_int(&mat.partial_group_min (&g).map_err(SKError::Io)?),
+                    AggOp::Max  => b.add_col_from_int(&mat.partial_group_max (&g).map_err(SKError::Io)?),
+                }.map_err(SKError::Io)?;
+            } else {
+                let b = dst_int.as_deref_mut().unwrap();
+                match spec.op {
+                    AggOp::Sum  => b.add_col_from    (&mat.partial_group_sum (&g).map_err(SKError::Io)?),
+                    AggOp::Min  => b.add_col_from    (&mat.partial_group_min (&g).map_err(SKError::Io)?),
+                    AggOp::Max  => b.add_col_from    (&mat.partial_group_max (&g).map_err(SKError::Io)?),
+                    AggOp::Any  => b.add_col_from_bit(&mat.partial_group_any (&g, threshold).map_err(SKError::Io)?),
+                    AggOp::All  => b.add_col_from_bit(&mat.partial_group_all (&g, threshold).map_err(SKError::Io)?),
+                    AggOp::None => b.add_col_from_bit(&mat.partial_group_none(&g, threshold).map_err(SKError::Io)?),
+                }.map_err(SKError::Io)?;
             }
         }
     } else {
         let mat = PersistentBitMatrix::open(src_layer_dir).map_err(SKError::Io)?;
-        for slot in 0..n {
-            mat.fill_row(slot, &mut src_buf);
-            for (col, spec) in specs.iter().enumerate() {
-                builders[col].set_val(slot, aggregate(spec.op, &spec.indices, &src_buf, threshold));
+        for spec in specs {
+            let g = ColGroup::new(&spec.label, spec.indices.clone());
+            if output_presence {
+                let b = dst_bit.as_deref_mut().unwrap();
+                match spec.op {
+                    AggOp::Any  => b.add_col_from    (&mat.partial_group_any (&g, 1).map_err(SKError::Io)?),
+                    AggOp::All  => b.add_col_from    (&mat.partial_group_all (&g, 1).map_err(SKError::Io)?),
+                    AggOp::None => b.add_col_from    (&mat.partial_group_none(&g, 1).map_err(SKError::Io)?),
+                    AggOp::Sum  => b.add_col_from_int(&mat.partial_group_sum (&g).map_err(SKError::Io)?),
+                    AggOp::Min  => b.add_col_from_int(&mat.partial_group_min (&g).map_err(SKError::Io)?),
+                    AggOp::Max  => b.add_col_from_int(&mat.partial_group_max (&g).map_err(SKError::Io)?),
+                }.map_err(SKError::Io)?;
+            } else {
+                let b = dst_int.as_deref_mut().unwrap();
+                match spec.op {
+                    AggOp::Sum  => b.add_col_from    (&mat.partial_group_sum (&g).map_err(SKError::Io)?),
+                    AggOp::Min  => b.add_col_from    (&mat.partial_group_min (&g).map_err(SKError::Io)?),
+                    AggOp::Max  => b.add_col_from    (&mat.partial_group_max (&g).map_err(SKError::Io)?),
+                    AggOp::Any  => b.add_col_from_bit(&mat.partial_group_any (&g, 1).map_err(SKError::Io)?),
+                    AggOp::All  => b.add_col_from_bit(&mat.partial_group_all (&g, 1).map_err(SKError::Io)?),
+                    AggOp::None => b.add_col_from_bit(&mat.partial_group_none(&g, 1).map_err(SKError::Io)?),
+                }.map_err(SKError::Io)?;
             }
         }
     }
@@ -168,7 +142,7 @@ impl KmerPartition {
         src: &KmerPartition,
         i: usize,
         specs: &[OutputCol],
-        n_src_genomes: usize,
+        _n_src_genomes: usize,
         threshold: u32,
         output_presence: bool,
         in_place: bool,
@@ -188,7 +162,6 @@ impl KmerPartition {
             fs::create_dir_all(&dst_index_dir)?;
         }
 
-        let n_out = specs.len();
         let data_subdir = if output_presence { "presence" } else { "counts" };
 
         for l in 0..src_meta.n_layers {
@@ -201,7 +174,7 @@ impl KmerPartition {
             let presence_dir = src_layer_dir.join("presence");
             let src_is_count = counts_dir.exists() && !presence_dir.exists();
 
-            // Determine number of slots from the source matrix.
+            // Determine number of slots and detect implicit layers.
             let n = if counts_dir.exists() {
                 PersistentCompactIntMatrix::open(&src_layer_dir).map_err(SKError::Io)?.n()
             } else if presence_dir.exists() {
@@ -216,7 +189,7 @@ impl KmerPartition {
             };
 
             // Choose the output data directory (temp name for in-place).
-            let (dst_data_dir, final_data_dir) = if in_place {
+            let (dst_data_dir, final_data_dir): (PathBuf, PathBuf) = if in_place {
                 let tmp  = dst_layer_dir.join(format!("{data_subdir}_new"));
                 let perm = dst_layer_dir.join(data_subdir);
                 (tmp, perm)
@@ -231,37 +204,22 @@ impl KmerPartition {
             }
             fs::create_dir_all(&dst_data_dir)?;
 
-            // Initialise packed-format skeleton.
-            if output_presence {
-                PersistentBitMatrixBuilder::new(n, &dst_data_dir)
-                    .map_err(SKError::Io)?.close().map_err(SKError::Io)?;
+            let (mut dst_bit, mut dst_int) = if output_presence {
+                (Some(PersistentBitMatrixBuilder::new(n, &dst_data_dir).map_err(SKError::Io)?), None)
             } else {
-                PersistentCompactIntMatrixBuilder::new(n, &dst_data_dir)
-                    .map_err(SKError::Io)?.close().map_err(SKError::Io)?;
-            }
-
-            // Create column builders.
-            let mut builders: Vec<ColBuilder> = (0..n_out)
-                .map(|col| -> SKResult<ColBuilder> {
-                    if output_presence {
-                        Ok(ColBuilder::Bit(PersistentBitVecBuilder::new(
-                            n, &col_path_bit(&dst_data_dir, col),
-                        )?))
-                    } else {
-                        Ok(ColBuilder::Int(PersistentCompactIntVecBuilder::new(
-                            n, &col_path_int(&dst_data_dir, col),
-                        )?))
-                    }
-                })
-                .collect::<SKResult<_>>()?;
+                (None, Some(PersistentCompactIntMatrixBuilder::new(n, &dst_data_dir).map_err(SKError::Io)?))
+            };
 
             fill_builders(
-                &mut builders, specs, n, n_src_genomes,
-                &src_layer_dir, src_is_count, threshold,
+                specs, &src_layer_dir, src_is_count, threshold, output_presence,
+                dst_bit.as_mut(), dst_int.as_mut(),
             )?;
 
-            for b in builders { b.close()?; }
-            write_matrix_meta(&dst_data_dir, n, n_out).map_err(SKError::Io)?;
+            if output_presence {
+                dst_bit.unwrap().close().map_err(SKError::Io)?;
+            } else {
+                dst_int.unwrap().close().map_err(SKError::Io)?;
+            }
 
             // In-place: swap old data dir for new.
             if in_place {