From 9abb2db92fc453ddd87da19faadd527730591b8f Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Fri, 19 Jun 2026 09:20:14 +0200
Subject: [PATCH] refactor: replace explicit bit-setting loops with optimized
 bulk operations

Refactor bitmatrix, colgroup, and layer modules to replace manual iteration with concise `or_where` predicates and bulk inversion calls. This simplifies the codebase and leverages optimized internal implementations for improved performance.
---
 src/obicompactvec/src/bitmatrix.rs | 8 +-------
 src/obicompactvec/src/colgroup.rs  | 8 ++------
 src/obilayeredmap/src/layer.rs     | 4 +---
 3 files changed, 4 insertions(+), 16 deletions(-)

diff --git a/src/obicompactvec/src/bitmatrix.rs b/src/obicompactvec/src/bitmatrix.rs
index 55a4561..c054ae0 100644
--- a/src/obicompactvec/src/bitmatrix.rs
+++ b/src/obicompactvec/src/bitmatrix.rs
@@ -412,13 +412,7 @@ impl PersistentBitMatrixBuilder {
         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.or_where(src.view(), |v| v > 0);
         b.close()
     }
 
diff --git a/src/obicompactvec/src/colgroup.rs b/src/obicompactvec/src/colgroup.rs
index b8c5ec8..b1545e6 100644
--- a/src/obicompactvec/src/colgroup.rs
+++ b/src/obicompactvec/src/colgroup.rs
@@ -53,9 +53,7 @@ pub trait MatrixGroupOps {
         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.or_where(counts.view(), |v| v >= n_required);
         b.freeze()
     }
 
@@ -64,9 +62,7 @@ pub trait MatrixGroupOps {
         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.or_where(counts.view(), |v| v == 0);
         b.freeze()
     }
 }
diff --git a/src/obilayeredmap/src/layer.rs b/src/obilayeredmap/src/layer.rs
index 72b38ea..241feea 100644
--- a/src/obilayeredmap/src/layer.rs
+++ b/src/obilayeredmap/src/layer.rs
@@ -107,9 +107,7 @@ impl Layer<()> {
         fs::create_dir_all(&presence_dir).map_err(OLMError::Io)?;
         let mut mb = PersistentBitMatrixBuilder::new(n_kmers, &presence_dir).map_err(OLMError::Io)?;
         let mut col = mb.add_col().map_err(OLMError::Io)?;
-        for slot in 0..n_kmers {
-            col.set(slot, true);
-        }
+        col.not();
         col.close().map_err(OLMError::Io)?;
         mb.close().map_err(OLMError::Io)
     }