Start of a huge refactoring

src/obikindex/src/layer/content_layer.rs

@@ -240,6 +240,26 @@ impl KmerLayer {
         }
     }
 
+    // content_layer.rs, à côté de fill_sub_matrix_carries
+    /// Batch, genome-major column extraction — `out[g][i]` = genome `g`'s raw
+    /// value at `slots[i]` (count as-is, presence promoted to 0/1). Column-first,
+    /// like the underlying storage: one read pass per genome column, not one per
+    /// kmer.
+    pub fn fill_sub_matrix(&self, slots: &[usize], out: &mut [Vec<u32>]) {
+        match self {
+            KmerLayer::Count { layer, .. } => layer.fill_sub_matrix(slots, out),
+            KmerLayer::Presence { layer, .. } => {
+                let mut bools: Vec<Vec<bool>> = out.iter().map(|_| Vec::new()).collect();
+                layer.fill_sub_matrix(slots, &mut bools);
+                for (o, b) in out.iter_mut().zip(bools.iter()) {
+                    o.clear();
+                    o.extend(b.iter().map(|&v| v as u32));
+                }
+            }
+            KmerLayer::Empty { .. } => panic!("Layer::fill_sub_matrix() called on an Empty layer"),
+        }
+    }
+
     /// Raw MPHF lookup: kmer → slot, no membership check.
     pub fn hash(&self, kmer: CanonicalKmer) -> usize {
         match self {

src/obikindex/src/layer/mphf_layer.rs

@@ -412,6 +412,12 @@ impl MphfOnly {
     pub fn index(&self, kmer: CanonicalKmer) -> usize {
         self.0.index(&kmer.raw())
     }
+
+    /// Batch form of [`index`](Self::index) — one MPHF lookup pass over the
+    /// whole slice instead of one call per kmer.
+    pub fn index_batch(&self, kmers: &[CanonicalKmer]) -> Vec<usize> {
+        kmers.iter().map(|&k| self.index(k)).collect()
+    }
 }
 
 impl MphfLayer {

src/obikindex/src/partition/mod.rs

@@ -61,7 +61,7 @@ pub struct KmerPartition {
 impl KmerPartition {
     pub fn new(index: &KmerIndex, i: usize) -> Self {
         KmerPartition {
-            partition_dir: index.dir().join(format!("part_{i:05}")),
+            partition_dir: index_dir(index.dir(), i),
             id: i,
         }
     }