feat: add configurable block sizes and in-place reindex command

Propagate configurable block size (`block_bits`) through index and layer construction to control unitig chunking and optimize memory/performance trade-offs. Introduce an in-place `reindex` command and library method to convert indices between exact and approximate evidence formats. Add validation to reject merging indexes with mismatched evidence types, and update parallel kmer counting to use `AtomicUsize` for thread-safe aggregation. Includes CLI argument parsing, metadata persistence, and updated tests.

src/obikpartitionner/src/index_layer.rs

@@ -45,6 +45,7 @@ impl KmerPartition {
         max_ab: Option<u32>,
         with_counts: bool,
         evidence: &EvidenceKind,
+        block_bits: u8,
     ) -> Result<usize, SKError> {
         let part_dir = self.part_dir(i);
         let dedup_path = part_dir.join("dereplicated.skmer.zst");
@@ -109,7 +110,7 @@ impl KmerPartition {
         uw.close()?;
 
         if with_counts {
-            Layer::<PersistentCompactIntMatrix>::build(&layer_dir, |kmer| {
+            Layer::<PersistentCompactIntMatrix>::build(&layer_dir, block_bits, |kmer| {
                 match (&mphf1_opt, &counts1_opt) {
                     (Some(mphf), Some(counts)) => counts.get(mphf.index(&kmer.raw())),
                     _ => 1,
@@ -117,7 +118,7 @@ impl KmerPartition {
             })
             .map_err(olm_to_sk)?;
         } else {
-            Layer::<()>::build(&layer_dir).map_err(olm_to_sk)?;
+            Layer::<()>::build(&layer_dir, block_bits).map_err(olm_to_sk)?;
         }
 
         // For approximate evidence: replace the exact evidence bundle with a

src/obikpartitionner/src/merge_layer.rs

@@ -161,6 +161,7 @@ impl KmerPartition {
         sources: &[(&KmerPartition, usize)],
         mode: MergeMode,
         n_dst_genomes: usize,
+        block_bits: u8,
     ) -> SKResult<()> {
         let dst_index_dir = self.part_dir(i).join(INDEX_SUBDIR);
         if !dst_index_dir.exists() {
@@ -216,7 +217,7 @@ impl KmerPartition {
                 uw.write(&unitig)?;
             }
             uw.close()?;
-            Layer::<()>::build(&new_layer_dir).map_err(olm_to_sk)?;
+            Layer::<()>::build(&new_layer_dir, block_bits).map_err(olm_to_sk)?;
         }
         drop(g);
 

src/obikpartitionner/src/rebuild_layer.rs

@@ -96,6 +96,7 @@ impl KmerPartition {
         filters: &[Box<dyn KmerFilter>],
         mode: MergeMode,
         n_genomes: usize,
+        block_bits: u8,
     ) -> SKResult<()> {
         let src_index_dir = src.part_dir(i).join(INDEX_SUBDIR);
         if !src_index_dir.exists() {
@@ -145,7 +146,7 @@ impl KmerPartition {
         uw.close()?;
         drop(g);
 
-        Layer::<()>::build(&dst_layer_dir).map_err(olm_to_sk)?;
+        Layer::<()>::build(&dst_layer_dir, block_bits).map_err(olm_to_sk)?;
         let dst_mphf = MphfLayer::open(&dst_layer_dir).map_err(olm_to_sk)?;
 
         // ── Prepare matrix builders (one column per genome) ───────────────────