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/obikindex/src/merge.rs

@@ -9,6 +9,8 @@ use obisys::{Reporter, Stage};
 use rayon::prelude::*;
 use tracing::info;
 
+use obilayeredmap::EvidenceKind;
+
 use crate::error::{OKIError, OKIResult};
 use crate::index::KmerIndex;
 use crate::meta::{GenomeInfo, IndexMeta};
@@ -61,6 +63,9 @@ impl KmerIndex {
             }
         }
 
+        // ── Validate evidence compatibility ───────────────────────────────────
+        let evidence = validate_evidence_compat(sources)?;
+
         // ── Compute final genome labels (rename duplicates if requested) ───────
         let (source_labels, all_genomes) = compute_labels(sources, rename_duplicates)?;
 
@@ -91,6 +96,7 @@ impl KmerIndex {
         let mut meta = IndexMeta::read(output).map_err(OKIError::Io)?;
         meta.genomes = all_genomes;
         meta.config.with_counts = mode == MergeMode::Count;
+        meta.config.evidence = evidence;
         meta.write(output)?;
 
         // In presence/absence mode, purge counts/ directories inherited from
@@ -134,13 +140,14 @@ impl KmerIndex {
             let pb = partition_bar(n_partitions as u64);
 
             let dst_partition = &dst.partition;
+            let block_bits = dst.meta.config.block_bits;
 
             let errors: Vec<obiskio::SKError> = (0..n_partitions)
                 .into_par_iter()
                 .filter_map(|i| {
                     let srcs: Vec<(&obikpartitionner::KmerPartition, usize)> =
                         remaining_sources.iter().map(|s| (&s.partition, s.meta.genomes.len())).collect();
-                    let result = dst_partition.merge_partition(i, &srcs, mode, n_dst_genomes).err();
+                    let result = dst_partition.merge_partition(i, &srcs, mode, n_dst_genomes, block_bits).err();
                     pb.inc(1);
                     result
                 })
@@ -258,6 +265,34 @@ fn partition_bar(n: u64) -> ProgressBar {
     pb
 }
 
+/// Check that all sources share the same evidence kind.
+///
+/// Rules:
+/// - all `Exact`                        → OK, returns `Exact`
+/// - all `Approx { b, z }` same params  → OK, returns `Approx { b, z }`
+/// - mixed exact/approx or different approx params → `IncompatibleEvidence`
+fn validate_evidence_compat(sources: &[&KmerIndex]) -> OKIResult<EvidenceKind> {
+    let ref_ev = &sources[0].meta.config.evidence;
+    for src in &sources[1..] {
+        let ev = &src.meta.config.evidence;
+        let compat = match (ref_ev, ev) {
+            (EvidenceKind::Exact, EvidenceKind::Exact) => true,
+            (EvidenceKind::Approx { b: b1, z: z1 },
+             EvidenceKind::Approx { b: b2, z: z2 }) => b1 == b2 && z1 == z2,
+            _ => false,
+        };
+        if !compat {
+            return Err(OKIError::IncompatibleEvidence(format!(
+                "source {:?} has evidence {:?}, expected {:?} — \
+                 convert all sources to the same evidence kind first \
+                 (use the `reindex` command)",
+                src.root_path.display(), ev, ref_ev,
+            )));
+        }
+    }
+    Ok(ref_ev.clone())
+}
+
 fn copy_dir_all(src: &Path, dst: &Path) -> io::Result<()> {
     fs::create_dir_all(dst)?;
     for entry in fs::read_dir(src)? {