Add configurable sparsity flag to index finalization and merge CLI

Extends `KmerIndex::finalize_indexed` to accept a `sparse` boolean parameter, enabling control over whether output presence matrices are packed in a compact sparse format or stored densely. The merge command now exposes a `--dense` flag to invert this setting, defaulting to the existing sparse representation. Call sites in select and rebuild modules pass `false` to preserve current behavior. A benchmark lock file is also added for dependency tracking.

src/obikindex/src/index/builder.rs

@@ -52,9 +52,10 @@ pub trait IndexBuilder: Sized {
 
     /// Mark `output` as fully indexed, pack its column matrices, and reopen it.
     ///
-    /// Shared tail of the `select`/`rebuild` construction paths, once their
+    /// Shared tail of the `select`/`rebuild`/`merge` construction paths,
-    /// partitions have been written.
+    /// once their partitions have been written. `sparse` selects the
-    fn finalize_indexed<P: AsRef<Path>>(output: P, rep: &mut Reporter) -> OKIResult<Self>;
+    /// on-disk presence-matrix format (see `pack_matrices`).
+    fn finalize_indexed<P: AsRef<Path>>(output: P, rep: &mut Reporter, sparse: bool) -> OKIResult<Self>;
 
     /// Current construction state, read fresh from `index.meta` (see
     /// `DevDocMD/implementation/partition_layer_cache.md`, "(11)" — no
@@ -99,12 +100,12 @@ impl IndexBuilder for KmerIndex {
         Ok(idx)
     }
 
-    fn finalize_indexed<P: AsRef<Path>>(output: P, rep: &mut Reporter) -> OKIResult<Self> {
+    fn finalize_indexed<P: AsRef<Path>>(output: P, rep: &mut Reporter, sparse: bool) -> OKIResult<Self> {
         let output = output.as_ref();
         let idx = KmerIndex::open(output)?;
         idx.meta.mark_indexed().map_err(OKIError::Io)?;
         let t_pack = Stage::start("pack");
-        idx.pack_matrices(false)?;
+        idx.pack_matrices(sparse)?;
         rep.push(t_pack.stop());
         Ok(idx)
     }

src/obikmer2/src/cmd/merge/mod.rs

@@ -28,6 +28,10 @@ pub struct MergeArgs {
     /// Disambiguate duplicate genome labels by appending .1, .2, … instead of erroring
     #[arg(long, default_value_t = false)]
     pub rename_duplicates: bool,
+
+    /// Pack the output's presence matrices in the dense format instead of the default sparse one
+    #[arg(long, default_value_t = false)]
+    pub dense: bool,
 }
 
 pub fn run(args: MergeArgs) {
@@ -89,6 +93,7 @@ pub fn run(args: MergeArgs) {
     let mut merge = Merge::new(&source_refs, &args.output, mode)
         .force(args.force)
         .rename_duplicates(args.rename_duplicates)
+        .sparse(!args.dense)
         .on_progress(|_: Progress| pb.inc(1));
 
     let dst = merge.run().unwrap_or_else(|e| {

src/obikmerge/src/merge.rs

@@ -45,6 +45,7 @@ pub struct Merge<'a> {
     mode: MergeMode,
     force: bool,
     rename_duplicates: bool,
+    sparse: bool,
     reporter: Reporter,
     on_progress: Option<Box<dyn FnMut(Progress) + Send + 'a>>,
 }
@@ -57,6 +58,7 @@ impl<'a> Merge<'a> {
             mode,
             force: false,
             rename_duplicates: false,
+            sparse: true,
             reporter: Reporter::new(),
             on_progress: None,
         }
@@ -76,6 +78,13 @@ impl<'a> Merge<'a> {
         self
     }
 
+    /// Pack the merged output's presence matrices in the compact sparse
+    /// format rather than dense (default: `true`).
+    pub fn sparse(mut self, v: bool) -> Self {
+        self.sparse = v;
+        self
+    }
+
     /// Progress callback, called once per completed partition.
     pub fn on_progress(mut self, cb: impl FnMut(Progress) + Send + 'a) -> Self {
         self.on_progress = Some(Box::new(cb));
@@ -322,7 +331,7 @@ impl Algorithm for Merge<'_> {
 
         // ── Finalize: pack matrices, mark indexed, reopen ──────────────────────
         let t = Stage::start("finalize");
-        let dst = KmerIndex::finalize_indexed(&output, &mut self.reporter)?;
+        let dst = KmerIndex::finalize_indexed(&output, &mut self.reporter, self.sparse)?;
         self.reporter.push(t.stop());
 
         Ok(dst)

src/obikrebuild/src/rebuild.rs

@@ -74,6 +74,6 @@ impl KmerIndex {
 
         rep.push(t.stop());
 
-        KmerIndex::finalize_indexed(output, rep)
+        KmerIndex::finalize_indexed(output, rep, false)
     }
 }

src/obikselect/src/select.rs

@@ -82,7 +82,7 @@ impl KmerIndex {
         pb.finish_and_clear();
         rep.push(t.stop());
 
-        KmerIndex::finalize_indexed(output, rep)
+        KmerIndex::finalize_indexed(output, rep, false)
     }
 
     /// Rewrite the genome columns of this index in-place according to `specs`.