feat: implement partition-based merge command for k-mer indices

Implements a new `merge` command that aggregates k-mer counts and presence/absence matrices from multiple source indices using a parallelized, partition-based algorithm. Adds CLI progress bars and execution timing across the bootstrap, spectrum rebuild, and merge phases. Updates logging to report the aggregate genome count and introduces a bounds check in the perfect hash layer to safely return `None` for unknown k-mers, preventing out-of-bounds access in downstream operations.

src/obikindex/src/merge.rs

@@ -2,7 +2,9 @@ use std::collections::HashMap;
 use std::fs;
 use std::io;
 use std::path::Path;
+use std::time::Duration;
 
+use indicatif::{ProgressBar, ProgressStyle};
 use obisys::{Reporter, Stage};
 use rayon::prelude::*;
 use tracing::info;
@@ -31,6 +33,7 @@ impl KmerIndex {
         mode: MergeMode,
         force: bool,
         rename_duplicates: bool,
+        rep: &mut Reporter,
     ) -> OKIResult<Self> {
         let output = output.as_ref();
 
@@ -74,7 +77,14 @@ impl KmerIndex {
         }
 
         // ── Bootstrap: copy first source to output ────────────────────────────
-        info!("copying {} → {}", sources[0].root_path.display(), output.display());
+        info!(
+            "bootstrap: copying {} → {} ({} genome(s))",
+            sources[0].root_path.display(),
+            output.display(),
+            sources[0].meta.genomes.len(),
+        );
+        let t = Stage::start("bootstrap");
+        let pb = spinner("bootstrap — copying index …");
         copy_dir_all(&sources[0].root_path, output)?;
 
         // Rewrite index.meta with final genome labels and the effective mode.
@@ -88,9 +98,14 @@ impl KmerIndex {
         if mode == MergeMode::Presence {
             remove_dirs_named(output, "counts")?;
         }
+        pb.finish_and_clear();
+        rep.push(t.stop());
 
         // Rebuild spectrums/ from all sources using the (possibly renamed) labels.
         // Drop the spectrums/ that were copied from source_0 and rebuild from scratch.
+        info!("rebuilding spectrums for {} source(s)", sources.len());
+        let t = Stage::start("spectrums");
+        let pb = spinner("spectrums — copying …");
         let spectrums_dir = output.join("spectrums");
         if spectrums_dir.exists() {
             fs::remove_dir_all(&spectrums_dir)?;
@@ -98,6 +113,8 @@ impl KmerIndex {
         for (src, new_labels) in sources.iter().zip(&source_labels) {
             copy_spectrums(&src.root_path, output, &src.meta.genomes, new_labels)?;
         }
+        pb.finish_and_clear();
+        rep.push(t.stop());
 
         // Open the destination index.
         let dst = KmerIndex::open(output)?;
@@ -107,8 +124,13 @@ impl KmerIndex {
         // ── Merge each subsequent source partition-by-partition ───────────────
         let remaining_sources: Vec<&KmerIndex> = sources[1..].to_vec();
         if !remaining_sources.is_empty() {
-            let mut rep = Reporter::new();
+            let n_src_genomes: usize = remaining_sources.iter().map(|s| s.meta.genomes.len()).sum();
+            info!(
+                "merging {} partition(s) × {} additional source genome(s) into {} destination genome(s)",
+                n_partitions, n_src_genomes, n_dst_genomes,
+            );
             let t = Stage::start("merge_partitions");
+            let pb = partition_bar(n_partitions as u64);
 
             let dst_partition = &dst.partition;
 
@@ -117,10 +139,13 @@ impl KmerIndex {
                 .filter_map(|i| {
                     let srcs: Vec<(&obikpartitionner::KmerPartition, usize)> =
                         remaining_sources.iter().map(|s| (&s.partition, s.meta.genomes.len())).collect();
-                    dst_partition.merge_partition(i, &srcs, mode, n_dst_genomes).err()
+                    let result = dst_partition.merge_partition(i, &srcs, mode, n_dst_genomes).err();
+                    pb.inc(1);
+                    result
                 })
                 .collect();
 
+            pb.finish_and_clear();
             if let Some(e) = errors.into_iter().next() {
                 return Err(OKIError::Partition(e));
             }
@@ -206,6 +231,31 @@ fn remove_dirs_named(root: &Path, name: &str) -> io::Result<()> {
     Ok(())
 }
 
+fn spinner(msg: &'static str) -> ProgressBar {
+    let pb = ProgressBar::new_spinner();
+    pb.set_style(
+        ProgressStyle::with_template("{spinner} {msg}  {elapsed}")
+            .unwrap()
+            .tick_strings(&["⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏"]),
+    );
+    pb.set_message(msg);
+    pb.enable_steady_tick(Duration::from_millis(100));
+    pb
+}
+
+fn partition_bar(n: u64) -> ProgressBar {
+    let pb = ProgressBar::new(n);
+    pb.set_style(
+        ProgressStyle::with_template(
+            "{spinner} merge — {bar:40.cyan/blue} {pos}/{len} partitions  {elapsed}",
+        )
+        .unwrap()
+        .tick_strings(&["⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏"]),
+    );
+    pb.enable_steady_tick(Duration::from_millis(100));
+    pb
+}
+
 fn copy_dir_all(src: &Path, dst: &Path) -> io::Result<()> {
     fs::create_dir_all(dst)?;
     for entry in fs::read_dir(src)? {