Extract indexing stage into LayerBuilder with NUMA-aware scheduling

Introduce a dedicated LayerBuilder struct to orchestrate parallel layer 0 construction across partitions. The fluent API supports configurable abundance thresholds and intermediate artifact retention. Parallel execution is delegated to a NUMA-aware PartitionRunner scheduler, while progress reporting and stage timing are shifted to the command layer. A new mark_indexed method cleanly separates state tracking from orchestration by generating a completion sentinel.

src/obikphylo/src/siblings/tests.rs

@@ -8,6 +8,7 @@ use tempfile::tempdir;
 
 use obikindexer::algorithms::counter::Counter;
 use obikindexer::algorithms::dereplicator::Dereplicator;
+use obikindexer::algorithms::layer_builder::LayerBuilder;
 use obikindexer::algorithms::partitionner::PartitionRouter;
 use obikindex::{GenomeInfo, IndexConfig, KmerIndex, MergeMode};
 
@@ -70,7 +71,6 @@ fn build_single_genome_index(dir: &Path, label: &str, seq: &[u8]) -> KmerIndex {
     let mut idx = KmerIndex::create(&index_path, config, Some(GenomeInfo::new(label)))
         .expect("create");
 
-    let mut rep = Reporter::new();
     let stream = obiread::open_nuc_stream(fasta_path.to_str().unwrap(), K).expect("open fasta");
     let mut router = PartitionRouter::new(&mut idx);
     for page in stream {
@@ -86,7 +86,10 @@ fn build_single_genome_index(dir: &Path, label: &str, seq: &[u8]) -> KmerIndex {
     idx.mark_scattered().expect("mark_scattered");
     idx.write_spectrum(spectrum.f0, spectrum.f1, &spectrum.counts).expect("write_spectrum");
     idx.mark_counted().expect("mark_counted");
-    idx.build_layers(1, None, false, &mut rep).expect("build_layers");
+    LayerBuilder::new(&idx)
+        .run(None::<fn(obisys::Progress)>)
+        .expect("build_layers");
+    idx.mark_indexed().expect("mark_indexed");
     idx
 }