From 009a328c5818c781b0a3ce93608584c8fbafebbe Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Tue, 26 May 2026 09:43:45 +0200
Subject: [PATCH] refactor: handle kmer deduplication and layer initialization
 concurrently

Introduce a secondary layer iteration to open `SrcLayerData` alongside the unitig reader for concurrent metadata access. This refactors the merge routine to handle kmer deduplication and per-layer data initialization simultaneously. Also corrects a typo in `rebuild_layer.rs` where `openopen_sequential` is renamed to `open_sequential`.
---
 src/obikpartitionner/src/dump_layer.rs    | 4 ++--
 src/obikpartitionner/src/merge_layer.rs   | 4 ++--
 src/obikpartitionner/src/rebuild_layer.rs | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/obikpartitionner/src/dump_layer.rs b/src/obikpartitionner/src/dump_layer.rs
index eaf8231..6216360 100644
--- a/src/obikpartitionner/src/dump_layer.rs
+++ b/src/obikpartitionner/src/dump_layer.rs
@@ -44,7 +44,7 @@ impl KmerPartition {
             if !layer_dir.exists() { break; }
             l += 1;
             let mphf = MphfLayer::open(&layer_dir).map_err(olm_to_sk)?;
-            let reader = UnitigFileReader::open(&layer_dir.join("unitigs.bin"))?;
+            let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))?;
 
             let counts_dir  = layer_dir.join("counts");
             let presence_dir = layer_dir.join("presence");
@@ -97,7 +97,7 @@ impl KmerPartition {
             let layer_dir = index_dir.join(format!("layer_{layer}"));
             if !layer_dir.exists() { break; }
             let mphf = MphfLayer::open(&layer_dir).map_err(olm_to_sk)?;
-            let reader = UnitigFileReader::open(&layer_dir.join("unitigs.bin"))?;
+            let reader = UnitigFileReader::open_sequential(&layer_dir.join("unitigs.bin"))?;
 
             let counts_dir   = layer_dir.join("counts");
             let presence_dir = layer_dir.join("presence");
diff --git a/src/obikpartitionner/src/merge_layer.rs b/src/obikpartitionner/src/merge_layer.rs
index d9d5a38..fa6b1be 100644
--- a/src/obikpartitionner/src/merge_layer.rs
+++ b/src/obikpartitionner/src/merge_layer.rs
@@ -195,7 +195,7 @@ impl KmerPartition {
             for l in 0..src_meta.n_layers {
                 let unitigs_path = src_index_dir
                     .join(format!("layer_{l}")).join("unitigs.bin");
-                let reader = UnitigFileReader::open(&unitigs_path)?;
+                let reader = UnitigFileReader::open_sequential(&unitigs_path)?;
                 for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
                     if dst_map.query(kmer).is_none() {
                         g.push(kmer);
@@ -303,7 +303,7 @@ impl KmerPartition {
 
             for l in 0..src_meta.n_layers {
                 let src_layer_dir = src_index_dir.join(format!("layer_{l}"));
-                let reader = UnitigFileReader::open(&src_layer_dir.join("unitigs.bin"))?;
+                let reader = UnitigFileReader::open_sequential(&src_layer_dir.join("unitigs.bin"))?;
                 let src_data = SrcLayerData::open(&src_layer_dir, mode)?;
 
                 for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
diff --git a/src/obikpartitionner/src/rebuild_layer.rs b/src/obikpartitionner/src/rebuild_layer.rs
index eb30cb2..29ca5d5 100644
--- a/src/obikpartitionner/src/rebuild_layer.rs
+++ b/src/obikpartitionner/src/rebuild_layer.rs
@@ -116,7 +116,7 @@ impl KmerPartition {
             let unitigs_path = src_layer_dir.join("unitigs.bin");
             if !unitigs_path.exists() { continue; }
 
-            let reader = UnitigFileReader::open(&unitigs_path)?;
+            let reader = UnitigFileReader::open_sequential(&unitigs_path)?;
             let src_data = SrcLayerData::open(&src_layer_dir, mode)?;
 
             for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
@@ -181,7 +181,7 @@ impl KmerPartition {
             let unitigs_path = src_layer_dir.join("unitigs.bin");
             if !unitigs_path.exists() { continue; }
 
-            let reader = UnitigFileReader::open(&unitigs_path)?;
+            let reader = UnitigFileReader::open_sequential(&unitigs_path)?;
             let src_data = SrcLayerData::open(&src_layer_dir, mode)?;
 
             for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {