Merge pull request 'Implement NUMA topology detection and CPU budget capping' (#74) from push-tnkxqmwztnmm into main

Reviewed-on: #74

.gitea/workflows/ci.yml

@@ -1,9 +1,8 @@
-name: CI
+pname: CI
 
 on:
-  push:
-    branches: ['**']
   pull_request:
+    branches: ['main']
 
 jobs:
   build:
@@ -26,8 +25,8 @@ jobs:
             ~/.cargo/registry
             ~/.cargo/git
             src/target
-          key: ${{ runner.os }}-cargo-${{ hashFiles('src/Cargo.lock') }}
-          restore-keys: ${{ runner.os }}-cargo-
+          key: ${{ runner.os }}-cargo-v2-${{ hashFiles('src/Cargo.lock') }}
+          restore-keys: ${{ runner.os }}-cargo-v2-
 
       - name: Build
         run: cargo build --release

.gitea/workflows/release.yml

@@ -3,10 +3,35 @@ name: Release
 on:
   push:
     tags:
-      - 'v*'
+      - "v*"
 
 jobs:
-  build-linux-static:
+  create-release:
+    runs-on: ubuntu-latest
+    outputs:
+      release_id: ${{ steps.create.outputs.release_id }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Create Gitea release
+        id: create
+        env:
+          GITEA_TOKEN: ${{ secrets.GITEATOKEN }}
+          TAG: ${{ github.ref_name }}
+        run: |
+          sudo apt-get update -qq && sudo apt-get install -y -qq jq
+          body=$(git for-each-ref --format='%(contents)' "refs/tags/$TAG")
+          release_id=$(curl -s -X POST \
+            "${{ github.server_url }}/api/v1/repos/${{ github.repository }}/releases" \
+            -H "Authorization: token $GITEA_TOKEN" \
+            -H "Content-Type: application/json" \
+            -d "{\"tag_name\":\"$TAG\",\"name\":\"$TAG\",\"body\":$(echo "$body" | jq -Rs .)}" | jq -r '.id')
+          echo "release_id=$release_id" >> $GITHUB_OUTPUT
+
+  build-linux-x86_64:
+    needs: create-release
     runs-on: ubuntu-latest
     defaults:
       run:
@@ -14,13 +39,22 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Install Rust + musl target
+      - name: Install Rust + zigbuild
         run: |
           curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --default-toolchain stable
           echo "$HOME/.cargo/bin" >> $GITHUB_PATH
-          sudo apt-get update -qq && sudo apt-get install -y -qq musl-tools jq
+          sudo apt-get update -qq && sudo apt-get install -y -qq jq
+          pip install ziglang --quiet --break-system-packages
+          $HOME/.cargo/bin/cargo install cargo-zigbuild
           $HOME/.cargo/bin/rustup target add x86_64-unknown-linux-musl
 
+      - name: Create musl C/C++ wrappers
+        run: |
+          ZIG=$(python3 -c "import ziglang, os; print(os.path.join(os.path.dirname(ziglang.__file__), 'zig'))")
+          printf '#!/bin/sh\nexec "%s" cc -target x86_64-linux-musl "$@"\n' "$ZIG" | sudo tee /usr/local/bin/x86_64-linux-musl-gcc > /dev/null
+          printf '#!/bin/sh\nexec "%s" c++ -target x86_64-linux-musl "$@"\n' "$ZIG" | sudo tee /usr/local/bin/x86_64-linux-musl-g++ > /dev/null
+          sudo chmod +x /usr/local/bin/x86_64-linux-musl-gcc /usr/local/bin/x86_64-linux-musl-g++
+
       - name: Cache cargo registry
         uses: actions/cache@v4
         with:
@@ -32,25 +66,62 @@ jobs:
           restore-keys: linux-musl-cargo-
 
       - name: Build static binary
-        run: cargo build --release --target x86_64-unknown-linux-musl
+        env:
+          PKG_CONFIG_ALLOW_CROSS: "1"
+        run: cargo zigbuild --release --target x86_64-unknown-linux-musl
 
-      - name: Prepare artifact
+      - name: Prepare and upload artifact
+        env:
+          GITEA_TOKEN: ${{ secrets.GITEATOKEN }}
+          RELEASE_ID: ${{ needs.create-release.outputs.release_id }}
         run: |
           mkdir -p /tmp/dist
           cp target/x86_64-unknown-linux-musl/release/obikmer /tmp/dist/obikmer-linux-x86_64
           strip /tmp/dist/obikmer-linux-x86_64
-
-      - name: Create Gitea release and upload binary
-        env:
-          GITEA_TOKEN: ${{ secrets.GITEATOKEN }}
-          TAG: ${{ github.ref_name }}
-        run: |
-          release_id=$(curl -s -X POST \
-            "${{ github.server_url }}/api/v1/repos/${{ github.repository }}/releases" \
-            -H "Authorization: token $GITEA_TOKEN" \
-            -H "Content-Type: application/json" \
-            -d "{\"tag_name\":\"$TAG\",\"name\":\"$TAG\"}" | jq -r '.id')
           curl -s -X POST \
-            "${{ github.server_url }}/api/v1/repos/${{ github.repository }}/releases/$release_id/assets" \
+            "${{ github.server_url }}/api/v1/repos/${{ github.repository }}/releases/$RELEASE_ID/assets" \
             -H "Authorization: token $GITEA_TOKEN" \
             -F "attachment=@/tmp/dist/obikmer-linux-x86_64"
+
+  build-macos-arm64:
+    needs: create-release
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Login to registry
+        run: echo "${{ secrets.REGISTRYTOKEN }}" | docker login registry.metabarcoding.org -u ${{ secrets.REGISTRYUSER }} --password-stdin
+
+      - name: Cache cargo registry
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+            src/target
+          key: macos-arm64-cargo-${{ hashFiles('src/Cargo.lock') }}
+          restore-keys: macos-arm64-cargo-
+
+      - name: Build macOS binary
+        run: |
+          CID=$(docker create \
+            -w /src/src \
+            registry.metabarcoding.org/cibuilder/rustcrossosx:latest \
+            cargo build --release --target aarch64-apple-darwin --no-default-features)
+          docker cp . "$CID:/src"
+          docker start -a "$CID"
+          STATUS=$(docker wait "$CID")
+          mkdir -p /tmp/dist
+          docker cp "$CID:/src/src/target/aarch64-apple-darwin/release/obikmer" /tmp/dist/obikmer-macos-arm64
+          docker rm "$CID" > /dev/null
+          [ "$STATUS" -eq 0 ]
+
+      - name: Prepare and upload artifact
+        env:
+          GITEA_TOKEN: ${{ secrets.GITEATOKEN }}
+          RELEASE_ID: ${{ needs.create-release.outputs.release_id }}
+        run: |
+          curl -s -X POST \
+            "${{ github.server_url }}/api/v1/repos/${{ github.repository }}/releases/$RELEASE_ID/assets" \
+            -H "Authorization: token $GITEA_TOKEN" \
+            -F "attachment=@/tmp/dist/obikmer-macos-arm64"

.gitignore

@@ -1,21 +1,46 @@
 .venv/
+.DS_Store
+.claude/
+.kilo/
+.serena/
+.zed/
+.ast-cache/
+CLAUDE.md
+memory/
+sandbox/
 src/target
 data-stress
 *.fasta
 *.fasta.gz
+*.fastq
+*.fastq.gz
+*.vcf
 *.zst
 *.zst.meta
 *.pb
-./**/*.json
+**/*.json
 *.bin
+*.log
+*.csv
+*.meta
+*.pfiv
+*.done
+*.efh
+*.efl
+*.bin.idx
+*.prsb
 Betula_exilis--IGA-24-33
-benchmark/genomes
-benchmark/simulated_data
-benchmark/specimen_index_presence
-benchmark/specimen_index_count
-benchmark/global_index_presence
-benchmark/global_index_count
-benchmark/stats
-benchmark/reference_index
-benchmark/specific_index_count
-benchmark/specific_index_presence
+benchmark/run/
+TNT
+phyg
+biblio
+*.tnt
+*.tre
+*.phy
+*.treefile
+*.bionj
+*.iqtree
+*.mldist
+*.parstree
+*.ckp.gz
+*.model

.kilo/plans/1778319532254-eager-panda.md

@@ -1,87 +0,0 @@
-# Plan d'amélioration technique - obiskio
-
-## 1. Contexte et objectifs
-- **Objectif** : Renforcer la robustesse, la maintenabilité et les performances de la crate `obiskio`.
-- **Priorités** : 
-  1. Gestion des erreurs
-  2. Optimisation de la mémoire du pool
-  3. Robustesse concurrente
-  4. Couverture de tests
-  5. Documentation
-
----
-
-## 2. Axes d'amélioration détaillés
-
-### 2.1 Gestion des erreurs
-- **Problème** : `SKError` ne couvre pas tous les cas (format invalide, taille maximale, CRC)
-- **Actions** :
-  - Ajouter variante `ParseError(String)` dans `src/error.rs`
-  - Valider les tailles de SuperKmer avant parsing
-  - Remplacer `expect()` par `unwrap_or_else` avec messages explicites
-  - Documenter chaque variante d’erreur dans le README
-
-### 2.2 Optimisation du pool de fichiers
-- **Problème** : `SKFilePool` utilise un `Vec<WriteEntry>` non contraint et n’effectue pas de nettoyage en cas d’erreur
-- **Actions** :
-  - Implémenter un `LimitedVec` avec limite stricte à `MAX_POOL_SIZE`
-  - Créer `clear_memory()` qui supprime les entrées orphelines
-  - Ajouter `evict_lru_threshold()` pour éviction proactive
-  - Introduire un `RwLock` pour les opérations de lecture massives
-
-### 2.3 Robustesse concurrente
-- **Problème** : Risque de deadlocks dans `SKFileWriter::write_batch()` et `SKFileReader::reopen_and_seek()`
-- **Actions** :
-  - Remplacer `Mutex` par `RwLock` pour les accès en lecture
-  - Ajouter un compteur de blocage et logs de timeout
-  - Utiliser `std::thread::park_timeout` pour débloquer
-  - Insérer `debug_assert!` sur les états invariants
-
-### 2.4 Couverture de tests
-- **Problème** : Absence de benchmarks, de tests de migration, de résilience de fichiers corrompus
-- **Actions** :
-  - Benchmarks I/O sur 10k+ SuperKmer avec `criterion`
-  - Tests de migration de version de fichier `.meta` → `.v2.meta`
-  - Tests de corruption volontaire (truncature, inversion de bits)
-  - Tests de stress sur pool saturation (100 threads)
-
-### 2.5 Documentation & exemples
-- **Actions** :
-  - Ajouter des examples dans chaque module (`# Examples`)
-  - Documenter la logique LRU avec diagrammes Mermaid
-  - Créer un guide « How to recover from eviction »
-  - Mettre à jour le `README.md` avec tableau des variantes d’erreur
-
----
-
-## 3. Plan d'exécution (Roadmap)
-
-| Sprint | Durée | Livrables clés |
-|--------|-------|----------------|
-| **S1** | 2 jours | Refactorisation `SKError`, ajout de tests unitaires |
-| **S2** | 3 jours | Implémentation `clear_memory()` + `LimitedVec` |
-| **S3** | 2 jours | Passage à `RwLock`, ajout de compteurs de blocage |
-| **S4** | 2 jours | Benchmarks + tests de migration |
-| **S5** | 1 jour | Documentation finale & mise à jour du README |
-
----
-
-## 4. Dépendances externes
-- Mettre à jour `niffler` vers la version 2.0 (performance compression)
-- Évaluer `bincode` vs `serde_json` pour les métas (I/O)
-- Ajouter dépendance `criterion` (dev‑dependencies)
-
----
-
-## 5. KPI de suivi
-- **Couverture de tests** : ≥85 % des chemins critiques
-- **Latence moyenne d’écriture** : ↓15 % après optimisation du pool
-- **Taux d’erreurs résolues** : 100 % des nouvelles variantes couvertes
-- **Temps de build CI** : ≤5 min pour l’ensemble des benchmarks
-
----
-
-## 6. Validation finale
-- Revue de code avec `cargo clippy -- -D warnings`
-- Analyse de toxicité avec `cargo deny open-source-licenses`
-- Vérification de la conformité aux standards de naming du projet

.serena/.gitignore

@@ -1,2 +0,0 @@
-/cache
-/project.local.yml

.serena/project.yml

@@ -1,133 +0,0 @@
-# the name by which the project can be referenced within Serena
-project_name: "obikmer"
-
-
-# list of languages for which language servers are started; choose from:
-#   al                  angular             ansible             bash                clojure
-#   cpp                 cpp_ccls            crystal             csharp              csharp_omnisharp
-#   dart                elixir              elm                 erlang              fortran
-#   fsharp              go                  groovy              haskell             haxe
-#   hlsl                html                java                json                julia
-#   kotlin              lean4               lua                 luau                markdown
-#   matlab              msl                 nix                 ocaml               pascal
-#   perl                php                 php_phpactor        powershell          python
-#   python_jedi         python_ty           r                   rego                ruby
-#   ruby_solargraph     rust                scala               scss                solidity
-#   svelte              swift               systemverilog       terraform           toml
-#   typescript          typescript_vts      vue                 yaml                zig
-#   (This list may be outdated. For the current list, see values of Language enum here:
-#   https://github.com/oraios/serena/blob/main/src/solidlsp/ls_config.py
-#   For some languages, there are alternative language servers, e.g. csharp_omnisharp, ruby_solargraph.)
-# Note:
-#   - For C, use cpp
-#   - For JavaScript, use typescript
-#   - For Angular projects, use angular (subsumes typescript+html; requires `npm install` in the project root)
-#   - For Svelte projects, use svelte (subsumes typescript/javascript for .svelte projects; requires npm)
-#   - For SCSS / Sass / plain CSS, use scss (some-sass-language-server handles all three)
-#   - For Free Pascal/Lazarus, use pascal
-# Special requirements:
-#   Some languages require additional setup/installations.
-#   See here for details: https://oraios.github.io/serena/01-about/020_programming-languages.html#language-servers
-# When using multiple languages, the first language server that supports a given file will be used for that file.
-# The first language is the default language and the respective language server will be used as a fallback.
-# Note that when using the JetBrains backend, language servers are not used and this list is correspondingly ignored.
-languages:
-- rust
-
-# the encoding used by text files in the project
-# For a list of possible encodings, see https://docs.python.org/3.11/library/codecs.html#standard-encodings
-encoding: "utf-8"
-
-# line ending convention to use when writing source files.
-# Possible values: unset (use global setting), "lf", "crlf", or "native" (platform default)
-# This does not affect Serena's own files (e.g. memories and configuration files), which always use native line endings.
-line_ending:
-
-# The language backend to use for this project.
-# If not set, the global setting from serena_config.yml is used.
-# Valid values: LSP, JetBrains
-# Note: the backend is fixed at startup. If a project with a different backend
-# is activated post-init, an error will be returned.
-language_backend:
-
-# whether to use project's .gitignore files to ignore files
-ignore_all_files_in_gitignore: true
-
-# advanced configuration option allowing to configure language server-specific options.
-# Maps the language key to the options.
-# Have a look at the docstring of the constructors of the LS implementations within solidlsp (e.g., for C# or PHP) to see which options are available.
-# No documentation on options means no options are available.
-ls_specific_settings: {}
-
-# list of additional workspace folder paths for cross-package reference support (e.g. in monorepos).
-# Paths can be absolute or relative to the project root.
-# Each folder is registered as an LSP workspace folder, enabling language servers to discover
-# symbols and references across package boundaries.
-# Currently supported for: TypeScript.
-# Example:
-#   additional_workspace_folders:
-#     - ../sibling-package
-#     - ../shared-lib
-additional_workspace_folders: []
-
-# list of additional paths to ignore in this project.
-# Same syntax as gitignore, so you can use * and **.
-# Note: global ignored_paths from serena_config.yml are also applied additively.
-ignored_paths: []
-
-# whether the project is in read-only mode
-# If set to true, all editing tools will be disabled and attempts to use them will result in an error
-# Added on 2025-04-18
-read_only: false
-
-# list of tool names to exclude.
-# This extends the existing exclusions (e.g. from the global configuration)
-# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
-excluded_tools: []
-
-# list of tools to include that would otherwise be disabled (particularly optional tools that are disabled by default).
-# This extends the existing inclusions (e.g. from the global configuration).
-# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
-included_optional_tools: []
-
-# fixed set of tools to use as the base tool set (if non-empty), replacing Serena's default set of tools.
-# This cannot be combined with non-empty excluded_tools or included_optional_tools.
-# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
-fixed_tools: []
-
-# list of mode names that are to be activated by default, overriding the setting in the global configuration.
-# The full set of modes to be activated is base_modes (from global config) + default_modes + added_modes.
-# If the setting is undefined/empty, the default_modes from the global configuration (serena_config.yml) apply.
-# Otherwise, this overrides the setting from the global configuration (serena_config.yml).
-# Therefore, you can set this to [] if you do not want the default modes defined in the global config to apply
-# for this project.
-# This setting can, in turn, be overridden by CLI parameters (--mode).
-# See https://oraios.github.io/serena/02-usage/050_configuration.html#modes
-default_modes:
-
-# list of mode names to be activated additionally for this project, e.g. ["query-projects"]
-# The full set of modes to be activated is base_modes (from global config) + default_modes + added_modes.
-# See https://oraios.github.io/serena/02-usage/050_configuration.html#modes
-added_modes:
-
-# initial prompt for the project. It will always be given to the LLM upon activating the project
-# (contrary to the memories, which are loaded on demand).
-initial_prompt: ""
-
-# time budget (seconds) per tool call for the retrieval of additional symbol information
-# such as docstrings or parameter information.
-# This overrides the corresponding setting in the global configuration; see the documentation there.
-# If null or missing, use the setting from the global configuration.
-symbol_info_budget:
-
-# list of regex patterns which, when matched, mark a memory entry as read‑only.
-# Extends the list from the global configuration, merging the two lists.
-read_only_memory_patterns: []
-
-# list of regex patterns for memories to completely ignore.
-# Matching memories will not appear in list_memories or activate_project output
-# and cannot be accessed via read_memory or write_memory.
-# To access ignored memory files, use the read_file tool on the raw file path.
-# Extends the list from the global configuration, merging the two lists.
-# Example: ["_archive/.*", "_episodes/.*"]
-ignored_memory_patterns: []

.zed/tasks.json

@@ -1,59 +0,0 @@
-// Project tasks configuration. See https://zed.dev/docs/tasks for documentation.
-//
-// Example:
-[
-  {
-    "label": "Example task",
-    "command": "for i in {1..5}; do echo \"Hello $i/5\"; sleep 1; done",
-    //"args": [],
-    // Env overrides for the command, will be appended to the terminal's environment from the settings.
-    "env": { "foo": "bar" },
-    // Current working directory to spawn the command into, defaults to current project root.
-    //"cwd": "/path/to/working/directory",
-    // Whether to use a new terminal tab or reuse the existing one to spawn the process, defaults to `false`.
-    "use_new_terminal": false,
-    // Whether to allow multiple instances of the same task to be run, or rather wait for the existing ones to finish, defaults to `false`.
-    "allow_concurrent_runs": false,
-    // What to do with the terminal pane and tab, after the command was started:
-    // * `always` — always show the task's pane, and focus the corresponding tab in it (default)
-    // * `no_focus` — always show the task's pane, add the task's tab in it, but don't focus it
-    // * `never` — do not alter focus, but still add/reuse the task's tab in its pane
-    "reveal": "always",
-    // Where to place the task's terminal item after starting the task:
-    // * `dock` — in the terminal dock, "regular" terminal items' place (default)
-    // * `center` — in the central pane group, "main" editor area
-    "reveal_target": "dock",
-    // What to do with the terminal pane and tab, after the command had finished:
-    // * `never` — Do nothing when the command finishes (default)
-    // * `always` — always hide the terminal tab, hide the pane also if it was the last tab in it
-    // * `on_success` — hide the terminal tab on task success only, otherwise behaves similar to `always`
-    "hide": "never",
-    // Which shell to use when running a task inside the terminal.
-    // May take 3 values:
-    // 1. (default) Use the system's default terminal configuration in /etc/passwd
-    //      "shell": "system"
-    // 2. A program:
-    //      "shell": {
-    //        "program": "sh"
-    //      }
-    // 3. A program with arguments:
-    //     "shell": {
-    //         "with_arguments": {
-    //           "program": "/bin/bash",
-    //           "args": ["--login"]
-    //         }
-    //     }
-    "shell": "system",
-    // Whether to show the task line in the output of the spawned task, defaults to `true`.
-    "show_summary": true,
-    // Whether to show the command line in the output of the spawned task, defaults to `true`.
-    "show_command": true,
-    // Which edited buffers to save before running the task:
-    // * `all` — save all edited buffers
-    // * `current` — save currently active buffer only
-    // * `none` — don't save any buffers
-    "save": "none",
-    // Represents the tags for inline runnable indicators, or spawning multiple tasks at once.
-    // "tags": []
-  },
-]

CLAUDE.md

@@ -1,101 +0,0 @@
-**PROMPT**
-
-Tu es ma base de connaissance et mon bloc-notes intelligent sur le projet **obikmer**. Tu ne proposes pas, tu ne codes pas spontanément — tu réponds à mes questions et tu structures mes idées au fur et à mesure que je les exprime.
-
-**Règle absolue : une question appelle une réponse, pas une action.**
-Ne modifier aucun fichier à moins d'une demande explicite de modification. En particulier : observer un bug ou une incohérence dans le code montré ne constitue pas un mandat pour le corriger. Le code montré peut refléter une intention en cours — modifier sans mandat risque d'introduire un vrai bug là où tu croyais corriger.
-
-**Règle absolue : ne jamais substituer une dépendance ou une bibliothèque sans validation explicite.**
-Si une dépendance demandée pose problème (erreur de compilation, bug, API manquante), exposer le problème et proposer des alternatives — ne jamais switcher silencieusement vers une autre bibliothèque. Le choix des dépendances est une décision d'architecture qui appartient au développeur.
-
-**Règle absolue : le code existant est une hypothèse, pas une vérité.**
-Quand une nouvelle construction (type, itérateur, abstraction) rend du code historique injustifié, le signaler immédiatement et proposer de le supprimer — ne pas conserver les deux en parallèle par inertie. Le développeur demande explicitement de remettre en cause le code base : ne pas attendre qu'il insiste.
-
-Tu maintiens en **anglais**, dense et sans remplissage, les documents suivants :
-- `docmd/index.md` — document de discussion de base, enrichi progressivement au fil de nos échanges ; il reflète l'état courant de la réflexion sur le projet
-- les autres fichiers Markdown dans `docmd/` selon leur thème respectif
-
-Les snippets de code y sont courts et illustrent uniquement des principes architecturaux. Nos échanges se font en **français**.
-
----
-
-## Contexte du projet
-
-`obikmer` est un outil Rust de manipulation, comptage, indexation et opérations ensemblistes sur des séquences ADN représentées comme des ensembles de kmers.
-
-**Contraintes fondamentales**
-- Efficacité maximale en calcul, mémoire et disque
-- Données métagénomiques : plusieurs dizaines de Gbases, milliards de kmers
-- k impair, k ∈ [11, 31], fixé à l'exécution
-- Formats d'entrée : FASTA, FASTQ, gzip, streaming stdin
-
-**Opérations prioritaires**
-- Comptage de kmers (fréquences)
-- Recherche / requête rapide
-- Opérations ensemblistes (union, intersection, diff)
-
-**Ce qui a déjà été discuté**
-- Encodage 2 bits/base → kmer tient dans un `u64`
-- Forme canonique : `min(kmer, revcomp)` pour réduire l'espace de moitié
-
----
-
-## Infrastructure de documentation
-
-La documentation est gérée via **MkDocs + thème Material**, avec publication sur **GitHub Pages**.
-
-**Structure des répertoires**
-
-```
-docmd/          ← sources Markdown + mkdocs.yml
-docmd/mkdocs.yml
-doc/            ← site HTML généré (servi par GitHub Pages)
-.venv/          ← environnement Python (ignoré par git)
-```
-
-**Configuration `docmd/mkdocs.yml`**
-- `docs_dir: .` (sources = `docmd/` lui-même)
-- `site_dir: ../doc` (sortie = `doc/`)
-
-**Commandes Makefile**
-
-| Commande | Effet |
-|---|---|
-| `make doc` | Construit le HTML dans `doc/` |
-| `make doc-serve` | Serveur local avec rechargement automatique |
-| `make clean-doc` | Supprime `doc/` |
-| `make clean` | Supprime `doc/` et `.venv/` |
-
-Le `.venv/` est dans `.gitignore`. Le répertoire `doc/` (sortie HTML) est versionné pour GitHub Pages.
-
-Lors de l'ajout de nouveaux fichiers Markdown dans `docmd/`, mettre à jour la section `nav:` de `docmd/mkdocs.yml`.
-
----
-
-Je continue à poser mes questions et à guider la discussion.
-
----
-
-## MCP Tools
-
-**Règle absolue : avant tout travail de code, appeler `mcp__serena__initial_instructions` pour charger les instructions Serena.**
-
-### Hiérarchie des outils pour ce projet Rust
-
-**Navigation et édition de code → serena en priorité**
-- Trouver un symbole, une déclaration, les implémentations d'un trait : `mcp__serena__find_symbol`, `mcp__serena__find_declaration`, `mcp__serena__find_implementations`
-- Trouver les usages d'un symbole : `mcp__serena__find_referencing_symbols`
-- Diagnostics LSP (erreurs de compilation) : `mcp__serena__get_diagnostics_for_file`
-- Vue d'ensemble d'un fichier : `mcp__serena__get_symbols_overview`
-- Modifier le corps d'une fonction/impl : `mcp__serena__replace_symbol_body`
-- Ne pas utiliser `cclsp` quand serena couvre le besoin
-
-**Analyse architecturale → jcodemunch**
-- Hotspots, couplage, dead code, dépendances entre modules
-- Utiliser avant de refactorer une zone critique
-
-**Raisonnement complexe → sequential-thinking**
-- Décisions d'architecture, choix d'algorithme, trade-offs non triviaux
-
-**Documentation de crates → context7**
-- Toujours consulter avant d'utiliser une API de bibliothèque externe

DevDoc/architecture/index_architecture.refs/index.html

@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
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+  
+  
     
     
     
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
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+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -381,10 +436,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
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             <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -672,14 +727,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../../implementation/obilayeredmap/" class="md-nav__link">
+      <a href="../../implementation/layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -784,14 +839,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../../implementation/merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -827,10 +1022,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
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+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1110,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -991,10 +1270,10 @@
 <h1 id="coverage-architectureindex_architecturemd">Coverage: architecture/index_architecture.md</h1>
 <h2 id="code-couvert">Code couvert</h2>
 <ul>
-<li><code>obilayeredmap/src/layer.rs</code> — Layer<D>, trait LayerData, modes () / PersistentCompactIntMatrix / PersistentBitMatrix</li>
-<li><code>obilayeredmap/src/mphf_layer.rs</code> — MphfLayer, EvidenceKind (Exact / Approx), LayerEvidence enum</li>
-<li><code>obilayeredmap/src/map.rs</code> — LayeredMap<D></li>
-<li><code>obilayeredmap/src/meta.rs</code> — LayerMeta, PartitionMeta</li>
+<li><code>obikindex/src/layer/typed_layer.rs</code> — Layer<D>, trait LayerData, modes () / PersistentCompactIntMatrix / PersistentBitMatrix</li>
+<li><code>obikindex/src/layer/mphf_layer.rs</code> — MphfLayer, EvidenceKind (Exact / Approx), LayerEvidence enum</li>
+<li><code>obikindex/src/layer/map.rs</code> — LayeredMap<D></li>
+<li><code>obikindex/src/layer/meta.rs</code> — LayerMeta, PartitionMeta</li>
 <li><code>obikindex/src/meta.rs</code> — IndexConfig (kmer_size, n_bits, with_counts, evidence, block_bits), IndexMeta</li>
 <li><code>obikindex/src/index.rs</code> — KmerIndex, build_layers</li>
 <li><code>obicompactvec/src/</code> — PersistentCompactIntMatrix, PersistentBitMatrix (DataStore implementations)</li>

DevDoc/architecture/index_architecture/index.html

@@ -12,6 +12,8 @@
         <link rel="prev" href="../sequences/invariant/">
       
       
+        <link rel="next" href="../siblings/">
+      
       
         
       
@@ -180,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
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             <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -361,6 +390,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -383,10 +440,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
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             <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -674,14 +731,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../../implementation/obilayeredmap/" class="md-nav__link">
+      <a href="../../implementation/layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -786,14 +843,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../../implementation/merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -831,10 +1028,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" checked>
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
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             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1159,6 +1356,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       

DevDoc/architecture/query.refs/index.html

@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -187,10 +214,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -208,8 +235,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -381,10 +436,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -402,8 +457,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -672,14 +727,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../../implementation/obilayeredmap/" class="md-nav__link">
+      <a href="../../implementation/layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -784,14 +839,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../../implementation/merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -827,10 +1022,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +1043,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1110,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -992,7 +1271,7 @@
 <h2 id="code-couvert">Code couvert</h2>
 <ul>
 <li><code>obikmer/src/cmd/query.rs</code> — commande query, format de sortie</li>
-<li><code>obikpartitionner/src/query_layer.rs</code> — routage de la requête à travers les partitions</li>
+<li><code>obikindex/src/partition/query_layer.rs</code> — routage de la requête à travers les partitions</li>
 <li><code>obiread/src/lib.rs</code> — lecture des séquences d'entrée pour la requête</li>
 </ul>
 <h2 id="notes">Notes</h2>

DevDoc/architecture/sequences/invariant.refs/index.html

@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -187,10 +214,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -208,8 +235,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -381,10 +436,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -402,8 +457,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -672,14 +727,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../implementation/obilayeredmap/" class="md-nav__link">
+      <a href="../../../implementation/layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -784,14 +839,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../../../implementation/merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -827,10 +1022,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +1043,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1110,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       

DevDoc/architecture/sequences/invariant/index.html

@@ -9,7 +9,7 @@
       
       
       
-        <link rel="prev" href="../../../implementation/rebuild_filter/">
+        <link rel="prev" href="../../../implementation/partition_layer_cache/">
       
       
         <link rel="next" href="../../index_architecture/">
@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -212,8 +239,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -385,10 +440,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -406,8 +461,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -676,14 +731,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../implementation/obilayeredmap/" class="md-nav__link">
+      <a href="../../../implementation/layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -788,14 +843,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../../../implementation/merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -833,10 +1028,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" checked>
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -854,8 +1049,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -931,6 +1126,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       

DevDoc/assets/javascripts/lunr/min/lunr.da.min.js

@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Danish` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.da=function(){this.pipeline.reset(),this.pipeline.add(e.da.trimmer,e.da.stopWordFilter,e.da.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.da.stemmer))},e.da.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.da.trimmer=e.trimmerSupport.generateTrimmer(e.da.wordCharacters),e.Pipeline.registerFunction(e.da.trimmer,"trimmer-da"),e.da.stemmer=function(){var r=e.stemmerSupport.Among,i=e.stemmerSupport.SnowballProgram,n=new function(){function e(){var e,r=f.cursor+3;if(d=f.limit,0<=r&&r<=f.limit){for(a=r;;){if(e=f.cursor,f.in_grouping(w,97,248)){f.cursor=e;break}if(f.cursor=e,e>=f.limit)return;f.cursor++}for(;!f.out_grouping(w,97,248);){if(f.cursor>=f.limit)return;f.cursor++}d=f.cursor,d<a&&(d=a)}}function n(){var e,r;if(f.cursor>=d&&(r=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,e=f.find_among_b(c,32),f.limit_backward=r,e))switch(f.bra=f.cursor,e){case 1:f.slice_del();break;case 2:f.in_grouping_b(p,97,229)&&f.slice_del()}}function t(){var e,r=f.limit-f.cursor;f.cursor>=d&&(e=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,f.find_among_b(l,4)?(f.bra=f.cursor,f.limit_backward=e,f.cursor=f.limit-r,f.cursor>f.limit_backward&&(f.cursor--,f.bra=f.cursor,f.slice_del())):f.limit_backward=e)}function s(){var e,r,i,n=f.limit-f.cursor;if(f.ket=f.cursor,f.eq_s_b(2,"st")&&(f.bra=f.cursor,f.eq_s_b(2,"ig")&&f.slice_del()),f.cursor=f.limit-n,f.cursor>=d&&(r=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,e=f.find_among_b(m,5),f.limit_backward=r,e))switch(f.bra=f.cursor,e){case 1:f.slice_del(),i=f.limit-f.cursor,t(),f.cursor=f.limit-i;break;case 2:f.slice_from("løs")}}function o(){var e;f.cursor>=d&&(e=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,f.out_grouping_b(w,97,248)?(f.bra=f.cursor,u=f.slice_to(u),f.limit_backward=e,f.eq_v_b(u)&&f.slice_del()):f.limit_backward=e)}var a,d,u,c=[new r("hed",-1,1),new r("ethed",0,1),new r("ered",-1,1),new r("e",-1,1),new r("erede",3,1),new r("ende",3,1),new r("erende",5,1),new r("ene",3,1),new r("erne",3,1),new r("ere",3,1),new r("en",-1,1),new r("heden",10,1),new r("eren",10,1),new r("er",-1,1),new r("heder",13,1),new r("erer",13,1),new r("s",-1,2),new r("heds",16,1),new r("es",16,1),new r("endes",18,1),new r("erendes",19,1),new r("enes",18,1),new r("ernes",18,1),new r("eres",18,1),new r("ens",16,1),new r("hedens",24,1),new r("erens",24,1),new r("ers",16,1),new r("ets",16,1),new r("erets",28,1),new r("et",-1,1),new r("eret",30,1)],l=[new r("gd",-1,-1),new r("dt",-1,-1),new r("gt",-1,-1),new r("kt",-1,-1)],m=[new r("ig",-1,1),new r("lig",0,1),new r("elig",1,1),new r("els",-1,1),new r("løst",-1,2)],w=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,48,0,128],p=[239,254,42,3,0,0,0,0,0,0,0,0,0,0,0,0,16],f=new i;this.setCurrent=function(e){f.setCurrent(e)},this.getCurrent=function(){return f.getCurrent()},this.stem=function(){var r=f.cursor;return e(),f.limit_backward=r,f.cursor=f.limit,n(),f.cursor=f.limit,t(),f.cursor=f.limit,s(),f.cursor=f.limit,o(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return n.setCurrent(e),n.stem(),n.getCurrent()}):(n.setCurrent(e),n.stem(),n.getCurrent())}}(),e.Pipeline.registerFunction(e.da.stemmer,"stemmer-da"),e.da.stopWordFilter=e.generateStopWordFilter("ad af alle alt anden at blev blive bliver da de dem den denne der deres det dette dig din disse dog du efter eller en end er et for fra ham han hans har havde have hende hendes her hos hun hvad hvis hvor i ikke ind jeg jer jo kunne man mange med meget men mig min mine mit mod ned noget nogle nu når og også om op os over på selv sig sin sine sit skal skulle som sådan thi til ud under var vi vil ville vor være været".split(" ")),e.Pipeline.registerFunction(e.da.stopWordFilter,"stopWordFilter-da")}});

DevDoc/assets/javascripts/lunr/min/lunr.hi.min.js

@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.hi=function(){this.pipeline.reset(),this.pipeline.add(e.hi.trimmer,e.hi.stopWordFilter,e.hi.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.hi.stemmer))},e.hi.wordCharacters="ऀ-ःऄ-एऐ-टठ-यर-िी-ॏॐ-य़ॠ-९॰-ॿa-zA-Zａ-ｚＡ-Ｚ0-9０-９",e.hi.trimmer=e.trimmerSupport.generateTrimmer(e.hi.wordCharacters),e.Pipeline.registerFunction(e.hi.trimmer,"trimmer-hi"),e.hi.stopWordFilter=e.generateStopWordFilter("अत अपना अपनी अपने अभी अंदर आदि आप इत्यादि इन इनका इन्हीं इन्हें इन्हों इस इसका इसकी इसके इसमें इसी इसे उन उनका उनकी उनके उनको उन्हीं उन्हें उन्हों उस उसके उसी उसे एक एवं एस ऐसे और कई कर करता करते करना करने करें कहते कहा का काफ़ी कि कितना किन्हें किन्हों किया किर किस किसी किसे की कुछ कुल के को कोई कौन कौनसा गया घर जब जहाँ जा जितना जिन जिन्हें जिन्हों जिस जिसे जीधर जैसा जैसे जो तक तब तरह तिन तिन्हें तिन्हों तिस तिसे तो था थी थे दबारा दिया दुसरा दूसरे दो द्वारा न नके नहीं ना निहायत नीचे ने पर पहले पूरा पे फिर बनी बही बहुत बाद बाला बिलकुल भी भीतर मगर मानो मे में यदि यह यहाँ यही या यिह ये रखें रहा रहे ऱ्वासा लिए लिये लेकिन व वग़ैरह वर्ग वह वहाँ वहीं वाले वुह वे वो सकता सकते सबसे सभी साथ साबुत साभ सारा से सो संग ही हुआ हुई हुए है हैं हो होता होती होते होना होने".split(" ")),e.hi.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var r=e.wordcut;r.init(),e.hi.tokenizer=function(i){if(!arguments.length||null==i||void 0==i)return[];if(Array.isArray(i))return i.map(function(r){return isLunr2?new e.Token(r.toLowerCase()):r.toLowerCase()});var t=i.toString().toLowerCase().replace(/^\s+/,"");return r.cut(t).split("|")},e.Pipeline.registerFunction(e.hi.stemmer,"stemmer-hi"),e.Pipeline.registerFunction(e.hi.stopWordFilter,"stopWordFilter-hi")}});

DevDoc/assets/javascripts/lunr/min/lunr.hy.min.js

@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.hy=function(){this.pipeline.reset(),this.pipeline.add(e.hy.trimmer,e.hy.stopWordFilter)},e.hy.wordCharacters="[A-Za-z԰-֏ff-ﭏ]",e.hy.trimmer=e.trimmerSupport.generateTrimmer(e.hy.wordCharacters),e.Pipeline.registerFunction(e.hy.trimmer,"trimmer-hy"),e.hy.stopWordFilter=e.generateStopWordFilter("դու և եք էիր էիք հետո նաև նրանք որը վրա է որ պիտի են այս մեջ ն իր ու ի այդ որոնք այն կամ էր մի ես համար այլ իսկ էին ենք հետ ին թ էինք մենք նրա նա դուք եմ էի ըստ որպես ում".split(" ")),e.Pipeline.registerFunction(e.hy.stopWordFilter,"stopWordFilter-hy"),e.hy.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}(),e.Pipeline.registerFunction(e.hy.stemmer,"stemmer-hy")}});

DevDoc/assets/javascripts/lunr/min/lunr.ja.min.js

@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var r="2"==e.version[0];e.ja=function(){this.pipeline.reset(),this.pipeline.add(e.ja.trimmer,e.ja.stopWordFilter,e.ja.stemmer),r?this.tokenizer=e.ja.tokenizer:(e.tokenizer&&(e.tokenizer=e.ja.tokenizer),this.tokenizerFn&&(this.tokenizerFn=e.ja.tokenizer))};var t=new e.TinySegmenter;e.ja.tokenizer=function(i){var n,o,s,p,a,u,m,l,c,f;if(!arguments.length||null==i||void 0==i)return[];if(Array.isArray(i))return i.map(function(t){return r?new e.Token(t.toLowerCase()):t.toLowerCase()});for(o=i.toString().toLowerCase().replace(/^\s+/,""),n=o.length-1;n>=0;n--)if(/\S/.test(o.charAt(n))){o=o.substring(0,n+1);break}for(a=[],s=o.length,c=0,l=0;c<=s;c++)if(u=o.charAt(c),m=c-l,u.match(/\s/)||c==s){if(m>0)for(p=t.segment(o.slice(l,c)).filter(function(e){return!!e}),f=l,n=0;n<p.length;n++)r?a.push(new e.Token(p[n],{position:[f,p[n].length],index:a.length})):a.push(p[n]),f+=p[n].length;l=c+1}return a},e.ja.stemmer=function(){return function(e){return e}}(),e.Pipeline.registerFunction(e.ja.stemmer,"stemmer-ja"),e.ja.wordCharacters="一二三四五六七八九十百千万億兆一-龠々〆ヵヶぁ-んァ-ヴーｱ-ﾝﾞa-zA-Zａ-ｚＡ-Ｚ0-9０-９",e.ja.trimmer=e.trimmerSupport.generateTrimmer(e.ja.wordCharacters),e.Pipeline.registerFunction(e.ja.trimmer,"trimmer-ja"),e.ja.stopWordFilter=e.generateStopWordFilter("これ それ あれ この その あの ここ そこ あそこ こちら どこ だれ なに なん 何 私 貴方 貴方方 我々 私達 あの人 あのかた 彼女 彼 です あります おります います は が の に を で え から まで より も どの と し それで しかし".split(" ")),e.Pipeline.registerFunction(e.ja.stopWordFilter,"stopWordFilter-ja"),e.jp=e.ja,e.Pipeline.registerFunction(e.jp.stemmer,"stemmer-jp"),e.Pipeline.registerFunction(e.jp.trimmer,"trimmer-jp"),e.Pipeline.registerFunction(e.jp.stopWordFilter,"stopWordFilter-jp")}});

DevDoc/assets/javascripts/lunr/min/lunr.jp.min.js

@@ -0,0 +1 @@
+module.exports=require("./lunr.ja");

DevDoc/assets/javascripts/lunr/min/lunr.kn.min.js

@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.kn=function(){this.pipeline.reset(),this.pipeline.add(e.kn.trimmer,e.kn.stopWordFilter,e.kn.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.kn.stemmer))},e.kn.wordCharacters="ಀ-಄ಅ-ಔಕ-ಹಾ-ೌ಼-ಽೕ-ೖೝ-ೞೠ-ೡೢ-ೣ೤೥೦-೯ೱ-ೳ",e.kn.trimmer=e.trimmerSupport.generateTrimmer(e.kn.wordCharacters),e.Pipeline.registerFunction(e.kn.trimmer,"trimmer-kn"),e.kn.stopWordFilter=e.generateStopWordFilter("ಮತ್ತು ಈ ಒಂದು ರಲ್ಲಿ ಹಾಗೂ ಎಂದು ಅಥವಾ ಇದು ರ ಅವರು ಎಂಬ ಮೇಲೆ ಅವರ ತನ್ನ ಆದರೆ ತಮ್ಮ ನಂತರ ಮೂಲಕ ಹೆಚ್ಚು ನ ಆ ಕೆಲವು ಅನೇಕ ಎರಡು ಹಾಗು ಪ್ರಮುಖ ಇದನ್ನು ಇದರ ಸುಮಾರು ಅದರ ಅದು ಮೊದಲ ಬಗ್ಗೆ ನಲ್ಲಿ ರಂದು ಇತರ ಅತ್ಯಂತ ಹೆಚ್ಚಿನ ಸಹ ಸಾಮಾನ್ಯವಾಗಿ ನೇ ಹಲವಾರು ಹೊಸ ದಿ ಕಡಿಮೆ ಯಾವುದೇ ಹೊಂದಿದೆ ದೊಡ್ಡ ಅನ್ನು ಇವರು ಪ್ರಕಾರ ಇದೆ ಮಾತ್ರ ಕೂಡ ಇಲ್ಲಿ ಎಲ್ಲಾ ವಿವಿಧ ಅದನ್ನು ಹಲವು ರಿಂದ ಕೇವಲ ದ ದಕ್ಷಿಣ ಗೆ ಅವನ ಅತಿ ನೆಯ ಬಹಳ ಕೆಲಸ ಎಲ್ಲ ಪ್ರತಿ ಇತ್ಯಾದಿ ಇವು ಬೇರೆ ಹೀಗೆ ನಡುವೆ ಇದಕ್ಕೆ ಎಸ್ ಇವರ ಮೊದಲು ಶ್ರೀ ಮಾಡುವ ಇದರಲ್ಲಿ ರೀತಿಯ ಮಾಡಿದ ಕಾಲ ಅಲ್ಲಿ ಮಾಡಲು ಅದೇ ಈಗ ಅವು ಗಳು ಎ ಎಂಬುದು ಅವನು ಅಂದರೆ ಅವರಿಗೆ ಇರುವ ವಿಶೇಷ ಮುಂದೆ ಅವುಗಳ ಮುಂತಾದ ಮೂಲ ಬಿ ಮೀ ಒಂದೇ ಇನ್ನೂ ಹೆಚ್ಚಾಗಿ ಮಾಡಿ ಅವರನ್ನು ಇದೇ ಯ ರೀತಿಯಲ್ಲಿ ಜೊತೆ ಅದರಲ್ಲಿ ಮಾಡಿದರು ನಡೆದ ಆಗ ಮತ್ತೆ ಪೂರ್ವ ಆತ ಬಂದ ಯಾವ ಒಟ್ಟು ಇತರೆ ಹಿಂದೆ ಪ್ರಮಾಣದ ಗಳನ್ನು ಕುರಿತು ಯು ಆದ್ದರಿಂದ ಅಲ್ಲದೆ ನಗರದ ಮೇಲಿನ ಏಕೆಂದರೆ ರಷ್ಟು ಎಂಬುದನ್ನು ಬಾರಿ ಎಂದರೆ ಹಿಂದಿನ ಆದರೂ ಆದ ಸಂಬಂಧಿಸಿದ ಮತ್ತೊಂದು ಸಿ ಆತನ ".split(" ")),e.kn.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var r=e.wordcut;r.init(),e.kn.tokenizer=function(t){if(!arguments.length||null==t||void 0==t)return[];if(Array.isArray(t))return t.map(function(r){return isLunr2?new e.Token(r.toLowerCase()):r.toLowerCase()});var n=t.toString().toLowerCase().replace(/^\s+/,"");return r.cut(n).split("|")},e.Pipeline.registerFunction(e.kn.stemmer,"stemmer-kn"),e.Pipeline.registerFunction(e.kn.stopWordFilter,"stopWordFilter-kn")}});

DevDoc/assets/javascripts/lunr/min/lunr.multi.min.js

@@ -0,0 +1 @@
+!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){e.multiLanguage=function(){for(var t=Array.prototype.slice.call(arguments),i=t.join("-"),r="",n=[],s=[],p=0;p<t.length;++p)"en"==t[p]?(r+="\\w",n.unshift(e.stopWordFilter),n.push(e.stemmer),s.push(e.stemmer)):(r+=e[t[p]].wordCharacters,e[t[p]].stopWordFilter&&n.unshift(e[t[p]].stopWordFilter),e[t[p]].stemmer&&(n.push(e[t[p]].stemmer),s.push(e[t[p]].stemmer)));var o=e.trimmerSupport.generateTrimmer(r);return e.Pipeline.registerFunction(o,"lunr-multi-trimmer-"+i),n.unshift(o),function(){this.pipeline.reset(),this.pipeline.add.apply(this.pipeline,n),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add.apply(this.searchPipeline,s))}}}});

DevDoc/assets/javascripts/lunr/min/lunr.no.min.js

@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Norwegian` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.no=function(){this.pipeline.reset(),this.pipeline.add(e.no.trimmer,e.no.stopWordFilter,e.no.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.no.stemmer))},e.no.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.no.trimmer=e.trimmerSupport.generateTrimmer(e.no.wordCharacters),e.Pipeline.registerFunction(e.no.trimmer,"trimmer-no"),e.no.stemmer=function(){var r=e.stemmerSupport.Among,n=e.stemmerSupport.SnowballProgram,i=new function(){function e(){var e,r=w.cursor+3;if(a=w.limit,0<=r||r<=w.limit){for(s=r;;){if(e=w.cursor,w.in_grouping(d,97,248)){w.cursor=e;break}if(e>=w.limit)return;w.cursor=e+1}for(;!w.out_grouping(d,97,248);){if(w.cursor>=w.limit)return;w.cursor++}a=w.cursor,a<s&&(a=s)}}function i(){var e,r,n;if(w.cursor>=a&&(r=w.limit_backward,w.limit_backward=a,w.ket=w.cursor,e=w.find_among_b(m,29),w.limit_backward=r,e))switch(w.bra=w.cursor,e){case 1:w.slice_del();break;case 2:n=w.limit-w.cursor,w.in_grouping_b(c,98,122)?w.slice_del():(w.cursor=w.limit-n,w.eq_s_b(1,"k")&&w.out_grouping_b(d,97,248)&&w.slice_del());break;case 3:w.slice_from("er")}}function t(){var e,r=w.limit-w.cursor;w.cursor>=a&&(e=w.limit_backward,w.limit_backward=a,w.ket=w.cursor,w.find_among_b(u,2)?(w.bra=w.cursor,w.limit_backward=e,w.cursor=w.limit-r,w.cursor>w.limit_backward&&(w.cursor--,w.bra=w.cursor,w.slice_del())):w.limit_backward=e)}function o(){var e,r;w.cursor>=a&&(r=w.limit_backward,w.limit_backward=a,w.ket=w.cursor,e=w.find_among_b(l,11),e?(w.bra=w.cursor,w.limit_backward=r,1==e&&w.slice_del()):w.limit_backward=r)}var s,a,m=[new r("a",-1,1),new r("e",-1,1),new r("ede",1,1),new r("ande",1,1),new r("ende",1,1),new r("ane",1,1),new r("ene",1,1),new r("hetene",6,1),new r("erte",1,3),new r("en",-1,1),new r("heten",9,1),new r("ar",-1,1),new r("er",-1,1),new r("heter",12,1),new r("s",-1,2),new r("as",14,1),new r("es",14,1),new r("edes",16,1),new r("endes",16,1),new r("enes",16,1),new r("hetenes",19,1),new r("ens",14,1),new r("hetens",21,1),new r("ers",14,1),new r("ets",14,1),new r("et",-1,1),new r("het",25,1),new r("ert",-1,3),new r("ast",-1,1)],u=[new r("dt",-1,-1),new r("vt",-1,-1)],l=[new r("leg",-1,1),new r("eleg",0,1),new r("ig",-1,1),new r("eig",2,1),new r("lig",2,1),new r("elig",4,1),new r("els",-1,1),new r("lov",-1,1),new r("elov",7,1),new r("slov",7,1),new r("hetslov",9,1)],d=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,48,0,128],c=[119,125,149,1],w=new n;this.setCurrent=function(e){w.setCurrent(e)},this.getCurrent=function(){return w.getCurrent()},this.stem=function(){var r=w.cursor;return e(),w.limit_backward=r,w.cursor=w.limit,i(),w.cursor=w.limit,t(),w.cursor=w.limit,o(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return i.setCurrent(e),i.stem(),i.getCurrent()}):(i.setCurrent(e),i.stem(),i.getCurrent())}}(),e.Pipeline.registerFunction(e.no.stemmer,"stemmer-no"),e.no.stopWordFilter=e.generateStopWordFilter("alle at av bare begge ble blei bli blir blitt både båe da de deg dei deim deira deires dem den denne der dere deres det dette di din disse ditt du dykk dykkar då eg ein eit eitt eller elles en enn er et ett etter for fordi fra før ha hadde han hans har hennar henne hennes her hjå ho hoe honom hoss hossen hun hva hvem hver hvilke hvilken hvis hvor hvordan hvorfor i ikke ikkje ikkje ingen ingi inkje inn inni ja jeg kan kom korleis korso kun kunne kva kvar kvarhelst kven kvi kvifor man mange me med medan meg meget mellom men mi min mine mitt mot mykje ned no noe noen noka noko nokon nokor nokre nå når og også om opp oss over på samme seg selv si si sia sidan siden sin sine sitt sjøl skal skulle slik so som som somme somt så sånn til um upp ut uten var vart varte ved vere verte vi vil ville vore vors vort vår være være vært å".split(" ")),e.Pipeline.registerFunction(e.no.stopWordFilter,"stopWordFilter-no")}});

DevDoc/assets/javascripts/lunr/min/lunr.sa.min.js

@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.sa=function(){this.pipeline.reset(),this.pipeline.add(e.sa.trimmer,e.sa.stopWordFilter,e.sa.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.sa.stemmer))},e.sa.wordCharacters="ऀ-ःऄ-एऐ-टठ-यर-िी-ॏॐ-य़ॠ-९॰-ॿ꣠-꣱ꣲ-ꣷ꣸-ꣻ꣼-ꣽꣾ-ꣿᆰ0-ᆰ9",e.sa.trimmer=e.trimmerSupport.generateTrimmer(e.sa.wordCharacters),e.Pipeline.registerFunction(e.sa.trimmer,"trimmer-sa"),e.sa.stopWordFilter=e.generateStopWordFilter('तथा अयम्‌ एकम्‌ इत्यस्मिन्‌ तथा तत्‌ वा अयम्‌ इत्यस्य ते आहूत उपरि तेषाम्‌  किन्तु तेषाम्‌ तदा इत्यनेन अधिकः इत्यस्य तत्‌ केचन बहवः द्वि तथा महत्वपूर्णः अयम्‌ अस्य  विषये अयं अस्ति तत्‌ प्रथमः विषये इत्युपरि इत्युपरि इतर अधिकतमः अधिकः अपि सामान्यतया ठ इतरेतर नूतनम्‌ द  न्यूनम्‌ कश्चित्‌ वा विशालः द  सः अस्ति तदनुसारम् तत्र अस्ति केवलम्‌ अपि अत्र सर्वे विविधाः तत्‌ बहवः यतः इदानीम्‌ द  दक्षिण इत्यस्मै तस्य उपरि नथ अतीव कार्यम्‌ सर्वे एकैकम्‌ इत्यादि। एते सन्ति  उत इत्थम्‌ मध्ये एतदर्थं . स कस्य प्रथमः श्री. करोति अस्मिन् प्रकारः निर्मिता कालः तत्र कर्तुं  समान अधुना ते सन्ति स एकः अस्ति सः अर्थात् तेषां कृते . स्थितम्  विशेषः अग्रिम तेषाम्‌ समान स्रोतः ख म समान इदानीमपि अधिकतया करोतु ते समान इत्यस्य वीथी सह यस्मिन्  कृतवान्‌ धृतः तदा पुनः पूर्वं सः आगतः किम्‌ कुल इतर पुरा  मात्रा स विषये उ अतएव अपि नगरस्य  उपरि यतः प्रतिशतं  कतरः कालः साधनानि भूत तथापि जात सम्बन्धि अन्यत्‌ ग अतः अस्माकं स्वकीयाः अस्माकं इदानीं अन्तः इत्यादयः भवन्तः इत्यादयः एते एताः तस्य अस्य इदम् एते तेषां तेषां तेषां तान् तेषां तेषां तेषां समानः सः एकः च तादृशाः बहवः अन्ये च वदन्ति यत् कियत् कस्मै  कस्मै  यस्मै  यस्मै  यस्मै  यस्मै न अतिनीचः किन्तु प्रथमं सम्पूर्णतया  ततः चिरकालानन्तरं पुस्तकं सम्पूर्णतया अन्तः  किन्तु अत्र वा इह इव श्रद्धाय अवशिष्यते  परन्तु अन्ये वर्गाः सन्ति ते सन्ति शक्नुवन्ति सर्वे मिलित्वा सर्वे एकत्र"'.split(" ")),e.sa.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var r=e.wordcut;r.init(),e.sa.tokenizer=function(t){if(!arguments.length||null==t||void 0==t)return[];if(Array.isArray(t))return t.map(function(r){return isLunr2?new e.Token(r.toLowerCase()):r.toLowerCase()});var i=t.toString().toLowerCase().replace(/^\s+/,"");return r.cut(i).split("|")},e.Pipeline.registerFunction(e.sa.stemmer,"stemmer-sa"),e.Pipeline.registerFunction(e.sa.stopWordFilter,"stopWordFilter-sa")}});

DevDoc/assets/javascripts/lunr/min/lunr.stemmer.support.min.js

@@ -0,0 +1 @@
+!function(r,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(r.lunr)}(this,function(){return function(r){r.stemmerSupport={Among:function(r,t,i,s){if(this.toCharArray=function(r){for(var t=r.length,i=new Array(t),s=0;s<t;s++)i[s]=r.charCodeAt(s);return i},!r&&""!=r||!t&&0!=t||!i)throw"Bad Among initialisation: s:"+r+", substring_i: "+t+", result: "+i;this.s_size=r.length,this.s=this.toCharArray(r),this.substring_i=t,this.result=i,this.method=s},SnowballProgram:function(){var r;return{bra:0,ket:0,limit:0,cursor:0,limit_backward:0,setCurrent:function(t){r=t,this.cursor=0,this.limit=t.length,this.limit_backward=0,this.bra=this.cursor,this.ket=this.limit},getCurrent:function(){var t=r;return r=null,t},in_grouping:function(t,i,s){if(this.cursor<this.limit){var e=r.charCodeAt(this.cursor);if(e<=s&&e>=i&&(e-=i,t[e>>3]&1<<(7&e)))return this.cursor++,!0}return!1},in_grouping_b:function(t,i,s){if(this.cursor>this.limit_backward){var e=r.charCodeAt(this.cursor-1);if(e<=s&&e>=i&&(e-=i,t[e>>3]&1<<(7&e)))return this.cursor--,!0}return!1},out_grouping:function(t,i,s){if(this.cursor<this.limit){var e=r.charCodeAt(this.cursor);if(e>s||e<i)return this.cursor++,!0;if(e-=i,!(t[e>>3]&1<<(7&e)))return this.cursor++,!0}return!1},out_grouping_b:function(t,i,s){if(this.cursor>this.limit_backward){var e=r.charCodeAt(this.cursor-1);if(e>s||e<i)return this.cursor--,!0;if(e-=i,!(t[e>>3]&1<<(7&e)))return this.cursor--,!0}return!1},eq_s:function(t,i){if(this.limit-this.cursor<t)return!1;for(var s=0;s<t;s++)if(r.charCodeAt(this.cursor+s)!=i.charCodeAt(s))return!1;return this.cursor+=t,!0},eq_s_b:function(t,i){if(this.cursor-this.limit_backward<t)return!1;for(var s=0;s<t;s++)if(r.charCodeAt(this.cursor-t+s)!=i.charCodeAt(s))return!1;return this.cursor-=t,!0},find_among:function(t,i){for(var s=0,e=i,n=this.cursor,u=this.limit,o=0,h=0,c=!1;;){for(var a=s+(e-s>>1),f=0,l=o<h?o:h,_=t[a],m=l;m<_.s_size;m++){if(n+l==u){f=-1;break}if(f=r.charCodeAt(n+l)-_.s[m])break;l++}if(f<0?(e=a,h=l):(s=a,o=l),e-s<=1){if(s>0||e==s||c)break;c=!0}}for(;;){var _=t[s];if(o>=_.s_size){if(this.cursor=n+_.s_size,!_.method)return _.result;var b=_.method();if(this.cursor=n+_.s_size,b)return _.result}if((s=_.substring_i)<0)return 0}},find_among_b:function(t,i){for(var s=0,e=i,n=this.cursor,u=this.limit_backward,o=0,h=0,c=!1;;){for(var a=s+(e-s>>1),f=0,l=o<h?o:h,_=t[a],m=_.s_size-1-l;m>=0;m--){if(n-l==u){f=-1;break}if(f=r.charCodeAt(n-1-l)-_.s[m])break;l++}if(f<0?(e=a,h=l):(s=a,o=l),e-s<=1){if(s>0||e==s||c)break;c=!0}}for(;;){var _=t[s];if(o>=_.s_size){if(this.cursor=n-_.s_size,!_.method)return _.result;var b=_.method();if(this.cursor=n-_.s_size,b)return _.result}if((s=_.substring_i)<0)return 0}},replace_s:function(t,i,s){var e=s.length-(i-t),n=r.substring(0,t),u=r.substring(i);return r=n+s+u,this.limit+=e,this.cursor>=i?this.cursor+=e:this.cursor>t&&(this.cursor=t),e},slice_check:function(){if(this.bra<0||this.bra>this.ket||this.ket>this.limit||this.limit>r.length)throw"faulty slice operation"},slice_from:function(r){this.slice_check(),this.replace_s(this.bra,this.ket,r)},slice_del:function(){this.slice_from("")},insert:function(r,t,i){var s=this.replace_s(r,t,i);r<=this.bra&&(this.bra+=s),r<=this.ket&&(this.ket+=s)},slice_to:function(){return this.slice_check(),r.substring(this.bra,this.ket)},eq_v_b:function(r){return this.eq_s_b(r.length,r)}}}},r.trimmerSupport={generateTrimmer:function(r){var t=new RegExp("^[^"+r+"]+"),i=new RegExp("[^"+r+"]+$");return function(r){return"function"==typeof r.update?r.update(function(r){return r.replace(t,"").replace(i,"")}):r.replace(t,"").replace(i,"")}}}}});

DevDoc/assets/javascripts/lunr/min/lunr.sv.min.js

@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Swedish` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.sv=function(){this.pipeline.reset(),this.pipeline.add(e.sv.trimmer,e.sv.stopWordFilter,e.sv.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.sv.stemmer))},e.sv.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.sv.trimmer=e.trimmerSupport.generateTrimmer(e.sv.wordCharacters),e.Pipeline.registerFunction(e.sv.trimmer,"trimmer-sv"),e.sv.stemmer=function(){var r=e.stemmerSupport.Among,n=e.stemmerSupport.SnowballProgram,t=new function(){function e(){var e,r=w.cursor+3;if(o=w.limit,0<=r||r<=w.limit){for(a=r;;){if(e=w.cursor,w.in_grouping(l,97,246)){w.cursor=e;break}if(w.cursor=e,w.cursor>=w.limit)return;w.cursor++}for(;!w.out_grouping(l,97,246);){if(w.cursor>=w.limit)return;w.cursor++}o=w.cursor,o<a&&(o=a)}}function t(){var e,r=w.limit_backward;if(w.cursor>=o&&(w.limit_backward=o,w.cursor=w.limit,w.ket=w.cursor,e=w.find_among_b(u,37),w.limit_backward=r,e))switch(w.bra=w.cursor,e){case 1:w.slice_del();break;case 2:w.in_grouping_b(d,98,121)&&w.slice_del()}}function i(){var e=w.limit_backward;w.cursor>=o&&(w.limit_backward=o,w.cursor=w.limit,w.find_among_b(c,7)&&(w.cursor=w.limit,w.ket=w.cursor,w.cursor>w.limit_backward&&(w.bra=--w.cursor,w.slice_del())),w.limit_backward=e)}function s(){var e,r;if(w.cursor>=o){if(r=w.limit_backward,w.limit_backward=o,w.cursor=w.limit,w.ket=w.cursor,e=w.find_among_b(m,5))switch(w.bra=w.cursor,e){case 1:w.slice_del();break;case 2:w.slice_from("lös");break;case 3:w.slice_from("full")}w.limit_backward=r}}var a,o,u=[new r("a",-1,1),new r("arna",0,1),new r("erna",0,1),new r("heterna",2,1),new r("orna",0,1),new r("ad",-1,1),new r("e",-1,1),new r("ade",6,1),new r("ande",6,1),new r("arne",6,1),new r("are",6,1),new r("aste",6,1),new r("en",-1,1),new r("anden",12,1),new r("aren",12,1),new r("heten",12,1),new r("ern",-1,1),new r("ar",-1,1),new r("er",-1,1),new r("heter",18,1),new r("or",-1,1),new r("s",-1,2),new r("as",21,1),new r("arnas",22,1),new r("ernas",22,1),new r("ornas",22,1),new r("es",21,1),new r("ades",26,1),new r("andes",26,1),new r("ens",21,1),new r("arens",29,1),new r("hetens",29,1),new r("erns",21,1),new r("at",-1,1),new r("andet",-1,1),new r("het",-1,1),new r("ast",-1,1)],c=[new r("dd",-1,-1),new r("gd",-1,-1),new r("nn",-1,-1),new r("dt",-1,-1),new r("gt",-1,-1),new r("kt",-1,-1),new r("tt",-1,-1)],m=[new r("ig",-1,1),new r("lig",0,1),new r("els",-1,1),new r("fullt",-1,3),new r("löst",-1,2)],l=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,24,0,32],d=[119,127,149],w=new n;this.setCurrent=function(e){w.setCurrent(e)},this.getCurrent=function(){return w.getCurrent()},this.stem=function(){var r=w.cursor;return e(),w.limit_backward=r,w.cursor=w.limit,t(),w.cursor=w.limit,i(),w.cursor=w.limit,s(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return t.setCurrent(e),t.stem(),t.getCurrent()}):(t.setCurrent(e),t.stem(),t.getCurrent())}}(),e.Pipeline.registerFunction(e.sv.stemmer,"stemmer-sv"),e.sv.stopWordFilter=e.generateStopWordFilter("alla allt att av blev bli blir blivit de dem den denna deras dess dessa det detta dig din dina ditt du där då efter ej eller en er era ert ett från för ha hade han hans har henne hennes hon honom hur här i icke ingen inom inte jag ju kan kunde man med mellan men mig min mina mitt mot mycket ni nu när någon något några och om oss på samma sedan sig sin sina sitta själv skulle som så sådan sådana sådant till under upp ut utan vad var vara varför varit varje vars vart vem vi vid vilka vilkas vilken vilket vår våra vårt än är åt över".split(" ")),e.Pipeline.registerFunction(e.sv.stopWordFilter,"stopWordFilter-sv")}});

DevDoc/assets/javascripts/lunr/min/lunr.ta.min.js

@@ -0,0 +1 @@
+!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.ta=function(){this.pipeline.reset(),this.pipeline.add(e.ta.trimmer,e.ta.stopWordFilter,e.ta.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.ta.stemmer))},e.ta.wordCharacters="஀-உஊ-ஏஐ-ஙச-ட஠-னப-யர-ஹ஺-ிீ-௉ொ-௏ௐ-௙௚-௟௠-௩௪-௯௰-௹௺-௿a-zA-Zａ-ｚＡ-Ｚ0-9０-９",e.ta.trimmer=e.trimmerSupport.generateTrimmer(e.ta.wordCharacters),e.Pipeline.registerFunction(e.ta.trimmer,"trimmer-ta"),e.ta.stopWordFilter=e.generateStopWordFilter("அங்கு அங்கே அது அதை அந்த அவர் அவர்கள் அவள் அவன் அவை ஆக ஆகவே ஆகையால் ஆதலால் ஆதலினால் ஆனாலும் ஆனால் இங்கு இங்கே இது இதை இந்த இப்படி இவர் இவர்கள் இவள் இவன் இவை இவ்வளவு உனக்கு உனது உன் உன்னால் எங்கு எங்கே எது எதை எந்த எப்படி எவர் எவர்கள் எவள் எவன் எவை எவ்வளவு எனக்கு எனது எனவே என் என்ன என்னால் ஏது ஏன் தனது தன்னால் தானே தான் நாங்கள் நாம் நான் நீ நீங்கள்".split(" ")),e.ta.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var t=e.wordcut;t.init(),e.ta.tokenizer=function(r){if(!arguments.length||null==r||void 0==r)return[];if(Array.isArray(r))return r.map(function(t){return isLunr2?new e.Token(t.toLowerCase()):t.toLowerCase()});var i=r.toString().toLowerCase().replace(/^\s+/,"");return t.cut(i).split("|")},e.Pipeline.registerFunction(e.ta.stemmer,"stemmer-ta"),e.Pipeline.registerFunction(e.ta.stopWordFilter,"stopWordFilter-ta")}});

DevDoc/assets/javascripts/lunr/min/lunr.te.min.js

@@ -0,0 +1 @@
+!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.te=function(){this.pipeline.reset(),this.pipeline.add(e.te.trimmer,e.te.stopWordFilter,e.te.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.te.stemmer))},e.te.wordCharacters="ఀ-ఄఅ-ఔక-హా-ౌౕ-ౖౘ-ౚౠ-ౡౢ-ౣ౦-౯౸-౿఼ఽ్ౝ౷౤౥",e.te.trimmer=e.trimmerSupport.generateTrimmer(e.te.wordCharacters),e.Pipeline.registerFunction(e.te.trimmer,"trimmer-te"),e.te.stopWordFilter=e.generateStopWordFilter("అందరూ అందుబాటులో అడగండి అడగడం అడ్డంగా అనుగుణంగా అనుమతించు అనుమతిస్తుంది అయితే ఇప్పటికే ఉన్నారు ఎక్కడైనా ఎప్పుడు ఎవరైనా ఎవరో ఏ ఏదైనా ఏమైనప్పటికి ఒక ఒకరు కనిపిస్తాయి కాదు కూడా గా గురించి చుట్టూ చేయగలిగింది తగిన తర్వాత దాదాపు దూరంగా నిజంగా పై ప్రకారం ప్రక్కన మధ్య మరియు మరొక మళ్ళీ మాత్రమే మెచ్చుకో వద్ద వెంట వేరుగా వ్యతిరేకంగా సంబంధం".split(" ")),e.te.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var t=e.wordcut;t.init(),e.te.tokenizer=function(r){if(!arguments.length||null==r||void 0==r)return[];if(Array.isArray(r))return r.map(function(t){return isLunr2?new e.Token(t.toLowerCase()):t.toLowerCase()});var i=r.toString().toLowerCase().replace(/^\s+/,"");return t.cut(i).split("|")},e.Pipeline.registerFunction(e.te.stemmer,"stemmer-te"),e.Pipeline.registerFunction(e.te.stopWordFilter,"stopWordFilter-te")}});

DevDoc/assets/javascripts/lunr/min/lunr.th.min.js

@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var r="2"==e.version[0];e.th=function(){this.pipeline.reset(),this.pipeline.add(e.th.trimmer),r?this.tokenizer=e.th.tokenizer:(e.tokenizer&&(e.tokenizer=e.th.tokenizer),this.tokenizerFn&&(this.tokenizerFn=e.th.tokenizer))},e.th.wordCharacters="[฀-๿]",e.th.trimmer=e.trimmerSupport.generateTrimmer(e.th.wordCharacters),e.Pipeline.registerFunction(e.th.trimmer,"trimmer-th");var t=e.wordcut;t.init(),e.th.tokenizer=function(i){if(!arguments.length||null==i||void 0==i)return[];if(Array.isArray(i))return i.map(function(t){return r?new e.Token(t):t});var n=i.toString().replace(/^\s+/,"");return t.cut(n).split("|")}}});

DevDoc/assets/javascripts/lunr/min/lunr.vi.min.js

@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.vi=function(){this.pipeline.reset(),this.pipeline.add(e.vi.stopWordFilter,e.vi.trimmer)},e.vi.wordCharacters="[A-Za-ẓ̀͐́͑̉̃̓ÂâÊêÔôĂ-ăĐ-đƠ-ơƯ-ư]",e.vi.trimmer=e.trimmerSupport.generateTrimmer(e.vi.wordCharacters),e.Pipeline.registerFunction(e.vi.trimmer,"trimmer-vi"),e.vi.stopWordFilter=e.generateStopWordFilter("là cái nhưng mà".split(" "))}});

DevDoc/assets/javascripts/lunr/min/lunr.zh.min.js

@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r(require("@node-rs/jieba")):r()(e.lunr)}(this,function(e){return function(r,t){if(void 0===r)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===r.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var i="2"==r.version[0];r.zh=function(){this.pipeline.reset(),this.pipeline.add(r.zh.trimmer,r.zh.stopWordFilter,r.zh.stemmer),i?this.tokenizer=r.zh.tokenizer:(r.tokenizer&&(r.tokenizer=r.zh.tokenizer),this.tokenizerFn&&(this.tokenizerFn=r.zh.tokenizer))},r.zh.tokenizer=function(n){if(!arguments.length||null==n||void 0==n)return[];if(Array.isArray(n))return n.map(function(e){return i?new r.Token(e.toLowerCase()):e.toLowerCase()});t&&e.load(t);var o=n.toString().trim().toLowerCase(),s=[];e.cut(o,!0).forEach(function(e){s=s.concat(e.split(" "))}),s=s.filter(function(e){return!!e});var u=0;return s.map(function(e,t){if(i){var n=o.indexOf(e,u),s={};return s.position=[n,e.length],s.index=t,u=n,new r.Token(e,s)}return e})},r.zh.wordCharacters="\\w一-龥",r.zh.trimmer=r.trimmerSupport.generateTrimmer(r.zh.wordCharacters),r.Pipeline.registerFunction(r.zh.trimmer,"trimmer-zh"),r.zh.stemmer=function(){return function(e){return e}}(),r.Pipeline.registerFunction(r.zh.stemmer,"stemmer-zh"),r.zh.stopWordFilter=r.generateStopWordFilter("的 一 不 在 人 有 是 为 為 以 于 於 上 他 而 后 後 之 来 來 及 了 因 下 可 到 由 这 這 与 與 也 此 但 并 並 个 個 其 已 无 無 小 我 们 們 起 最 再 今 去 好 只 又 或 很 亦 某 把 那 你 乃 它 吧 被 比 别 趁 当 當 从 從 得 打 凡 儿 兒 尔 爾 该 該 各 给 給 跟 和 何 还 還 即 几 幾 既 看 据 據 距 靠 啦 另 么 麽 每 嘛 拿 哪 您 凭 憑 且 却 卻 让 讓 仍 啥 如 若 使 谁 誰 虽 雖 随 隨 同 所 她 哇 嗡 往 些 向 沿 哟 喲 用 咱 则 則 怎 曾 至 致 着 著 诸 諸 自".split(" ")),r.Pipeline.registerFunction(r.zh.stopWordFilter,"stopWordFilter-zh")}});

DevDoc/assets/javascripts/lunr/tinyseg.js

@@ -0,0 +1,206 @@
+/**
+ * export the module via AMD, CommonJS or as a browser global
+ * Export code from https://github.com/umdjs/umd/blob/master/returnExports.js
+ */
+;(function (root, factory) {
+    if (typeof define === 'function' && define.amd) {
+        // AMD. Register as an anonymous module.
+        define(factory)
+    } else if (typeof exports === 'object') {
+        /**
+         * Node. Does not work with strict CommonJS, but
+         * only CommonJS-like environments that support module.exports,
+         * like Node.
+         */
+        module.exports = factory()
+    } else {
+        // Browser globals (root is window)
+        factory()(root.lunr);
+    }
+}(this, function () {
+    /**
+     * Just return a value to define the module export.
+     * This example returns an object, but the module
+     * can return a function as the exported value.
+     */
+
+    return function(lunr) {
+        // TinySegmenter 0.1 -- Super compact Japanese tokenizer in Javascript
+        // (c) 2008 Taku Kudo <taku@chasen.org>
+        // TinySegmenter is freely distributable under the terms of a new BSD licence.
+        // For details, see http://chasen.org/~taku/software/TinySegmenter/LICENCE.txt
+
+        function TinySegmenter() {
+          var patterns = {
+            "[一二三四五六七八九十百千万億兆]":"M",
+            "[一-龠々〆ヵヶ]":"H",
+            "[ぁ-ん]":"I",
+            "[ァ-ヴーｱ-ﾝﾞｰ]":"K",
+            "[a-zA-Zａ-ｚＡ-Ｚ]":"A",
+            "[0-9０-９]":"N"
+          }
+          this.chartype_ = [];
+          for (var i in patterns) {
+            var regexp = new RegExp(i);
+            this.chartype_.push([regexp, patterns[i]]);
+          }
+
+          this.BIAS__ = -332
+          this.BC1__ = {"HH":6,"II":2461,"KH":406,"OH":-1378};
+          this.BC2__ = {"AA":-3267,"AI":2744,"AN":-878,"HH":-4070,"HM":-1711,"HN":4012,"HO":3761,"IA":1327,"IH":-1184,"II":-1332,"IK":1721,"IO":5492,"KI":3831,"KK":-8741,"MH":-3132,"MK":3334,"OO":-2920};
+          this.BC3__ = {"HH":996,"HI":626,"HK":-721,"HN":-1307,"HO":-836,"IH":-301,"KK":2762,"MK":1079,"MM":4034,"OA":-1652,"OH":266};
+          this.BP1__ = {"BB":295,"OB":304,"OO":-125,"UB":352};
+          this.BP2__ = {"BO":60,"OO":-1762};
+          this.BQ1__ = {"BHH":1150,"BHM":1521,"BII":-1158,"BIM":886,"BMH":1208,"BNH":449,"BOH":-91,"BOO":-2597,"OHI":451,"OIH":-296,"OKA":1851,"OKH":-1020,"OKK":904,"OOO":2965};
+          this.BQ2__ = {"BHH":118,"BHI":-1159,"BHM":466,"BIH":-919,"BKK":-1720,"BKO":864,"OHH":-1139,"OHM":-181,"OIH":153,"UHI":-1146};
+          this.BQ3__ = {"BHH":-792,"BHI":2664,"BII":-299,"BKI":419,"BMH":937,"BMM":8335,"BNN":998,"BOH":775,"OHH":2174,"OHM":439,"OII":280,"OKH":1798,"OKI":-793,"OKO":-2242,"OMH":-2402,"OOO":11699};
+          this.BQ4__ = {"BHH":-3895,"BIH":3761,"BII":-4654,"BIK":1348,"BKK":-1806,"BMI":-3385,"BOO":-12396,"OAH":926,"OHH":266,"OHK":-2036,"ONN":-973};
+          this.BW1__ = {",と":660,",同":727,"B1あ":1404,"B1同":542,"、と":660,"、同":727,"」と":1682,"あっ":1505,"いう":1743,"いっ":-2055,"いる":672,"うし":-4817,"うん":665,"から":3472,"がら":600,"こう":-790,"こと":2083,"こん":-1262,"さら":-4143,"さん":4573,"した":2641,"して":1104,"すで":-3399,"そこ":1977,"それ":-871,"たち":1122,"ため":601,"った":3463,"つい":-802,"てい":805,"てき":1249,"でき":1127,"です":3445,"では":844,"とい":-4915,"とみ":1922,"どこ":3887,"ない":5713,"なっ":3015,"など":7379,"なん":-1113,"にし":2468,"には":1498,"にも":1671,"に対":-912,"の一":-501,"の中":741,"ませ":2448,"まで":1711,"まま":2600,"まる":-2155,"やむ":-1947,"よっ":-2565,"れた":2369,"れで":-913,"をし":1860,"を見":731,"亡く":-1886,"京都":2558,"取り":-2784,"大き":-2604,"大阪":1497,"平方":-2314,"引き":-1336,"日本":-195,"本当":-2423,"毎日":-2113,"目指":-724,"Ｂ１あ":1404,"Ｂ１同":542,"｣と":1682};
+          this.BW2__ = {"..":-11822,"11":-669,"――":-5730,"−−":-13175,"いう":-1609,"うか":2490,"かし":-1350,"かも":-602,"から":-7194,"かれ":4612,"がい":853,"がら":-3198,"きた":1941,"くな":-1597,"こと":-8392,"この":-4193,"させ":4533,"され":13168,"さん":-3977,"しい":-1819,"しか":-545,"した":5078,"して":972,"しな":939,"その":-3744,"たい":-1253,"たた":-662,"ただ":-3857,"たち":-786,"たと":1224,"たは":-939,"った":4589,"って":1647,"っと":-2094,"てい":6144,"てき":3640,"てく":2551,"ては":-3110,"ても":-3065,"でい":2666,"でき":-1528,"でし":-3828,"です":-4761,"でも":-4203,"とい":1890,"とこ":-1746,"とと":-2279,"との":720,"とみ":5168,"とも":-3941,"ない":-2488,"なが":-1313,"など":-6509,"なの":2614,"なん":3099,"にお":-1615,"にし":2748,"にな":2454,"によ":-7236,"に対":-14943,"に従":-4688,"に関":-11388,"のか":2093,"ので":-7059,"のに":-6041,"のの":-6125,"はい":1073,"はが":-1033,"はず":-2532,"ばれ":1813,"まし":-1316,"まで":-6621,"まれ":5409,"めて":-3153,"もい":2230,"もの":-10713,"らか":-944,"らし":-1611,"らに":-1897,"りし":651,"りま":1620,"れた":4270,"れて":849,"れば":4114,"ろう":6067,"われ":7901,"を通":-11877,"んだ":728,"んな":-4115,"一人":602,"一方":-1375,"一日":970,"一部":-1051,"上が":-4479,"会社":-1116,"出て":2163,"分の":-7758,"同党":970,"同日":-913,"大阪":-2471,"委員":-1250,"少な":-1050,"年度":-8669,"年間":-1626,"府県":-2363,"手権":-1982,"新聞":-4066,"日新":-722,"日本":-7068,"日米":3372,"曜日":-601,"朝鮮":-2355,"本人":-2697,"東京":-1543,"然と":-1384,"社会":-1276,"立て":-990,"第に":-1612,"米国":-4268,"１１":-669};
+          this.BW3__ = {"あた":-2194,"あり":719,"ある":3846,"い.":-1185,"い。":-1185,"いい":5308,"いえ":2079,"いく":3029,"いた":2056,"いっ":1883,"いる":5600,"いわ":1527,"うち":1117,"うと":4798,"えと":1454,"か.":2857,"か。":2857,"かけ":-743,"かっ":-4098,"かに":-669,"から":6520,"かり":-2670,"が,":1816,"が、":1816,"がき":-4855,"がけ":-1127,"がっ":-913,"がら":-4977,"がり":-2064,"きた":1645,"けど":1374,"こと":7397,"この":1542,"ころ":-2757,"さい":-714,"さを":976,"し,":1557,"し、":1557,"しい":-3714,"した":3562,"して":1449,"しな":2608,"しま":1200,"す.":-1310,"す。":-1310,"する":6521,"ず,":3426,"ず、":3426,"ずに":841,"そう":428,"た.":8875,"た。":8875,"たい":-594,"たの":812,"たり":-1183,"たる":-853,"だ.":4098,"だ。":4098,"だっ":1004,"った":-4748,"って":300,"てい":6240,"てお":855,"ても":302,"です":1437,"でに":-1482,"では":2295,"とう":-1387,"とし":2266,"との":541,"とも":-3543,"どう":4664,"ない":1796,"なく":-903,"など":2135,"に,":-1021,"に、":-1021,"にし":1771,"にな":1906,"には":2644,"の,":-724,"の、":-724,"の子":-1000,"は,":1337,"は、":1337,"べき":2181,"まし":1113,"ます":6943,"まっ":-1549,"まで":6154,"まれ":-793,"らし":1479,"られ":6820,"るる":3818,"れ,":854,"れ、":854,"れた":1850,"れて":1375,"れば":-3246,"れる":1091,"われ":-605,"んだ":606,"んで":798,"カ月":990,"会議":860,"入り":1232,"大会":2217,"始め":1681,"市":965,"新聞":-5055,"日,":974,"日、":974,"社会":2024,"ｶ月":990};
+          this.TC1__ = {"AAA":1093,"HHH":1029,"HHM":580,"HII":998,"HOH":-390,"HOM":-331,"IHI":1169,"IOH":-142,"IOI":-1015,"IOM":467,"MMH":187,"OOI":-1832};
+          this.TC2__ = {"HHO":2088,"HII":-1023,"HMM":-1154,"IHI":-1965,"KKH":703,"OII":-2649};
+          this.TC3__ = {"AAA":-294,"HHH":346,"HHI":-341,"HII":-1088,"HIK":731,"HOH":-1486,"IHH":128,"IHI":-3041,"IHO":-1935,"IIH":-825,"IIM":-1035,"IOI":-542,"KHH":-1216,"KKA":491,"KKH":-1217,"KOK":-1009,"MHH":-2694,"MHM":-457,"MHO":123,"MMH":-471,"NNH":-1689,"NNO":662,"OHO":-3393};
+          this.TC4__ = {"HHH":-203,"HHI":1344,"HHK":365,"HHM":-122,"HHN":182,"HHO":669,"HIH":804,"HII":679,"HOH":446,"IHH":695,"IHO":-2324,"IIH":321,"III":1497,"IIO":656,"IOO":54,"KAK":4845,"KKA":3386,"KKK":3065,"MHH":-405,"MHI":201,"MMH":-241,"MMM":661,"MOM":841};
+          this.TQ1__ = {"BHHH":-227,"BHHI":316,"BHIH":-132,"BIHH":60,"BIII":1595,"BNHH":-744,"BOHH":225,"BOOO":-908,"OAKK":482,"OHHH":281,"OHIH":249,"OIHI":200,"OIIH":-68};
+          this.TQ2__ = {"BIHH":-1401,"BIII":-1033,"BKAK":-543,"BOOO":-5591};
+          this.TQ3__ = {"BHHH":478,"BHHM":-1073,"BHIH":222,"BHII":-504,"BIIH":-116,"BIII":-105,"BMHI":-863,"BMHM":-464,"BOMH":620,"OHHH":346,"OHHI":1729,"OHII":997,"OHMH":481,"OIHH":623,"OIIH":1344,"OKAK":2792,"OKHH":587,"OKKA":679,"OOHH":110,"OOII":-685};
+          this.TQ4__ = {"BHHH":-721,"BHHM":-3604,"BHII":-966,"BIIH":-607,"BIII":-2181,"OAAA":-2763,"OAKK":180,"OHHH":-294,"OHHI":2446,"OHHO":480,"OHIH":-1573,"OIHH":1935,"OIHI":-493,"OIIH":626,"OIII":-4007,"OKAK":-8156};
+          this.TW1__ = {"につい":-4681,"東京都":2026};
+          this.TW2__ = {"ある程":-2049,"いった":-1256,"ころが":-2434,"しょう":3873,"その後":-4430,"だって":-1049,"ていた":1833,"として":-4657,"ともに":-4517,"もので":1882,"一気に":-792,"初めて":-1512,"同時に":-8097,"大きな":-1255,"対して":-2721,"社会党":-3216};
+          this.TW3__ = {"いただ":-1734,"してい":1314,"として":-4314,"につい":-5483,"にとっ":-5989,"に当た":-6247,"ので,":-727,"ので、":-727,"のもの":-600,"れから":-3752,"十二月":-2287};
+          this.TW4__ = {"いう.":8576,"いう。":8576,"からな":-2348,"してい":2958,"たが,":1516,"たが、":1516,"ている":1538,"という":1349,"ました":5543,"ません":1097,"ようと":-4258,"よると":5865};
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+          
+          return this;
+        }
+        TinySegmenter.prototype.ctype_ = function(str) {
+          for (var i in this.chartype_) {
+            if (str.match(this.chartype_[i][0])) {
+              return this.chartype_[i][1];
+            }
+          }
+          return "O";
+        }
+
+        TinySegmenter.prototype.ts_ = function(v) {
+          if (v) { return v; }
+          return 0;
+        }
+
+        TinySegmenter.prototype.segment = function(input) {
+          if (input == null || input == undefined || input == "") {
+            return [];
+          }
+          var result = [];
+          var seg = ["B3","B2","B1"];
+          var ctype = ["O","O","O"];
+          var o = input.split("");
+          for (i = 0; i < o.length; ++i) {
+            seg.push(o[i]);
+            ctype.push(this.ctype_(o[i]))
+          }
+          seg.push("E1");
+          seg.push("E2");
+          seg.push("E3");
+          ctype.push("O");
+          ctype.push("O");
+          ctype.push("O");
+          var word = seg[3];
+          var p1 = "U";
+          var p2 = "U";
+          var p3 = "U";
+          for (var i = 4; i < seg.length - 3; ++i) {
+            var score = this.BIAS__;
+            var w1 = seg[i-3];
+            var w2 = seg[i-2];
+            var w3 = seg[i-1];
+            var w4 = seg[i];
+            var w5 = seg[i+1];
+            var w6 = seg[i+2];
+            var c1 = ctype[i-3];
+            var c2 = ctype[i-2];
+            var c3 = ctype[i-1];
+            var c4 = ctype[i];
+            var c5 = ctype[i+1];
+            var c6 = ctype[i+2];
+            score += this.ts_(this.UP1__[p1]);
+            score += this.ts_(this.UP2__[p2]);
+            score += this.ts_(this.UP3__[p3]);
+            score += this.ts_(this.BP1__[p1 + p2]);
+            score += this.ts_(this.BP2__[p2 + p3]);
+            score += this.ts_(this.UW1__[w1]);
+            score += this.ts_(this.UW2__[w2]);
+            score += this.ts_(this.UW3__[w3]);
+            score += this.ts_(this.UW4__[w4]);
+            score += this.ts_(this.UW5__[w5]);
+            score += this.ts_(this.UW6__[w6]);
+            score += this.ts_(this.BW1__[w2 + w3]);
+            score += this.ts_(this.BW2__[w3 + w4]);
+            score += this.ts_(this.BW3__[w4 + w5]);
+            score += this.ts_(this.TW1__[w1 + w2 + w3]);
+            score += this.ts_(this.TW2__[w2 + w3 + w4]);
+            score += this.ts_(this.TW3__[w3 + w4 + w5]);
+            score += this.ts_(this.TW4__[w4 + w5 + w6]);
+            score += this.ts_(this.UC1__[c1]);
+            score += this.ts_(this.UC2__[c2]);
+            score += this.ts_(this.UC3__[c3]);
+            score += this.ts_(this.UC4__[c4]);
+            score += this.ts_(this.UC5__[c5]);
+            score += this.ts_(this.UC6__[c6]);
+            score += this.ts_(this.BC1__[c2 + c3]);
+            score += this.ts_(this.BC2__[c3 + c4]);
+            score += this.ts_(this.BC3__[c4 + c5]);
+            score += this.ts_(this.TC1__[c1 + c2 + c3]);
+            score += this.ts_(this.TC2__[c2 + c3 + c4]);
+            score += this.ts_(this.TC3__[c3 + c4 + c5]);
+            score += this.ts_(this.TC4__[c4 + c5 + c6]);
+        //  score += this.ts_(this.TC5__[c4 + c5 + c6]);    
+            score += this.ts_(this.UQ1__[p1 + c1]);
+            score += this.ts_(this.UQ2__[p2 + c2]);
+            score += this.ts_(this.UQ3__[p3 + c3]);
+            score += this.ts_(this.BQ1__[p2 + c2 + c3]);
+            score += this.ts_(this.BQ2__[p2 + c3 + c4]);
+            score += this.ts_(this.BQ3__[p3 + c2 + c3]);
+            score += this.ts_(this.BQ4__[p3 + c3 + c4]);
+            score += this.ts_(this.TQ1__[p2 + c1 + c2 + c3]);
+            score += this.ts_(this.TQ2__[p2 + c2 + c3 + c4]);
+            score += this.ts_(this.TQ3__[p3 + c1 + c2 + c3]);
+            score += this.ts_(this.TQ4__[p3 + c2 + c3 + c4]);
+            var p = "O";
+            if (score > 0) {
+              result.push(word);
+              word = "";
+              p = "B";
+            }
+            p1 = p2;
+            p2 = p3;
+            p3 = p;
+            word += seg[i];
+          }
+          result.push(word);
+
+          return result;
+        }
+
+        lunr.TinySegmenter = TinySegmenter;
+    };
+
+}));

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DevDoc/implementation/chunkreader.refs/index.html

@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -187,10 +214,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -208,8 +235,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -381,10 +436,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -402,8 +457,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -672,14 +727,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -784,14 +839,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -827,10 +1022,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +1043,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1110,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       

DevDoc/implementation/chunkreader/index.html

@@ -77,12 +77,24 @@
   
 
     
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../installation/">
+<span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
   </span>
 </a>
 </li>
 <li class="md-nav__item md-nav__item--nested">
-<input class="md-nav__toggle md-toggle" id="__nav_2" type="checkbox"/>
-<label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+<input class="md-nav__toggle md-toggle" id="__nav_3" type="checkbox"/>
+<label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
 <span class="md-ellipsis">
     
   
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 </label>
-<nav aria-expanded="false" aria-labelledby="__nav_2_label" class="md-nav" data-md-level="1">
-<label class="md-nav__title" for="__nav_2">
+<nav aria-expanded="false" aria-labelledby="__nav_3_label" class="md-nav" data-md-level="1">
+<label class="md-nav__title" for="__nav_3">
 <span class="md-nav__icon md-icon"></span>
             
   
@@ -160,6 +172,18 @@
   
 
     
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../theory/evolutionary_distances/">
+<span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
   </span>
 </a>
 </li>
@@ -167,8 +191,8 @@
 </nav>
 </li>
 <li class="md-nav__item md-nav__item--active md-nav__item--nested">
-<input checked="" class="md-nav__toggle md-toggle" id="__nav_3" type="checkbox"/>
-<label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+<input checked="" class="md-nav__toggle md-toggle" id="__nav_4" type="checkbox"/>
+<label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
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 </label>
-<nav aria-expanded="true" aria-labelledby="__nav_3_label" class="md-nav" data-md-level="1">
-<label class="md-nav__title" for="__nav_3">
+<nav aria-expanded="true" aria-labelledby="__nav_4_label" class="md-nav" data-md-level="1">
+<label class="md-nav__title" for="__nav_4">
 <span class="md-nav__icon md-icon"></span>
             
   
@@ -296,6 +320,15 @@
     </span>
 </a>
 </li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#future-work-parallel-gzip-decompression-in-xopen">
+<span class="md-ellipsis">
+      
+        Future work — parallel gzip decompression in xopen
+      
+    </span>
+</a>
+</li>
 </ul>
 </nav>
 </li>
@@ -372,11 +405,11 @@
 </a>
 </li>
 <li class="md-nav__item">
-<a class="md-nav__link" href="../obilayeredmap/">
+<a class="md-nav__link" href="../layer_tier/">
 <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -420,11 +453,71 @@
 </a>
 </li>
 <li class="md-nav__item">
-<a class="md-nav__link" href="../rebuild_filter/">
+<a class="md-nav__link" href="../merge_parallelism/">
 <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism &amp; memory
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../filtering/">
+<span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../select/">
+<span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../obitaxonomy/">
+<span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../benchmark_query_testing/">
+<span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../partition_layer_cache/">
+<span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -435,8 +528,8 @@
 </nav>
 </li>
 <li class="md-nav__item md-nav__item--nested">
-<input class="md-nav__toggle md-toggle" id="__nav_4" type="checkbox"/>
-<label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+<input class="md-nav__toggle md-toggle" id="__nav_5" type="checkbox"/>
+<label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
 <span class="md-ellipsis">
     
   
@@ -447,8 +540,8 @@
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 <span class="md-nav__icon md-icon"></span>
 </label>
-<nav aria-expanded="false" aria-labelledby="__nav_4_label" class="md-nav" data-md-level="1">
-<label class="md-nav__title" for="__nav_4">
+<nav aria-expanded="false" aria-labelledby="__nav_5_label" class="md-nav" data-md-level="1">
+<label class="md-nav__title" for="__nav_5">
 <span class="md-nav__icon md-icon"></span>
             
   
@@ -478,6 +571,42 @@
   
 
     
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../architecture/siblings/">
+<span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../architecture/numa_worker_pools/">
+<span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../architecture/numa_partition_runner/">
+<span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
   </span>
 </a>
 </li>
@@ -552,6 +681,15 @@
     </span>
 </a>
 </li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#future-work-parallel-gzip-decompression-in-xopen">
+<span class="md-ellipsis">
+      
+        Future work — parallel gzip decompression in xopen
+      
+    </span>
+</a>
+</li>
 </ul>
 </nav>
 </div>
@@ -659,6 +797,16 @@ The stream path (<code>NucStream</code> / <code>NucPage</code>) is described in
     FoundAt      --&gt; InHeader  : other</code></pre>
 <p><code>restart</code> is updated each time a <code>+</code> is found. When any state fails its expected input, the scan jumps back to <code>restart</code> and continues from there — guaranteeing that a <code>@</code> in a quality line cannot be accepted as a record start, because the <code>\n+\n</code> structure immediately following it (going backward) will not be found.</p>
 <p>Returns the byte offset of the <code>@</code> that starts the last complete record.</p>
+<hr/>
+<h2 id="future-work-parallel-gzip-decompression-in-xopen">Future work — parallel gzip decompression in <code>xopen</code></h2>
+<p><code>obiread::xopen</code> (<code>xopen.rs</code>) decompresses gzip via <code>niffler</code> → <code>flate2</code>, which is single-threaded (standard DEFLATE has no parallel-decodable structure). For large local gzip inputs this single-threaded decompression can become the throughput bottleneck feeding the <code>query</code>/<code>index</code>/<code>superkmer</code> pipelines, since chunk/page production for a given file is serialized ahead of the worker pool.</p>
+<p>Candidate: special-case local, on-disk, gzip-magic-detected paths in <code>open_raw</code>/<code>xopen</code> to use <a href="https://github.com/alekseizarubin/rapidgzip-rs"><code>rapidgzip-rs</code></a> (<code>ReaderBuilder::new().parallelism(n).open(path)</code>, implements <code>Read + Seek</code>) instead of <code>niffler</code>, keeping <code>niffler</code> for every other case: <code>stdin</code> (<code>-</code>), HTTP(S) sources, and all non-gzip formats (bzip2, xz, zstd — less used in practice here).</p>
+<p>Constraints identified so far (not yet validated against real data):
+- Branch point must move earlier than the current <code>decompress()</code> call in <code>open_raw</code> — rapidgzip's fast path needs the file <strong>path</strong>, not an already-opened generic <code>Read</code>, so the gzip/local-file detection has to happen before the generic <code>File::open</code> + <code>niffler::send::get_reader</code> path is taken.
+- <code>stdin</code> and HTTP sources are not seekable — they stay on <code>niffler</code> regardless; the gain only applies to local on-disk <code>.gz</code> files.
+- <code>rapidgzip-sys</code> vendors a native C++ engine: requires CMake ≥ 3.17, a C++17 compiler, and <code>nasm</code> on x86 targets — a real build-toolchain addition, not just a pure-Rust crate.
+- Low maturity of the Rust binding at review time (2 GitHub stars, ~15 commits, April 2026 latest release) — the underlying C++ engine is validated (HPDC 2023 paper), but the binding itself has limited production track record.</p>
+<p>Decision: parked for now. Before adopting, validate on real data: throughput vs. <code>niffler</code> on representative large <code>.gz</code> inputs, and byte-for-byte correctness of decompressed output.</p>
 </article>
 </div>
 <script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>

DevDoc/implementation/evidence_elimination.refs/index.html

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+
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+    </li>
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 <h1 id="coverage-implementationevidence_eliminationmd">Coverage: implementation/evidence_elimination.md</h1>
 <h2 id="code-couvert">Code couvert</h2>
 <ul>
-<li><code>obilayeredmap/src/fingerprint.rs</code> — FingerprintVec, FingerprintVecWriter, stockage b bits/slot, matches()</li>
-<li><code>obilayeredmap/src/mphf_layer.rs</code> — build_approx_evidence(dir, b, z), find_approx()</li>
-<li><code>obilayeredmap/src/meta.rs</code> — EvidenceKind::Approx { b, z }, LayerMeta</li>
+<li><code>obikindex/src/layer/fingerprint.rs</code> — FingerprintVec, FingerprintVecWriter, stockage b bits/slot, matches()</li>
+<li><code>obikindex/src/layer/mphf_layer.rs</code> — build_approx_evidence(dir, b, z), find_approx()</li>
+<li><code>obikindex/src/layer/meta.rs</code> — EvidenceKind::Approx { b, z }, LayerMeta</li>
 <li><code>obikindex/src/reindex.rs</code> — KmerIndex::reindex(), conversion exact↔approx en place</li>
 <li><code>obikmer/src/cmd/reindex.rs</code> — CLI reindex, options --approx, -z, --evidence-bits, --fp, --block-size</li>
 <li><code>obikmer/src/cmd/index.rs</code> — resolve_approx_params(), options --approx, -z, --evidence-bits, --fp</li>

DevDoc/implementation/evidence_elimination/index.html

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-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
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+  
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+      <a href="../benchmark_query_testing/" class="md-nav__link">
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+    NUMA-aware partition runner
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+  
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DevDoc/implementation/filtering/index.html

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+        <title>Kmer filtering - obikmer</title>
       
     
     
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+              Kmer filtering
             
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+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -387,10 +442,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -408,8 +463,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -678,14 +733,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -787,6 +842,34 @@
                 
   
   
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
     
   
   
@@ -806,7 +889,7 @@
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Kmer filtering
   
 
     
@@ -824,7 +907,7 @@
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Kmer filtering
   
 
     
@@ -958,6 +1041,45 @@
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="Quorum flags">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#negative-counts-offset-from-group-size" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Negative counts — offset from group size
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#validation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Validation
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#conservative-rounding-of-fraction-thresholds" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Conservative rounding of fraction thresholds
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
@@ -969,6 +1091,45 @@
     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#command-specific-options" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Command-specific options
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Command-specific options">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#dump-head-n" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        dump --head N
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#phylo-presence-threshold-n" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        phylo --presence-threshold N
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
@@ -991,6 +1152,118 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1013,10 +1286,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -1034,8 +1307,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1101,6 +1374,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1243,6 +1600,45 @@
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="Quorum flags">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#negative-counts-offset-from-group-size" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Negative counts — offset from group size
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#validation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Validation
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#conservative-rounding-of-fraction-thresholds" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Conservative rounding of fraction thresholds
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1254,6 +1650,45 @@
     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#command-specific-options" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Command-specific options
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Command-specific options">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#dump-head-n" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        dump --head N
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#phylo-presence-threshold-n" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        phylo --presence-threshold N
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
@@ -1285,11 +1720,12 @@
 
 
 <h1 id="kmer-filtering-and-ingroupoutgroup-predicates">Kmer filtering and ingroup/outgroup predicates</h1>
-<p>The <code>rebuild</code>, <code>dump</code>, and <code>unitig</code> commands all share the same filtering
-system. Filters can select k-mers based on per-genome quorum counts, optionally
-restricted to <strong>ingroup</strong> and <strong>outgroup</strong> genome sets derived from genome
-metadata.</p>
-<p><code>rebuild</code> additionally accepts <code>--min-total-count</code> / <code>--max-total-count</code> filters
+<p>The <code>filter</code>, <code>dump</code>, and <code>unitig</code> commands share the same filtering system,
+implemented as a shared <code>FilterArgs</code> clap argument group embedded in each command
+via <code>#[command(flatten)]</code>. Filters select k-mers based on per-genome quorum
+counts, optionally restricted to <strong>ingroup</strong> and <strong>outgroup</strong> genome sets derived
+from genome metadata. All rules described here apply identically to all three commands.</p>
+<p><code>filter</code> additionally accepts <code>--min-total-count</code> / <code>--max-total-count</code> filters
 that operate on the sum of counts across all genomes.</p>
 <h2 id="predicate-syntax">Predicate syntax</h2>
 <p>Each <code>--ingroup</code> and <code>--outgroup</code> flag takes a predicate of the form:</p>
@@ -1327,16 +1763,44 @@ that operate on the sum of counts across all genomes.</p>
 </table>
 <p>Multiple values separated by <code>|</code> are always OR-ed within the predicate.</p>
 <h3 id="path-matching-and">Path matching (<code>~</code> and <code>!~</code>)</h3>
-<p>Metadata values can represent hierarchical taxonomic paths such as
+<p>Metadata values can represent hierarchical concept paths such as
 <code>/Eukaryota/Viridiplantae/Streptophyta/Betulaceae/Betula/nana</code>.</p>
+<p>Stored taxonomy values always start with <code>/</code> (the root of the path).
+Query patterns do <strong>not</strong> need to start with <code>/</code> — a leading <code>/</code> is an optional
+start anchor, not a requirement.</p>
+<table>
+<thead>
+<tr>
+<th>Pattern form</th>
+<th>Semantics</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>A/B</code></td>
+<td>contiguous sub-path A then B, anywhere in the value</td>
+</tr>
+<tr>
+<td><code>/A/B</code></td>
+<td>value starts with A then B</td>
+</tr>
+<tr>
+<td><code>A/B$</code></td>
+<td>value ends with A then B</td>
+</tr>
+<tr>
+<td><code>/A/B$</code></td>
+<td>value is exactly A then B</td>
+</tr>
+<tr>
+<td><code>A@x/B</code></td>
+<td>A with class <code>x</code> followed by B with any class</td>
+</tr>
+</tbody>
+</table>
 <ul>
-<li><strong>Absolute pattern</strong> (starts with <code>/</code>): the value must start with the pattern
-  at a segment boundary.
-  <code>taxon~/Betulaceae/Betula</code> matches <code>/Betulaceae/Betula/nana</code> and
-  <code>/Betulaceae/Betula</code> but not <code>/Betulaceae/Betuloides/…</code>.</li>
-<li><strong>Bare segment</strong> (no leading <code>/</code>): the value must contain the pattern as an
-  exact path component anywhere.
-  <code>taxon~Betula</code> matches any path that has <code>Betula</code> as one of its segments.</li>
+<li><code>taxon~/Betulaceae/Betula</code> matches any path that starts with <code>Betulaceae</code> then <code>Betula</code>.</li>
+<li><code>taxon~Betula</code> matches any path containing <code>Betula</code> as a segment, anywhere.</li>
 </ul>
 <h3 id="missing-metadata-key-na">Missing metadata key → NA</h3>
 <p>If a genome does not carry the queried metadata key, the predicate returns <strong>NA</strong>.
@@ -1422,12 +1886,12 @@ cannot be classified are <strong>ignored</strong> in all quorum counts.</p>
 <tr>
 <td><code>--min-count N</code></td>
 <td>ingroup</td>
-<td>k-mer present in at least N ingroup genomes</td>
+<td>k-mer present in at least N ingroup genomes (N may be negative, see below)</td>
 </tr>
 <tr>
 <td><code>--max-count N</code></td>
 <td>ingroup</td>
-<td>k-mer present in at most N ingroup genomes</td>
+<td>k-mer present in at most N ingroup genomes (N may be negative, see below)</td>
 </tr>
 <tr>
 <td><code>--min-frac F</code></td>
@@ -1442,12 +1906,12 @@ cannot be classified are <strong>ignored</strong> in all quorum counts.</p>
 <tr>
 <td><code>--min-outgroup-count N</code></td>
 <td>outgroup</td>
-<td>k-mer present in at least N outgroup genomes</td>
+<td>k-mer present in at least N outgroup genomes (N may be negative, see below)</td>
 </tr>
 <tr>
 <td><code>--max-outgroup-count N</code></td>
 <td>outgroup</td>
-<td>k-mer present in at most N outgroup genomes</td>
+<td>k-mer present in at most N outgroup genomes (N may be negative, see below)</td>
 </tr>
 <tr>
 <td><code>--min-outgroup-frac F</code></td>
@@ -1462,12 +1926,12 @@ cannot be classified are <strong>ignored</strong> in all quorum counts.</p>
 <tr>
 <td><code>--min-total-count N</code></td>
 <td>all genomes</td>
-<td>sum of per-genome counts ≥ N (<code>rebuild</code> only)</td>
+<td>sum of per-genome counts ≥ N (<code>filter</code> only)</td>
 </tr>
 <tr>
 <td><code>--max-total-count N</code></td>
 <td>all genomes</td>
-<td>sum of per-genome counts ≤ N (<code>rebuild</code> only)</td>
+<td>sum of per-genome counts ≤ N (<code>filter</code> only)</td>
 </tr>
 <tr>
 <td><code>--presence-threshold N</code></td>
@@ -1476,15 +1940,184 @@ cannot be classified are <strong>ignored</strong> in all quorum counts.</p>
 </tr>
 </tbody>
 </table>
-<p>Defaults: mins = 0 (no lower bound), max counts = group size, max fracs = 1.0
-(no upper bound). A filter with all defaults is a no-op.</p>
+<h3 id="negative-counts-offset-from-group-size">Negative counts — offset from group size</h3>
+<p>The four integer count flags (<code>--min-count</code>, <code>--max-count</code>, <code>--min-outgroup-count</code>,
+<code>--max-outgroup-count</code>) accept <strong>negative</strong> values, interpreted as an offset counted
+down from the group size <code>n</code>, resolved at run time once <code>n</code> is known:</p>
+<table>
+<thead>
+<tr>
+<th>Value</th>
+<th>Effective threshold</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>N ≥ 0</code></td>
+<td>literal absolute count <code>N</code></td>
+</tr>
+<tr>
+<td><code>-x</code> (x &gt; 0)</td>
+<td><code>max(1, n − x)</code> — "all but x"</td>
+</tr>
+</tbody>
+</table>
+<p><code>-1</code> literally means <em>all but one</em>, <code>-2</code> <em>all but two</em>, and so on. This expresses
+a quorum relative to the group size that a plain fraction cannot state exactly
+(e.g. "present in every genome except at most one" is <code>n−1</code>, which is <code>0.9</code> for
+<code>n = 10</code> but <code>0.857…</code> for <code>n = 7</code>).</p>
+<p>The threshold is <strong>floored at 1</strong>, never 0: the negative form always keeps
+constraining the group. Without the floor, <code>--min-count -1</code> on a singleton
+ingroup (<code>n = 1</code>) would resolve to <code>0</code> ("at least 0") and silently drop the
+constraint; the floor makes it <code>1</code> ("present in that one genome") instead.</p>
+<p>To express a count of <code>0</code> (e.g. "absent from the ingroup"), use the literal <code>0</code>,
+not a negative — <code>0</code> and <code>-0</code> are indistinguishable, so the offset form starts at
+<code>-1</code>.</p>
+<blockquote>
+<p><strong>Edge case</strong> — on an <em>empty</em> group (<code>n = 0</code>, e.g. a predicate matching no
+genome), a negative count still resolves to <code>1</code>, an impossible constraint that
+rejects every k-mer. This is consistent with an empty group letting nothing
+through, but differs from the "no constraint" behaviour of the fraction flags.</p>
+</blockquote>
+<p><strong>Conditional defaults</strong> — the defaults for <code>--min-frac</code> and <code>--max-outgroup-count</code> depend on two conditions:
+whether the corresponding group was declared, <strong>and</strong> whether any quorum flag for that group was explicitly set.</p>
+<blockquote>
+<p><strong>Rule</strong>: declaring a group activates the smart default <strong>only if no quorum flag for that group is explicitly set</strong>.
+As soon as any quorum flag for a group is present on the command line, all defaults for that group revert to no-op values.</p>
+</blockquote>
+<table>
+<thead>
+<tr>
+<th><code>--ingroup</code></th>
+<th>Any ingroup quorum flag?</th>
+<th><code>--min-frac</code> default</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>not set</td>
+<td>—</td>
+<td>0.0 (no-op)</td>
+</tr>
+<tr>
+<td>set</td>
+<td>no</td>
+<td><strong>1.0</strong> — all ingroup genomes must carry the k-mer</td>
+</tr>
+<tr>
+<td>set</td>
+<td>yes</td>
+<td>0.0 — user controls quorum explicitly</td>
+</tr>
+</tbody>
+</table>
+<table>
+<thead>
+<tr>
+<th><code>--outgroup</code></th>
+<th>Any outgroup quorum flag?</th>
+<th><code>--max-outgroup-count</code> default</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>not set</td>
+<td>—</td>
+<td>outgroup size (no-op)</td>
+</tr>
+<tr>
+<td>set</td>
+<td>no</td>
+<td><strong>0</strong> — no outgroup genome may carry the k-mer</td>
+</tr>
+<tr>
+<td>set</td>
+<td>yes</td>
+<td>outgroup size — user controls quorum explicitly</td>
+</tr>
+</tbody>
+</table>
+<p>"Any ingroup quorum flag" means any of: <code>--min-count</code>, <code>--max-count</code>, <code>--min-frac</code>, <code>--max-frac</code>.<br />
+"Any outgroup quorum flag" means any of: <code>--min-outgroup-count</code>, <code>--max-outgroup-count</code>, <code>--min-outgroup-frac</code>, <code>--max-outgroup-frac</code>.</p>
+<p><strong>Why this rule?</strong> Setting any quorum flag signals explicit intent — the defaults are there to help when the user omits quorum entirely, not to interfere with deliberate constraints. Mixing implicit and explicit quorum on the same group would risk silent incoherence (e.g. <code>--max-count 0</code> with an implicit <code>--min-frac 1.0</code>).</p>
+<p>All other bounds default to 0 / group size / 0.0 / 1.0 regardless of whether groups are declared.</p>
+<h3 id="validation">Validation</h3>
+<p>After resolving defaults, the following are checked and cause an immediate error:</p>
+<table>
+<thead>
+<tr>
+<th>Condition</th>
+<th>Error</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--min-count &gt; --max-count</code></td>
+<td>incoherent bounds</td>
+</tr>
+<tr>
+<td><code>--min-frac &gt; --max-frac</code></td>
+<td>incoherent bounds</td>
+</tr>
+<tr>
+<td><code>--min-outgroup-count &gt; --max-outgroup-count</code></td>
+<td>incoherent bounds</td>
+</tr>
+<tr>
+<td><code>--min-outgroup-frac &gt; --max-outgroup-frac</code></td>
+<td>incoherent bounds</td>
+</tr>
+<tr>
+<td>any fraction outside <code>[0.0, 1.0]</code></td>
+<td>invalid value</td>
+</tr>
+</tbody>
+</table>
+<p>The check applies to the <strong>effective</strong> values (after defaults are resolved), so an explicit <code>--max-frac 0.5</code> with an implicit <code>--min-frac 1.0</code> would have been caught — but the rule above prevents that situation from arising in the first place.</p>
 <p>Fractions are computed over the size of the classified group, not over total
 genome count. An empty group (no genome classified as ingroup/outgroup) never
 triggers a filter failure.</p>
+<h3 id="conservative-rounding-of-fraction-thresholds">Conservative rounding of fraction thresholds</h3>
+<p>When a fraction threshold <code>F</code> is applied to a group of size <code>N</code>, the effective
+integer threshold is determined by the direction of the bound:</p>
+<table>
+<thead>
+<tr>
+<th>Bound</th>
+<th>Effective count</th>
+<th>Rounding</th>
+<th>Rationale</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--min-frac F</code></td>
+<td>k-mer in ≥ ⌈F·N⌉ genomes</td>
+<td><strong>ceil</strong></td>
+<td>stricter — a kmer present in exactly ⌊F·N⌋ genomes does not meet the fraction</td>
+</tr>
+<tr>
+<td><code>--max-frac F</code></td>
+<td>k-mer in ≤ ⌊F·N⌋ genomes</td>
+<td><strong>floor</strong></td>
+<td>stricter — a kmer present in ⌈F·N⌉ genomes already exceeds the fraction</td>
+</tr>
+</tbody>
+</table>
+<p>The same rule applies symmetrically to <code>--min-outgroup-frac</code> (ceil) and
+<code>--max-outgroup-frac</code> (floor). The outgroup direction is not inverted: the
+conservative rounding depends only on whether the bound is a minimum or a
+maximum, not on which group it applies to.</p>
+<p><strong>Example</strong> — <code>--min-frac 0.5</code> with an ingroup of 3 genomes:
+<code>⌈0.5 × 3⌉ = ⌈1.5⌉ = 2</code> → at least 2 of 3 ingroup genomes must carry the k-mer.</p>
+<p><strong>Implementation note</strong> — the filter evaluates <code>n / denom &lt; min_frac</code> directly
+(integer <code>n</code>, float comparison) rather than pre-computing <code>⌈F·N⌉</code>. This is
+mathematically equivalent for integer counts: <code>n / N &lt; F</code> ↔ <code>n &lt; F·N</code> ↔
+<code>n ≤ ⌈F·N⌉ − 1</code> ↔ <code>n &lt; ⌈F·N⌉</code>. No explicit rounding is needed.</p>
 <h2 id="examples">Examples</h2>
 <p>Keep k-mers specific to <em>Betula nana</em> — present in at least 2 <em>B. nana</em> genomes
 and absent from every other genome in the index:</p>
-<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>rebuild<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;species=Betula_nana&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;*&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--min-count<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="se">\</span>
@@ -1492,7 +2125,7 @@ and absent from every other genome in the index:</p>
 </code></pre></div>
 <p>Keep k-mers found in at least 2 <em>Betula nana</em> genomes and absent from all
 other <em>Betula</em>:</p>
-<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>rebuild<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;species=Betula_nana&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;genus=Betula&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--min-count<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="se">\</span>
@@ -1500,21 +2133,28 @@ other <em>Betula</em>:</p>
 </code></pre></div>
 <p>Use taxonomic paths — keep k-mers present in ≥ 50 % of the <em>Betula</em> clade
 and in fewer than 10 % of everything outside <em>Betulaceae</em>:</p>
-<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>rebuild<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;taxon~/Betulaceae/Betula&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;taxon!~/Betulaceae&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--min-frac<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--max-outgroup-frac<span class="w"> </span><span class="m">0</span>.1
 </code></pre></div>
 <p>Multiple outgroup predicates (OR): exclude k-mers present in <em>Alnus</em> or <em>Carpinus</em>:</p>
-<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>rebuild<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;genus=Betula&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;genus=Alnus&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;genus=Carpinus&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--max-outgroup-count<span class="w"> </span><span class="m">0</span>
 </code></pre></div>
-<p>The same flags work identically for <code>dump</code> and <code>unitig</code>. To dump only k-mers
-specific to <em>Betula nana</em>:</p>
+<p>Noise-tolerant core — keep k-mers present in <em>all but one</em> ingroup genome
+(<code>-1</code> = <code>n−1</code>) and absent from <em>all but one</em> of the outgroup:</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;genus=Betula&quot;</span><span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;*&quot;</span><span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--min-count<span class="w"> </span>-1<span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--max-outgroup-count<span class="w"> </span>-1
+</code></pre></div>
+<p>To dump only k-mers specific to <em>Betula nana</em>:</p>
 <div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>dump<span class="w"> </span>myindex<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;species=Betula_nana&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;*&quot;</span><span class="w"> </span><span class="se">\</span>
@@ -1528,10 +2168,25 @@ specific to <em>Betula nana</em>:</p>
 <span class="w">  </span>--min-count<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--max-outgroup-count<span class="w"> </span><span class="m">0</span>
 </code></pre></div>
+<h2 id="command-specific-options">Command-specific options</h2>
+<h3 id="dump-head-n"><code>dump --head N</code></h3>
+<p>Stops output after the first N k-mers that pass all active filters.
+Iteration terminates immediately — subsequent partitions and layers are not scanned.
+Useful for quick inspection of large indexes without loading the entire dataset.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>dump<span class="w"> </span>myindex<span class="w"> </span>--head<span class="w"> </span><span class="m">100</span>
+obikmer<span class="w"> </span>dump<span class="w"> </span>myindex<span class="w"> </span>--head<span class="w"> </span><span class="m">20</span><span class="w"> </span>--ingroup<span class="w"> </span><span class="s2">&quot;species=Betula_nana&quot;</span><span class="w"> </span>--min-count<span class="w"> </span><span class="m">1</span>
+</code></pre></div>
+<h3 id="phylo-presence-threshold-n"><code>phylo --presence-threshold N</code></h3>
+<p>When computing Jaccard distance on a <strong>count index</strong>, a k-mer is considered present in a genome if its count is ≥ N (default 1).
+This option is independent of the <code>--presence-threshold</code> used in filtering.</p>
+<div class="highlight"><pre><span></span><code><span class="c1"># Jaccard treating kmers with count ≥ 2 as present</span>
+obikmer<span class="w"> </span>phylo<span class="w"> </span>myindex<span class="w"> </span>--metric<span class="w"> </span>jaccard<span class="w"> </span>--presence-threshold<span class="w"> </span><span class="m">2</span>
+</code></pre></div>
+<p>This parameter has no effect on presence/absence indexes (where values are already 0/1) or on metrics other than Jaccard.</p>
 <h2 id="implementation">Implementation</h2>
 <ul>
 <li>
-<p><strong><code>obikpartitionner::filter::GroupQuorumFilter</code></strong> — implements <code>KmerFilter</code>
+<p><strong><code>obikindex::partition::filter::GroupQuorumFilter</code></strong> — implements <code>KmerFilter</code>
   using pre-computed ingroup and outgroup index vectors. The heavy logic
   (predicate parsing, three-value evaluation, genome classification) happens
   once before any iteration; each k-mer row evaluation is a simple index
@@ -1539,14 +2194,14 @@ specific to <em>Betula nana</em>:</p>
 </li>
 <li>
 <p><strong><code>obikmer::cmd::predicate::FilterArgs</code></strong> — shared <code>clap</code> argument group
-  embedded via <code>#[command(flatten)]</code> in <code>RebuildArgs</code>, <code>DumpArgs</code>, and
+  embedded via <code>#[command(flatten)]</code> in <code>FilterArgs</code>, <code>DumpArgs</code>, and
   <code>UnitigArgs</code>. <code>FilterArgs::build_filters()</code> returns a ready-to-use filter
   list.</p>
 </li>
 <li>
-<p><strong><code>obikpartitionner::KmerPartition::iter_partition_kmers</code></strong> — accepts
+<p><strong><code>obikindex::partition::KmerPartition::iter_partition_kmers</code></strong> — accepts
   <code>filters: &amp;[Box&lt;dyn KmerFilter&gt;]</code> and applies them per-kmer before invoking
-  the callback. <code>rebuild</code>, <code>dump</code>, and <code>unitig</code> all go through this single
+  the callback. <code>filter</code>, <code>dump</code>, and <code>unitig</code> all go through this single
   entry point.</p>
 </li>
 </ul>

DevDoc/implementation/kmer.refs/index.html

@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
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+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -187,10 +214,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -208,8 +235,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
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+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
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+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -381,10 +436,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -402,8 +457,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
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+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -672,14 +727,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -784,14 +839,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -827,10 +1022,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
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+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +1043,8 @@
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           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
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+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1110,90 @@
 
               
             
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+  
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+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
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+            
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+  
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+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
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+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
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+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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DevDoc/implementation/kmer/index.html

@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
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@@ -363,6 +390,34 @@
 
               
             
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+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
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+    Central-position SNP distance (discussion)
+  
+
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+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
           </ul>
         </nav>
       
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -408,8 +463,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -813,14 +868,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -925,14 +980,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -968,10 +1163,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -989,8 +1184,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1056,6 +1251,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       

DevDoc/implementation/layer_tier.refs/index.html

@@ -19,7 +19,7 @@
     
     
       
-        <title>Obilayeredmap.refs - obikmer</title>
+        <title>Layer tier.refs - obikmer</title>
       
     
     
@@ -60,7 +60,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#coverage-implementationobilayeredmapmd" class="md-skip">
+        <a href="#coverage-implementationlayer_tiermd" class="md-skip">
           Skip to content
         </a>
       
@@ -96,7 +96,7 @@
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Obilayeredmap.refs
+              Layer tier.refs
             
           </span>
         </div>
@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -187,10 +214,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -208,8 +235,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -381,10 +436,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -402,8 +457,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -672,14 +727,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -784,14 +839,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -827,10 +1022,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +1043,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1110,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -988,15 +1267,15 @@
 
 
 <!-- coverage sidecar — ne pas ajouter au nav mkdocs -->
-<h1 id="coverage-implementationobilayeredmapmd">Coverage: implementation/obilayeredmap.md</h1>
+<h1 id="coverage-implementationlayer_tiermd">Coverage: implementation/layer_tier.md</h1>
 <h2 id="code-couvert">Code couvert</h2>
 <ul>
-<li><code>obilayeredmap/src/mphf_layer.rs</code> — MphfLayer, LayerEvidence enum (Exact/Approx), find(), find_exact(), find_approx()</li>
-<li><code>obilayeredmap/src/layer.rs</code> — Layer<D>, trait LayerData, modes () / PersistentCompactIntMatrix / PersistentBitMatrix, build(), build_evidence(), append_genome_column()</li>
-<li><code>obilayeredmap/src/map.rs</code> — LayeredMap<D>, push_layer(), query()</li>
-<li><code>obilayeredmap/src/evidence.rs</code> — Evidence, EvidenceWriter, encodage chunk_id:rank</li>
-<li><code>obilayeredmap/src/fingerprint.rs</code> — FingerprintVec, FingerprintVecWriter, matches()</li>
-<li><code>obilayeredmap/src/meta.rs</code> — LayerMeta, EvidenceKind (Exact / Approx { b, z })</li>
+<li><code>obikindex/src/layer/mphf_layer.rs</code> — MphfLayer, LayerEvidence enum (Exact/Approx), find(), find_exact(), find_approx()</li>
+<li><code>obikindex/src/layer/typed_layer.rs</code> — Layer<D>, trait LayerData, modes () / PersistentCompactIntMatrix / PersistentBitMatrix, build(), build_evidence(), append_genome_column()</li>
+<li><code>obikindex/src/layer/map.rs</code> — LayeredMap<D>, push_layer(), query()</li>
+<li><code>obikindex/src/layer/evidence.rs</code> — Evidence, EvidenceWriter, encodage chunk_id:rank</li>
+<li><code>obikindex/src/layer/fingerprint.rs</code> — FingerprintVec, FingerprintVecWriter, matches()</li>
+<li><code>obikindex/src/layer/meta.rs</code> — LayerMeta, EvidenceKind (Exact / Approx { b, z })</li>
 </ul>
 <h2 id="notes">Notes</h2>
 <p>FORT RISQUE DE DÉRIVE. C'est le fichier le plus affecté par les changements récents :

DevDoc/implementation/layer_tier/index.html

@@ -23,7 +23,7 @@
     
     
       
-        <title>obilayeredmap crate - obikmer</title>
+        <title>obikindex layer tier - obikmer</title>
       
     
     
@@ -64,7 +64,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#obilayeredmap-layered-kmer-index-crate" class="md-skip">
+        <a href="#obikindexlayer-the-layer-tier" class="md-skip">
           Skip to content
         </a>
       
@@ -100,7 +100,7 @@
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              obilayeredmap crate
+              obikindex layer tier
             
           </span>
         </div>
@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -212,8 +239,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -387,10 +442,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -408,8 +463,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -694,7 +749,7 @@
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -712,7 +767,7 @@
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -885,6 +940,67 @@
       </ul>
     </nav>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#layerd-raw-mapping-iteration-and-batch-access" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Layer\&lt;D> — raw mapping, iteration, and batch access
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Layer\&lt;D&gt; — raw mapping, iteration, and batch access">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#raw-kmer-slot-mapping" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Raw kmer → slot mapping
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#kmer-iteration" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Kmer iteration
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#batch-lookup-on-payload-vectorsviews" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Batch lookup on payload vectors/views
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#sub_matrix-fill_sub_matrix" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        sub_matrix / fill_sub_matrix
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
         <li class="md-nav__item">
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+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
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+  <a href="#kmer-iteration" class="md-nav__link">
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+  <a href="#batch-lookup-on-payload-vectorsviews" class="md-nav__link">
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+  <a href="#sub_matrix-fill_sub_matrix" class="md-nav__link">
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+  
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@@ -1550,9 +1951,9 @@
 
 
 
-<h1 id="obilayeredmap-layered-kmer-index-crate">obilayeredmap — layered kmer index crate</h1>
+<h1 id="obikindexlayer-the-layer-tier">obikindex::layer — the Layer tier</h1>
 <h2 id="purpose">Purpose</h2>
-<p><code>obilayeredmap</code> implements a persistent, incrementally extensible kmer index. Each layer covers a disjoint kmer set and wraps a <code>ptr_hash</code> MPHF with associated per-slot data. Adding a new dataset never rebuilds existing layers.</p>
+<p><code>obikindex::layer</code> (the <code>layer/</code> submodule of the <code>obikindex</code> crate — a standalone <code>obilayeredmap</code> crate until 2026-08-21, folded back in alongside <code>obikpartition</code> as part of a broader <code>Index { Partition { Layer } }</code> submodule regrouping) implements a persistent, incrementally extensible kmer index. Each layer covers a disjoint kmer set and wraps a <code>ptr_hash</code> MPHF with associated per-slot data. Adding a new dataset never rebuilds existing layers.</p>
 <hr />
 <h2 id="three-usage-modes">Three usage modes</h2>
 <p>The MPHF + evidence infrastructure is the same for all modes. The <strong>payload</strong> varies.</p>
@@ -1777,6 +2178,38 @@
 </code></pre></div>
 <p>Mode 3 (<code>PersistentBitMatrix</code>) has no <code>push_layer</code> on <code>LayeredMap</code>; callers build directly via <code>Layer&lt;PersistentBitMatrix&gt;::build_presence</code>.</p>
 <hr />
+<h2 id="layerd-raw-mapping-iteration-and-batch-access">Layer\&lt;D&gt; — raw mapping, iteration, and batch access</h2>
+<p>Beyond <code>query</code>/<code>find</code> (membership-checked), <code>Layer&lt;D&gt;</code> exposes lower-level access used by consumers that already know a kmer is in the layer (e.g. cross-partition sibling resolution) or that need to sweep every kmer/slot without paying for a membership check each time.</p>
+<h3 id="raw-kmer-slot-mapping">Raw kmer → slot mapping</h3>
+<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">index</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">kmer</span><span class="p">:</span><span class="w"> </span><span class="nc">CanonicalKmer</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="kt">usize</span>
+<span class="nc">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">index_batch</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">kmers</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="p">[</span><span class="n">CanonicalKmer</span><span class="p">])</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="kt">usize</span><span class="o">&gt;</span>
+</code></pre></div>
+<p>Pure MPHF mapping, no evidence/fingerprint check — equivalent to <code>MphfOnly::index</code>. Only meaningful when the caller already knows <code>kmer</code> belongs to the layer; on an absent kmer the MPHF still returns <em>some</em> slot (undefined, not <code>None</code>).</p>
+<h3 id="kmer-iteration">Kmer iteration</h3>
+<p>Four iterators, all built from <code>unitigs.bin</code> (physical layout order, <strong>not</strong> correlated with MPHF slot numbers):</p>
+<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">iter_kmers</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">KmerIter</span><span class="o">&lt;&#39;</span><span class="nb">_</span><span class="o">&gt;</span>
+<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">enumerate_kmers</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">Enumerate</span><span class="o">&lt;</span><span class="n">KmerIter</span><span class="o">&lt;&#39;</span><span class="nb">_</span><span class="o">&gt;&gt;</span><span class="w">              </span><span class="c1">// (order_index, kmer)</span>
+<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">iter_kmers_batch</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">n</span><span class="p">:</span><span class="w"> </span><span class="kt">usize</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">KmerBatchIter</span><span class="o">&lt;&#39;</span><span class="nb">_</span><span class="o">&gt;</span><span class="w">          </span><span class="c1">// Vec&lt;CanonicalKmer&gt; of size ≤ n</span>
+<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">enumerate_kmers_batch</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">n</span><span class="p">:</span><span class="w"> </span><span class="kt">usize</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">impl</span><span class="w"> </span><span class="nb">Iterator</span><span class="o">&lt;</span><span class="n">Item</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">(</span><span class="kt">usize</span><span class="p">,</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="n">CanonicalKmer</span><span class="o">&gt;</span><span class="p">)</span><span class="o">&gt;</span><span class="w"> </span><span class="o">+</span><span class="w"> </span><span class="nb">Send</span><span class="w"> </span><span class="o">+</span><span class="w"> </span><span class="o">&#39;</span><span class="nb">static</span>
+</code></pre></div>
+<p><code>KmerIter</code>/<code>KmerBatchIter</code> own a clone of the underlying <code>Arc&lt;UnitigFileReader&gt;</code> rather than borrowing <code>self</code> — <code>Send + 'static</code>, streamed from disk one kmer at a time, never materialised as a whole. Multiple instances can coexist concurrently, each with its own cursor. <code>enumerate_kmers_batch</code>'s index is the batch's starting offset in iteration order (a multiple of <code>n</code> except for the final, possibly shorter, batch).</p>
+<h3 id="batch-lookup-on-payload-vectorsviews">Batch lookup on payload vectors/views</h3>
+<p><code>PersistentCompactIntVec</code>, <code>PersistentBitVec</code>, <code>IntSliceView</code>, <code>BitSliceView</code> all expose:</p>
+<div class="highlight"><pre><span></span><code><span class="k">fn</span><span class="w"> </span><span class="nf">get_batch</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">slots</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="p">[</span><span class="kt">usize</span><span class="p">])</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="n">T</span><span class="o">&gt;</span>
+<span class="k">fn</span><span class="w"> </span><span class="nf">fill_batch</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">slots</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="p">[</span><span class="kt">usize</span><span class="p">],</span><span class="w"> </span><span class="n">out</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="nc">mut</span><span class="w"> </span><span class="p">[</span><span class="n">T</span><span class="p">])</span>
+</code></pre></div>
+<p>Both sort <code>slots</code> internally for sequential mmap access, then reorder results back to the caller's original order. <code>fill_batch</code> fills a caller-provided buffer, avoiding the <code>Vec</code> allocation.</p>
+<h3 id="sub_matrix-fill_sub_matrix">sub_matrix / fill_sub_matrix</h3>
+<div class="highlight"><pre><span></span><code><span class="c1">// Layer&lt;PersistentCompactIntMatrix&gt;</span>
+<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">sub_matrix</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">slots</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="p">[</span><span class="kt">usize</span><span class="p">])</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="nb">Vec</span><span class="o">&lt;</span><span class="kt">u32</span><span class="o">&gt;&gt;</span><span class="w">            </span><span class="c1">// column-first</span>
+<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">fill_sub_matrix</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">slots</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="p">[</span><span class="kt">usize</span><span class="p">],</span><span class="w"> </span><span class="n">out</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="nc">mut</span><span class="w"> </span><span class="p">[</span><span class="nb">Vec</span><span class="o">&lt;</span><span class="kt">u32</span><span class="o">&gt;</span><span class="p">])</span>
+
+<span class="c1">// Layer&lt;PersistentBitMatrix&gt; (and any D: BinaryMatrix, e.g. PersistentSparseBitMatrix)</span>
+<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">sub_matrix</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">slots</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="p">[</span><span class="kt">usize</span><span class="p">])</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="nb">Vec</span><span class="o">&lt;</span><span class="kt">bool</span><span class="o">&gt;&gt;</span>
+<span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">fill_sub_matrix</span><span class="p">(</span><span class="o">&amp;</span><span class="bp">self</span><span class="p">,</span><span class="w"> </span><span class="n">slots</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="p">[</span><span class="kt">usize</span><span class="p">],</span><span class="w"> </span><span class="n">out</span><span class="p">:</span><span class="w"> </span><span class="kp">&amp;</span><span class="nc">mut</span><span class="w"> </span><span class="p">[</span><span class="nb">Vec</span><span class="o">&lt;</span><span class="kt">bool</span><span class="o">&gt;</span><span class="p">])</span>
+</code></pre></div>
+<p>Column-first to match the on-disk column-major layout. <code>fill_sub_matrix</code> sorts <code>slots</code> once, then calls each column's <code>fill_batch</code> in turn — no redundant per-column sort. On <code>PersistentSparseBitMatrix</code> (k-mer-major, no column method) this degrades to a row-by-row decode; see <a href="../../architecture/siblings/">siblings.md</a>.</p>
+<hr />
 <h2 id="layeredstores-and-aggregation-traits">LayeredStore\&lt;S&gt; and aggregation traits</h2>
 <p><code>LayeredStore&lt;S&gt;</code> is a generic aggregation wrapper over <code>Vec&lt;S&gt;</code>. It propagates three traits from <code>obicompactvec::traits</code> up the hierarchy via blanket impls:</p>
 <div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">struct</span><span class="w"> </span><span class="nc">LayeredStore</span><span class="o">&lt;</span><span class="n">S</span><span class="o">&gt;</span><span class="p">(</span><span class="k">pub</span><span class="w"> </span><span class="nb">Vec</span><span class="o">&lt;</span><span class="n">S</span><span class="o">&gt;</span><span class="p">);</span>

DevDoc/implementation/merge.refs/index.html

@@ -178,6 +178,33 @@
   
   
   
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+      <a href="../../installation/" class="md-nav__link">
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@@ -672,14 +727,14 @@
   
   
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-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
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-    obilayeredmap crate
+    obikindex layer tier
   
 
     
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-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
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+      <a href="../obitaxonomy/" class="md-nav__link">
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+              
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+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
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+  
+    Sibling annex (discussion)
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+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
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+  
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+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
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+  <span class="md-ellipsis">
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+    NUMA-aware partition runner
+  
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@@ -992,9 +1271,9 @@
 <h2 id="code-couvert">Code couvert</h2>
 <ul>
 <li><code>obikindex/src/merge.rs</code> — <code>KmerIndex::merge()</code>, validation de compatibilité d'évidence, <code>validate_evidence_compat()</code></li>
-<li><code>obikpartitionner/src/merge_layer.rs</code> — <code>merge_partition()</code>, construction de la nouvelle layer, paramètre <code>block_bits</code></li>
-<li><code>obikpartitionner/src/rebuild_layer.rs</code> — <code>rebuild_partition()</code>, paramètre <code>block_bits</code></li>
-<li><code>obilayeredmap/src/layer.rs</code> — <code>Layer::append_genome_column()</code> (PersistentCompactIntMatrix et PersistentBitMatrix)</li>
+<li><code>obikindex/src/partition/merge_layer.rs</code> — <code>merge_partition()</code>, construction de la nouvelle layer, paramètre <code>block_bits</code></li>
+<li><code>obikindex/src/partition/rebuild_layer.rs</code> — <code>rebuild_partition()</code>, paramètre <code>block_bits</code></li>
+<li><code>obikindex/src/layer/typed_layer.rs</code> — <code>Layer::append_genome_column()</code> (PersistentCompactIntMatrix et PersistentBitMatrix)</li>
 <li><code>obicompactvec/src/intmatrix.rs</code> — <code>append_column</code> pour PersistentCompactIntMatrix</li>
 <li><code>obicompactvec/src/bitmatrix.rs</code> — <code>append_column</code> pour PersistentBitMatrix</li>
 </ul>

DevDoc/implementation/merge/index.html

@@ -12,7 +12,7 @@
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+      <a href="../../installation/" class="md-nav__link">
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+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
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-    obilayeredmap crate
+    obikindex layer tier
   
 
     
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     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#known-issue-not-yet-fixed-2026-08-28" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Known issue (not yet fixed, 2026-08-28)
+      
+    </span>
+  </a>
+  
 </li>
       
     </ul>
@@ -997,14 +1063,154 @@
   
   
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+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
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-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
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+
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+    </li>
+  
+
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+            
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+      <a href="../filtering/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
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+  </span>
+  
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+      <a href="../select/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
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+  
+    Select command
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+  </span>
+  
+  
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+
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+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
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+  
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+      <a href="../benchmark_query_testing/" class="md-nav__link">
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+    Benchmark: query-path testing
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+  
+    Partition and layer caching (discussion)
   
 
     
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+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
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+  
+  
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+
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+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
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+
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+    </li>
+  
+
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+            
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     </span>
   </a>
   
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#known-issue-not-yet-fixed-2026-08-28" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Known issue (not yet fixed, 2026-08-28)
+      
+    </span>
+  </a>
+  
 </li>
       
     </ul>
@@ -1516,6 +1817,14 @@ spectrums/
   &lt;label&gt;.json               ← one file per genome, rebuilt from all sources
 index.meta                   ← complete genome list + evidence kind written at bootstrap
 </code></pre></div>
+<p><code>mphf.bin</code>/<code>unitigs.bin</code>/<code>evidence.bin</code>/<code>unitigs.bin.idx</code>/<code>fingerprint.bin</code>/<code>layer_meta.json</code> marked "unchanged" above are hard-linked from the base source's own files during the bootstrap copy (2026-08-28), not copied — <code>merge_partition</code> never rewrites them for pre-existing layers, only the <code>presence</code>/<code>counts</code> subdirectory gets widened in place, so only that subdirectory is a real, independent copy. Falls back to a real copy per file if linking itself fails (different filesystems). Verified: source files are byte-identical (checksummed) before/after a normal merge.</p>
+<h2 id="known-issue-not-yet-fixed-2026-08-28">Known issue (not yet fixed, 2026-08-28)</h2>
+<p>Merging an index against itself — literally the same directory passed twice as separate source arguments (e.g. <code>obikmer merge -o out IDX IDX --rename-duplicates</code>) — panics deep in the MPHF's rank-select structure (<code>common_traits::select_in_word</code>, <code>assertion failed: rank &lt; self.count_ones()</code>), inside <code>MphfLayer::find</code> called from <code>merge_partition</code>'s "is this source kmer already in dst" check against the bootstrap-copied <code>dst_layers</code>. Root cause not identified; ruled out so far:</p>
+<ul>
+<li><strong>Not an empty-new-layer issue</strong>: a source contributing zero new kmers (verified both as the sole additional source and as a third, fully-redundant source in a 3-way merge) is handled correctly — no layer is created for it, no crash, exit 0.</li>
+<li><strong>Not caused by the hard-link change above</strong>: verified via checksum that a normal (two distinct sources) merge leaves every source file byte-identical.</li>
+</ul>
+<p>Only reproduces when <code>sources[0]</code> and <code>sources[1]</code> are the exact same on-disk path opened as two independent <code>KmerIndex</code> handles — an artificial scenario (nobody merges an index with itself intentionally), deprioritized rather than investigated further for now. Does terminate cleanly rather than hang, since <code>PartitionRunner</code>'s panic propagation fix (see <code>architecture/numa_partition_runner.md</code>) now surfaces it as a normal process panic/exit 101 instead of a silent deadlock.</p>
 
 
 

DevDoc/implementation/mphf.refs/index.html

@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
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+    Installation
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+    obikindex layer tier
   
 
     
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-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+      <a href="../filtering/" class="md-nav__link">
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+  
+    Kmer filtering
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+    
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+      <a href="../select/" class="md-nav__link">
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+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
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+
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+            
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+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
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+  </span>
+  
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+    </li>
+  
+
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+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
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+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
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+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
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+              
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+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
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+    
+  
+    Sibling annex (discussion)
+  
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+  
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+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
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+  </span>
+  
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+    </li>
+  
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+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
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+  </span>
+  
+  
+
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+    </li>
+  
+
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+            
           </ul>
         </nav>
       
@@ -991,8 +1270,8 @@
 <h1 id="coverage-implementationmphfmd">Coverage: implementation/mphf.md</h1>
 <h2 id="code-couvert">Code couvert</h2>
 <ul>
-<li><code>obilayeredmap/src/mphf_layer.rs</code> — type Mphf (PtrHash + CubicEps + CachelineEfVec + Xx64), construction en 2 passes, <code>build()</code>, <code>build_exact_evidence()</code>, <code>build_approx_evidence()</code>, <code>build_evidence()</code></li>
-<li><code>obikpartitionner/src/index_layer.rs</code> — <code>build_index_layer()</code> avec passage de <code>block_bits</code></li>
+<li><code>obikindex/src/layer/mphf_layer.rs</code> — type Mphf (PtrHash + CubicEps + CachelineEfVec + Xx64), construction en 2 passes, <code>build()</code>, <code>build_exact_evidence()</code>, <code>build_approx_evidence()</code>, <code>build_evidence()</code></li>
+<li><code>obikindex/src/partition/index_layer.rs</code> — <code>build_index_layer()</code> avec passage de <code>block_bits</code></li>
 </ul>
 <h2 id="notes">Notes</h2>
 <p>FORT RISQUE DE DÉRIVE. Changements récents :

DevDoc/implementation/mphf/index.html

@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
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+    Installation
+  
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+              
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+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
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+    
+  
+    Central-position SNP distance (discussion)
+  
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+    </li>
+  
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -891,14 +946,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -1003,14 +1058,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
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+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
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+  </span>
+  
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+    </li>
+  
+
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+            
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+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
+              
+                
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+  
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+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
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@@ -1134,6 +1329,90 @@
 
               
             
+              
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+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1354,7 +1633,7 @@
 <h2 id="why-two-phases-are-needed">Why two phases are needed</h2>
 <p>Kmer indexing per partition proceeds in two phases. The separation is necessary because the exact number of surviving unique kmers is not known until after counting and filtering low-abundance kmers.</p>
 <h3 id="phase-1-provisional-mphf-kmer-spectrum">Phase 1 — provisional MPHF + kmer spectrum</h3>
-<p>Implemented in <code>obikpartitionner::KmerPartition::count_kmer()</code> → <code>count_partition()</code>.</p>
+<p>Implemented in <code>obikindex::partition::KmerPartition::count_kmer()</code> → <code>count_partition()</code>.</p>
 <ol>
 <li><strong>External sort</strong>: read the dereplicated superkmer file; extract the raw <code>u64</code> canonical kmer value for every kmer of every superkmer. Sort in RAM-bounded chunks (adaptive budget: 40% of available RAM ÷ n_threads, minimum 1 M kmers per chunk), then k-way merge with inline dedup. Result: <code>sorted_unique.bin</code> — a flat array of f0 distinct sorted <code>u64</code> values. Exact kmer count f0 is known at this point.</li>
 <li><strong>Build provisional MPHF</strong> (ptr_hash, same configuration as phase 2) over <code>sorted_unique.bin</code> using <code>new_from_par_iter</code>. Delete <code>sorted_unique.bin</code> immediately after. Persist to <code>mphf1.bin</code>.</li>
@@ -1444,7 +1723,7 @@
 <hr />
 <h2 id="multilayer-index-architecture">Multilayer index architecture</h2>
 <h3 id="layer-structure">Layer structure</h3>
-<p>Each layer is a self-contained unit. See <a href="../obilayeredmap/">obilayeredmap</a> for the full on-disk layout. The MPHF-relevant files are:</p>
+<p>Each layer is a self-contained unit. See <a href="../layer_tier/">obikindex::layer</a> for the full on-disk layout. The MPHF-relevant files are:</p>
 <div class="highlight"><pre><span></span><code>layer_i/
   unitigs.bin      — packed 2-bit nucleotide sequences (kmer evidence source)
   unitigs.bin.idx  — random-access block index (block_bits controls granularity)
@@ -1479,7 +1758,7 @@ MphfLayer::build_approx_evidence(dir, b, z)
     Uses open_sequential(); never writes .idx
 </code></pre></div>
 <p>There is no <code>build_evidence</code> dispatch wrapper. Callers choose the appropriate post-hoc build directly.</p>
-<p>In <code>obikpartitionner</code>, <code>build_index_layer</code> receives <code>block_bits: u8</code> from <code>IndexConfig::block_bits</code> and forwards it directly to <code>Layer::build</code> and <code>Layer::build_approx_evidence</code>.</p>
+<p>In <code>obikindex::partition</code>, <code>build_index_layer</code> receives <code>block_bits: u8</code> from <code>IndexConfig::block_bits</code> and forwards it directly to <code>Layer::build</code> and <code>Layer::build_approx_evidence</code>.</p>
 <h3 id="membership-verification">Membership verification</h3>
 <p>ptr_hash maps any input to a valid slot — it does not natively detect absent keys. Membership is verified using the evidence entry:</p>
 <ul>

DevDoc/implementation/obipipeline.refs/index.html

@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
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+  
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+    Installation
+  
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
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+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
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+    obikindex layer tier
   
 
     
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+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
+              
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+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
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+  </span>
+  
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+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
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+            
+              
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+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
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+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
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+    </li>
+  
+
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+            
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+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
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+    </li>
+  
+
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+            
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+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
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             <span class="md-nav__icon md-icon"></span>
             
   
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+              
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+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
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+    
+  
+    Sibling annex (discussion)
+  
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+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -996,7 +1275,7 @@
 </ul>
 <h2 id="notes">Notes</h2>
 <p>Document stable (librairie générique, peu de risque de dérive).
-Vérifier si <code>obipipeline</code> est toujours utilisé dans la phase scatter de <code>obikpartitionner</code>
+Vérifier si <code>obipipeline</code> est toujours utilisé dans la phase scatter de <code>obikindex::partition</code>
 ou s'il a été remplacé par Rayon dans certains chemins.</p>
 
 

DevDoc/implementation/obipipeline/index.html

@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
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+  
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+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
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+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -212,8 +239,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
+              
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+  
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+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
           </ul>
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@@ -387,10 +442,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
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+          <label class="md-nav__title" for="__nav_4">
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@@ -841,14 +896,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -953,14 +1008,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -996,10 +1191,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1084,6 +1279,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       

DevDoc/implementation/persistent_bit_vec.refs/index.html

@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -187,10 +214,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
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+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -208,8 +235,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
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+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -381,10 +436,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -402,8 +457,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -672,14 +727,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -784,14 +839,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -827,10 +1022,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +1043,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1110,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       

DevDoc/implementation/persistent_bit_vec/index.html

@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -212,8 +239,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -387,10 +442,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -408,8 +463,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -678,14 +733,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -1065,14 +1120,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
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+  
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+
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+
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DevDoc/implementation/persistent_compact_int_vec.refs/index.html

@@ -178,6 +178,33 @@
   
   
   
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@@ -359,6 +386,34 @@
 
               
             
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+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
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-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
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+
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+
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+
+      </a>
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+      <a href="../partition_layer_cache/" class="md-nav__link">
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+  
+  
+  <span class="md-ellipsis">
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+    Partition and layer caching (discussion)
   
 
     
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+
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+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
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+  
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+  
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DevDoc/implementation/persistent_compact_int_vec/index.html

@@ -9,7 +9,7 @@
       
       
       
-        <link rel="prev" href="../obilayeredmap/">
+        <link rel="prev" href="../layer_tier/">
       
       
         <link rel="next" href="../persistent_bit_vec/">
@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
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+
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@@ -363,6 +390,34 @@
 
               
             
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+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
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+  
+
+      </a>
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+  
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     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
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     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
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+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
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+
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+  
+
+              
+            
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+  
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+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
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+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -1091,10 +1286,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
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             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1179,6 +1374,90 @@
 
               
             
+              
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+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
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+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       

DevDoc/implementation/pipeline.refs/index.html

@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+  
+    Installation
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+
+    
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+
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
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             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
+              
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+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
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@@ -672,14 +727,14 @@
   
   
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-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
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-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -784,14 +839,154 @@
   
   
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-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
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-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
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+      <a href="../filtering/" class="md-nav__link">
+        
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+    
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+    Kmer filtering
+  
+
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+  </span>
+  
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+
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+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
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+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
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+  </span>
+  
+  
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+    </li>
+  
+
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+              
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+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
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+  </span>
+  
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+    </li>
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+
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+            
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+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
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+              
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+  
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+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
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+    
+  
+    Sibling annex (discussion)
+  
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+    </li>
+  
+
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+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
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+  </span>
+  
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+    </li>
+  
+
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+            
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+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
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+  </span>
+  
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+
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+    </li>
+  
+
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+            
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         </nav>
       
@@ -991,12 +1270,12 @@
 <h1 id="coverage-implementationpipelinemd">Coverage: implementation/pipeline.md</h1>
 <h2 id="code-couvert">Code couvert</h2>
 <ul>
-<li><code>obikpartitionner/src/partition.rs</code> — estimation des paramètres (phase 0)</li>
+<li><code>obikindex/src/partition/partition.rs</code> — estimation des paramètres (phase 0)</li>
 <li><code>obiskbuilder/src/iter.rs</code> — scatter : filtre entropie, extraction superkmers, routage partition (phase 1)</li>
-<li><code>obikpartitionner/src/filter.rs</code> — déduplication bucket-sort (phase 2)</li>
-<li><code>obikpartitionner/src/kmer_sort.rs</code> — tri externe + agrégation de comptages (phase 3)</li>
+<li><code>obikindex/src/partition/filter.rs</code> — déduplication bucket-sort (phase 2)</li>
+<li><code>obikindex/src/partition/kmer_sort.rs</code> — tri externe + agrégation de comptages (phase 3)</li>
 <li><code>obidebruinj/src/debruijn.rs</code> — graphe De Bruijn, extraction des unitigs (phase 5)</li>
-<li><code>obikpartitionner/src/index_layer.rs</code> — construction MPHF + évidence (phase 6), paramètre <code>block_bits</code></li>
+<li><code>obikindex/src/partition/index_layer.rs</code> — construction MPHF + évidence (phase 6), paramètre <code>block_bits</code></li>
 <li><code>obikindex/src/index.rs</code> — <code>build_layers()</code>, <code>dereplicate_and_count()</code></li>
 </ul>
 <h2 id="notes">Notes</h2>

DevDoc/implementation/pipeline/index.html

@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
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+    Installation
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+              
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+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
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+    
+  
+    Central-position SNP distance (discussion)
+  
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+  </span>
+  
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+    </li>
+  
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             <span class="md-nav__icon md-icon"></span>
             
   
@@ -802,14 +857,14 @@
   
   
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-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
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-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
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+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
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+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
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             <span class="md-nav__icon md-icon"></span>
             
   
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+              
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+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
+              
+                
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+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
+              
+                
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+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
           </ul>
         </nav>
       
@@ -1323,7 +1602,7 @@ branching / dead-end → unitig start or end
       counts/                ← PersistentCompactIntMatrix (with_counts only)
 </code></pre></div>
 <p><strong>Cleanup:</strong> unless <code>--keep-intermediate</code> is set, <code>remove_build_artifacts</code> deletes <code>dereplicated.skmer.zst</code>, <code>mphf1.bin</code>, and <code>counts1.bin</code> after all partitions are indexed.</p>
-<p>See <a href="../obilayeredmap/">obilayeredmap</a> and <a href="../mphf/">MPHF selection</a> for data structure details.</p>
+<p>See <a href="../layer_tier/">obikindex::layer</a> and <a href="../mphf/">MPHF selection</a> for data structure details.</p>
 <p><strong>Query path (exact evidence):</strong></p>
 <div class="highlight"><pre><span></span><code>query kmer q
   → canonical_minimizer(q) → hash → PART → part_XXXXX/

DevDoc/implementation/storage.refs/index.html

@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
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@@ -672,14 +727,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -784,14 +839,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
+              
+                
+  
+  
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+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
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+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
+              
+                
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+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
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           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1110,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -993,7 +1272,7 @@
 <ul>
 <li><code>obikindex/src/meta.rs</code> — IndexMeta, IndexConfig (version, config, genomes)</li>
 <li><code>obikindex/src/index.rs</code> — layout sur disque : partitions/, index.meta</li>
-<li><code>obilayeredmap/src/meta.rs</code> — LayerMeta (evidence kind), PartitionMeta (n_layers)</li>
+<li><code>obikindex/src/layer/meta.rs</code> — LayerMeta (evidence kind), PartitionMeta (n_layers)</li>
 <li><code>obiskio/src/unitig_index.rs</code> — fichiers unitigs.bin + unitigs.bin.idx</li>
 </ul>
 <h2 id="notes">Notes</h2>

DevDoc/implementation/storage/index.html

@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -212,8 +239,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -387,10 +442,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -408,8 +463,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -874,14 +929,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -986,14 +1041,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -1029,10 +1224,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -1050,8 +1245,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1117,6 +1312,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       

DevDoc/implementation/superkmer.refs/index.html

@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -187,10 +214,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -208,8 +235,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -381,10 +436,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -402,8 +457,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -672,14 +727,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -784,14 +839,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -827,10 +1022,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +1043,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1110,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       

DevDoc/implementation/superkmer/index.html

@@ -9,7 +9,7 @@
       
       
       
-        <link rel="prev" href="../../theory/indexing/">
+        <link rel="prev" href="../../theory/evolutionary_distances/">
       
       
         <link rel="next" href="../kmer/">
@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -212,8 +239,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -387,10 +442,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -408,8 +463,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -780,14 +835,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -892,14 +947,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -935,10 +1130,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -956,8 +1151,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1023,6 +1218,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       

DevDoc/implementation/unitig_evidence.refs/index.html

@@ -178,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -187,10 +214,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -208,8 +235,8 @@
             <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -359,6 +386,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -381,10 +436,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -402,8 +457,8 @@
             <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -672,14 +727,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -784,14 +839,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -827,10 +1022,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -848,8 +1043,8 @@
             <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -915,6 +1110,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -992,7 +1271,7 @@
 <h2 id="code-couvert">Code couvert</h2>
 <ul>
 <li><code>obiskio/src/unitig_index.rs</code> — format unitigs.bin + unitigs.bin.idx, UnitigFileWriter, UnitigFileReader, build_unitig_idx(), DEFAULT_BLOCK_BITS=0, chemin chaud block_bits=0 dans chunk_start()</li>
-<li><code>obilayeredmap/src/evidence.rs</code> — encodage Evidence (chunk_id 25 bits | rank 7 bits), EvidenceWriter</li>
+<li><code>obikindex/src/layer/evidence.rs</code> — encodage Evidence (chunk_id 25 bits | rank 7 bits), EvidenceWriter</li>
 <li><code>obidebruinj/src/debruijn.rs</code> — extraction unitigs, chunking à MAX_KMERS_PER_CHUNK</li>
 </ul>
 <h2 id="notes">Notes</h2>

DevDoc/implementation/unitig_evidence/index.html

@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -191,10 +218,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
           
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
             
   
   
@@ -212,8 +239,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -363,6 +390,34 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -387,10 +442,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
         
           
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
             
   
   
@@ -408,8 +463,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -902,14 +957,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../layer_tier/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -1014,14 +1069,154 @@
   
   
     <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../benchmark_query_testing/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
   
 
     
@@ -1057,10 +1252,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
             
   
   
@@ -1078,8 +1273,8 @@
             <span class="md-nav__icon md-icon"></span>
           </label>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             
   
@@ -1145,6 +1340,90 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>