refactor(benchmark): consolidate generated artifacts under run/ directory

Restructure the benchmark pipeline to direct all simulated data, indices, statistics, and query outputs into a unified `run/` directory. Update Makefile targets, shell scripts, and Python utilities to resolve paths relative to this new base. Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.

.gitea/workflows/ci.yml

@@ -0,0 +1,35 @@
+pname: CI
+
+on:
+  pull_request:
+    branches: ['main']
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: src
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Rust
+        run: |
+          curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --default-toolchain stable
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+      - name: Cache cargo registry
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+            src/target
+          key: ${{ runner.os }}-cargo-v2-${{ hashFiles('src/Cargo.lock') }}
+          restore-keys: ${{ runner.os }}-cargo-v2-
+
+      - name: Build
+        run: cargo build --release
+
+      - name: Test
+        run: cargo test --release

.gitea/workflows/release.yml

@@ -0,0 +1,127 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  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" >> $GITHUB_OUTPUT
+
+  build-linux-x86_64:
+    needs: create-release
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: src
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Rust + zigbuild
+        run: |
+          curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --default-toolchain stable
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+          sudo apt-get update -qq && sudo apt-get install -y -qq 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:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+            src/target
+          key: linux-musl-cargo-${{ hashFiles('src/Cargo.lock') }}
+          restore-keys: linux-musl-cargo-
+
+      - name: Build static binary
+        env:
+          PKG_CONFIG_ALLOW_CROSS: "1"
+        run: cargo zigbuild --release --target x86_64-unknown-linux-musl
+
+      - name: Prepare and upload artifact
+        env:
+          GITEA_TOKEN: ${{ secrets.GITEATOKEN }}
+          RELEASE_ID: ${{ needs.create-release.outputs.release_id }}
+        run: |
+          mkdir -p /tmp/dist
+          cp target/x86_64-unknown-linux-musl/release/obikmer /tmp/dist/obikmer-linux-x86_64
+          strip /tmp/dist/obikmer-linux-x86_64
+          curl -s -X POST \
+            "${{ github.server_url }}/api/v1/repos/${{ github.repository }}/releases/$RELEASE_ID/assets" \
+            -H "Authorization: token $GITEA_TOKEN" \
+            -F "attachment=@/tmp/dist/obikmer-linux-x86_64"
+
+  build-macos-arm64:
+    needs: create-release
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Login to registry
+        run: echo "${{ 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

@@ -1,11 +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/run/
+TNT
+phyg
+biblio
+*.tnt
+*.tre
+*.phy
+*.treefile
+*.bionj
+*.iqtree
+*.mldist
+*.parstree
+*.ckp.gz
+*.model

.serena/.gitignore

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

.serena/project.yml

@@ -0,0 +1,169 @@
+# the name by which the project can be referenced within Serena/when chatting with the LLM.
+project_name: "obikmer"
+
+# 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.
+# The settings are considered only if the project is trusted (see global configuration to define trusted projects).
+# See https://oraios.github.io/serena/02-usage/050_configuration.html#language-server-specific-settings
+ls_specific_settings: {}
+
+# list of additional paths to ignore in this project.
+# Same syntax as gitignore, so you can use * and **.
+# Important: quote patterns that start with `*`, otherwise YAML treats them as aliases.
+# Example:
+#   ignored_paths:
+#     - "examples/**"
+#     - ".worktrees/**"
+#     - "**/bin/**"
+#     - "**/obj/**"
+# 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: []
+
+# list of additional workspace folder paths for cross-package reference support.
+# 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, but these folders are not indexed by Serena,
+# i.e. the respective symbols will not be found using Serena's symbol search tools.
+# Example:
+#   additional_workspace_folders:
+#     - ../sibling-package
+#     - ../shared-lib
+ls_additional_workspace_folders: []
+
+# list of language servers to start when using the LSP backend; choose from:
+#   ada                    al                     angular                ansible                bash
+#   bsl                    clojure                cpp                    cpp_ccls               crystal
+#   csharp                 csharp_omnisharp       cue                    dart                   deno
+#   elixir                 elm                    erlang                 fortran                fsharp
+#   gdscript               gleam                  go                     groovy                 haskell
+#   haxe                   hlsl                   html                   java                   json
+#   julia                  kotlin                 latex                  lean4                  lua
+#   luau                   markdown               matlab                 msl                    nextflow
+#   nix                    ocaml                  pascal                 perl                   php
+#   php_phpactor           php_phpantom           powershell             python                 python_basedpyright
+#   python_jedi            python_pyrefly         python_ty              qml                    r
+#   rego                   ruby                   ruby_solargraph        rust                   scala
+#   scss                   solidity               svelte                 swift                  systemverilog
+#   terraform              toml                   typescript             typescript_vts         vue
+#   wolfram                yaml                   zig
+#   (This list may be outdated; generated with scripts/print_language_list.py;
+#   For the current list, see values of the LanguageServerId enum here:
+#   https://github.com/oraios/serena/blob/main/src/solidlsp/ls_config.py)
+# For some languages, there are several 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 Deno projects, use deno (serves the same .ts/.js files as typescript; requires the deno CLI on PATH)
+#   - For SCSS / Sass / plain CSS, use scss (some-sass-language-server handles all three)
+#   - For Free Pascal/Lazarus, use pascal
+# Special requirements:
+#   Some language servers require additional setup/installations.
+#   See here for details: https://oraios.github.io/serena/01-about/020_programming-languages.html#language-servers
+# When using multiple language servers, the first language server that supports a given file will be used for that file.
+# The first language server 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.
+language_servers:
+- rust
+
+# list of workspace folder paths (LSP backend only).
+# These folders will be used to build up Serena's symbol index.
+# Paths must be within the project root and should thus be relative to the project root.
+# Furthermore, the paths should not be filtered by ignore settings.
+# Default setting: The entire project root folder (".") is considered.
+# In (large) monorepos, this can be used to index only subfolders of the project root, e.g.
+#   ls_workspace_folders:
+#     - "./subproject1"
+#     - "./subproject2"
+ls_workspace_folders:
+- .
+
+# optional shell command to run before the language backend (LSP or JetBrains) is initialised.
+# the command runs in the project root directory and is only executed if the project is trusted
+# (see trusted_project_path_patterns in the global configuration).
+# serena waits for the command to exit: a non-zero exit code is logged as an error but does not
+# abort activation. a per-project timeout (activation_command_timeout, default 180s) is the safety
+# backstop for non-terminating commands; on expiry the process is killed and activation continues.
+# example: activation_command: "npx nx run-many -t build"
+activation_command:
+
+# maximum time in seconds to wait for activation_command to complete before killing it (default 180s).
+# must be a positive number.
+activation_command_timeout: 180.0

CLAUDE.md

@@ -1,75 +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.

DevDoc/architecture/sequences/invariant/index.html

@@ -9,7 +9,7 @@
       
       
       
-        <link rel="prev" href="../../../implementation/persistent_bit_vec/">
+        <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>
             
   
@@ -648,14 +703,42 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../implementation/obilayeredmap/" class="md-nav__link">
+      <a href="../../../implementation/evidence_elimination/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    Evidence elimination (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/layer_tier/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obikindex layer tier
   
 
     
@@ -725,6 +808,202 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/merge/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    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)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -749,10 +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">
             
   
   
@@ -770,8 +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>
             
   
@@ -847,6 +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};
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+            if (str.match(this.chartype_[i][0])) {
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+        TinySegmenter.prototype.ts_ = function(v) {
+          if (v) { return v; }
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+        TinySegmenter.prototype.segment = function(input) {
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+          for (var i = 4; i < seg.length - 3; ++i) {
+            var score = this.BIAS__;
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+            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;
+    };
+
+}));

DevDoc/assets/stylesheets/palette.ab4e12ef.min.css.map

@@ -0,0 +1 @@
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DevDoc/implementation/chunkreader.refs/index.html

@@ -9,10 +9,6 @@
       
       
       
-        <link rel="prev" href="../obipipeline/">
-      
-      
-        <link rel="next" href="../mphf/">
       
       
         
@@ -23,7 +19,7 @@
     
     
       
-        <title>On-disk storage - obikmer</title>
+        <title>Chunkreader.refs - obikmer</title>
       
     
     
@@ -64,7 +60,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#on-disk-collection-structure" class="md-skip">
+        <a href="#coverage-implementationchunkreadermd" class="md-skip">
           Skip to content
         </a>
       
@@ -100,7 +96,7 @@
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              On-disk storage
+              Chunkreader.refs
             
           </span>
         </div>
@@ -182,6 +178,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -191,10 +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">
             
   
   
@@ -212,8 +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>
             
   
@@ -363,6 +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>
       
@@ -374,8 +425,6 @@
       
   
   
-    
-  
   
   
     
@@ -383,14 +432,14 @@
     
     
     
-    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
+    <li class="md-nav__item md-nav__item--nested">
       
         
         
-        <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" >
         
           
-          <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 +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="true">
-          <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>
             
   
@@ -563,19 +612,10 @@
                 
   
   
-    
   
   
-  
-    <li class="md-nav__item md-nav__item--active">
-      
-      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
-      
-      
-        
-      
-      
-      <a href="./" class="md-nav__link md-nav__link--active">
+    <li class="md-nav__item">
+      <a href="../storage/" class="md-nav__link">
         
   
   
@@ -591,7 +631,6 @@
   
 
       </a>
-      
     </li>
   
 
@@ -660,14 +699,42 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../evidence_elimination/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    Evidence elimination (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../layer_tier/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obikindex layer tier
   
 
     
@@ -737,6 +804,202 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    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)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -759,10 +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">
             
   
   
@@ -780,8 +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>
             
   
@@ -847,6 +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>
       
@@ -874,6 +1221,36 @@
     
   
   
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#code-couvert" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Code couvert
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#notes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Notes
+      
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
 </nav>
                   </div>
                 </div>
@@ -889,9 +1266,16 @@
 
 
 
-<h1 id="on-disk-collection-structure">On-disk collection structure</h1>
-<p>See <a href="../obilayeredmap/">obilayeredmap crate</a> for the current on-disk layout.</p>
-<p>The index root contains one <code>part_XXXXX/</code> directory per partition, each holding one or more <code>layer_N/</code> directories. Each layer directory contains <code>mphf.bin</code>, <code>unitigs.bin</code>, <code>unitigs.bin.idx</code>, <code>evidence.bin</code>, and optionally a <code>counts/</code> or <code>presence/</code> payload directory.</p>
+<!-- coverage sidecar — ne pas ajouter au nav mkdocs -->
+<h1 id="coverage-implementationchunkreadermd">Coverage: implementation/chunkreader.md</h1>
+<h2 id="code-couvert">Code couvert</h2>
+<ul>
+<li><code>obiread/src/chunk.rs</code> — SeqChunkIter, détection de frontières FASTA/FASTQ, state machines</li>
+<li><code>obikrope/src/lib.rs</code> — type Rope (Vec<Bytes>), opérations zero-copy</li>
+</ul>
+<h2 id="notes">Notes</h2>
+<p>Document stable (la stratégie de chunking rope ne devrait pas avoir changé).
+Vérifier que le split FASTA/FASTQ reste correct si de nouveaux formats ont été ajoutés.</p>
 
 
 

DevDoc/implementation/chunkreader/index.html

@@ -77,12 +77,24 @@
   
 
     
+  </span>
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@@ -454,19 +628,28 @@
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@@ -498,6 +681,15 @@
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@@ -506,68 +698,77 @@
 <div class="md-content" data-md-component="content">
 <article class="md-content__inner md-typeset">
 <h1 id="chunk-reader-implementation">Chunk reader — implementation</h1>
-<p>The <code>obiread</code> crate provides a streaming iterator that reads FASTA or FASTQ files in fixed-size blocks and yields self-contained chunks, each ending on a complete sequence record boundary. Chunks are consumed in parallel by downstream workers.</p>
-<h2 id="output-type-rope">Output type: rope</h2>
-<p>Each chunk is a <code>Vec&lt;Bytes&gt;</code> — a <strong>rope</strong>: a list of reference-counted byte slices that are not necessarily contiguous in memory. The consumer iterates over the slices in order.</p>
-<p>Using <code>bytes::Bytes</code> means the split at the record boundary is O(1): <code>Bytes::split_to(n)</code> adjusts a reference counter, not memory. No <code>memcpy</code> in the common case.</p>
-<h2 id="allocation-policy">Allocation policy</h2>
+<p><code>obiread</code> exposes two distinct sequence reading paths, each optimised for a different use case.</p>
+<h2 id="two-reading-paths">Two reading paths</h2>
 <table>
 <thead>
 <tr>
-<th>Case</th>
-<th>Cost</th>
+<th>Path</th>
+<th>API</th>
+<th>Output unit</th>
+<th>Per-record identity</th>
+<th>Use case</th>
 </tr>
 </thead>
 <tbody>
 <tr>
-<td>Boundary found in the current block (common)</td>
-<td>zero extra allocation — <code>split_to</code> only</td>
+<td><strong>Record path</strong></td>
+<td><code>read_sequence_chunks</code> → <code>parse_chunk</code></td>
+<td><code>SeqRecord</code> (id + raw sequence + normalised rope)</td>
+<td>yes</td>
+<td><code>query</code> — must read complete records</td>
 </tr>
 <tr>
-<td>Boundary straddles multiple blocks (sequence &gt; block size, rare)</td>
-<td>one allocation to pack the rope into a flat buffer</td>
-</tr>
-<tr>
-<td>EOF flush</td>
-<td>zero extra allocation</td>
+<td><strong>Stream path</strong></td>
+<td><code>open_nuc_stream</code></td>
+<td><code>NucPage</code> (flat normalised byte buffer)</td>
+<td>no</td>
+<td><code>index</code>, <code>superkmer</code> — bulk throughput</td>
 </tr>
 </tbody>
 </table>
+<p>The record path uses <code>Rope</code>-backed chunks and is described in detail below.
+The stream path (<code>NucStream</code> / <code>NucPage</code>) is described in the scatter section of <a href="../pipeline/">pipeline</a>.</p>
+<hr/>
+<h2 id="record-path-chunk-reader">Record path: chunk reader</h2>
+<p>The chunk reader reads FASTA or FASTQ files in fixed-size blocks and yields self-contained chunks, each ending on a complete sequence record boundary. <code>parse_chunk</code> then converts each chunk into a <code>Vec&lt;SeqRecord&gt;</code>, where each record carries its identifier, raw sequence bytes, and a normalised rope ready for superkmer building.</p>
+<p>This path is mandatory for <code>query</code>, where superkmers must be tracked back to their originating sequence (id, kmer offset) for output annotation.</p>
+<h2 id="output-type-rope">Output type: Rope</h2>
+<p>Each chunk is a <code>Rope</code> — a segmented byte sequence: a <code>Vec</code> of blocks, where each block is a <code>Vec&lt;Cell&lt;u8&gt;&gt;</code>. The consumer iterates over the blocks via a forward or backward cursor.</p>
+<p><code>Rope::split_off(pos)</code> splits at an absolute byte offset in O(log n) (binary search over block-start index). If <code>pos</code> falls inside a block, that block is split in two via <code>Vec::split_off</code> — no <code>memcpy</code> in the common case.</p>
 <h2 id="seqchunkiter">SeqChunkIter</h2>
 <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">SeqChunkIter</span><span class="o">&lt;</span><span class="n">R</span><span class="p">:</span><span class="w"> </span><span class="nc">Read</span><span class="o">&gt;</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="cm">/* private */</span><span class="w"> </span><span class="p">}</span>
 
 <span class="k">impl</span><span class="o">&lt;</span><span class="n">R</span><span class="p">:</span><span class="w"> </span><span class="nc">Read</span><span class="o">&gt;</span><span class="w"> </span><span class="nb">Iterator</span><span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="n">SeqChunkIter</span><span class="o">&lt;</span><span class="n">R</span><span class="o">&gt;</span><span class="w"> </span><span class="p">{</span>
-<span class="w">    </span><span class="k">type</span><span class="w"> </span><span class="nc">Item</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">io</span><span class="p">::</span><span class="nb">Result</span><span class="o">&lt;</span><span class="nb">Vec</span><span class="o">&lt;</span><span class="n">Bytes</span><span class="o">&gt;&gt;</span><span class="p">;</span>
+<span class="w">    </span><span class="k">type</span><span class="w"> </span><span class="nc">Item</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">io</span><span class="p">::</span><span class="nb">Result</span><span class="o">&lt;</span><span class="n">Rope</span><span class="o">&gt;</span><span class="p">;</span>
 <span class="p">}</span>
 
 <span class="k">pub</span><span class="w"> </span><span class="k">fn</span><span class="w"> </span><span class="nf">fasta_chunks</span><span class="o">&lt;</span><span class="n">R</span><span class="p">:</span><span class="w"> </span><span class="nc">Read</span><span class="o">&gt;</span><span class="p">(</span><span class="n">source</span><span class="p">:</span><span class="w"> </span><span class="nc">R</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">SeqChunkIter</span><span class="o">&lt;</span><span class="n">R</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">fastq_chunks</span><span class="o">&lt;</span><span class="n">R</span><span class="p">:</span><span class="w"> </span><span class="nc">Read</span><span class="o">&gt;</span><span class="p">(</span><span class="n">source</span><span class="p">:</span><span class="w"> </span><span class="nc">R</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="nc">SeqChunkIter</span><span class="o">&lt;</span><span class="n">R</span><span class="o">&gt;</span>
 </code></pre></div>
 <p><code>next()</code> loop:</p>
-<div class="highlight"><pre><span></span><code>1. read one block of block_size bytes → push onto rope
-2. probe check: if the boundary marker ("\n&gt;" or "\n@") is absent from the
-   last block, skip the splitter (avoids a full backward scan for nothing)
-3. call splitter on last block
-   if found at offset n:
-       remainder = last_block.split_to(n)    ← O(1), zero copy
-       return std::mem::take(&amp;mut self.rope)  ← the chunk
-4. if rope.len() &gt; 1 (multi-block accumulation):
-       pack rope into one flat buffer         ← one alloc
-       retry splitter on flat buffer
-5. if EOF: flush remaining rope as final chunk
+<div class="highlight"><pre><span></span><code>1. read one block of block_size bytes → push onto Rope
+2. call splitter(rope) → Option&lt;abs_offset&gt;
+   if Some(pos):
+       tail = rope.split_off(pos)    ← O(log n), may split one block
+       chunk = mem::replace(&amp;mut rope, tail)
+       return Some(Ok(chunk))
+3. if EOF and rope non-empty: return Some(Ok(rope)) as final chunk
+4. if EOF and rope empty: return None
 </code></pre></div>
+<p>The <code>Splitter</code> function signature is <code>fn(&amp;Rope) -&gt; Option&lt;usize&gt;</code>. It returns the absolute byte offset of the start of the last complete record, or <code>None</code> if no boundary was found in the accumulated rope (need more data).</p>
 <h2 id="boundary-detection-fasta">Boundary detection — FASTA</h2>
-<p>Backward scan with a 2-state machine. Searches for <code>&gt;</code> immediately preceded by <code>\n</code> or <code>\r</code>:</p>
+<p>Backward scan with a 2-state machine. Searches (right to left) for <code>&gt;</code> followed by <code>\n</code> or <code>\r</code> (i.e., a <code>&gt;</code> that is preceded by a newline in forward order):</p>
 <pre class="mermaid"><code>stateDiagram-v2
     direction LR
     [*]      --&gt; Scanning
     Scanning --&gt; FoundGt  : '&gt;'
     FoundGt  --&gt; Scanning : other
     FoundGt  --&gt; [*]      : '\\n' / '\\r' ✓</code></pre>
-<p>Returns the byte offset of the <code>&gt;</code> that starts the last complete record.</p>
+<p>Returns the byte offset of the <code>&gt;</code> that starts the last complete record. Returns <code>None</code> if only one <code>&gt;</code> is found (cannot confirm there is a prior complete record).</p>
 <h2 id="boundary-detection-fastq">Boundary detection — FASTQ</h2>
 <p>FASTQ records have a rigid 4-line structure (<code>@header</code>, sequence, <code>+</code>, quality). The <code>@</code> character (ASCII 64, Phred score 31) can appear legitimately in quality lines, making any forward heuristic unreliable. The backward scanner verifies the full structural context before accepting a candidate <code>@</code>.</p>
-<p>7-state machine (port of Go's <code>EndOfLastFastqEntry</code>), scanning from <strong>right to left</strong>. Each time a <code>+</code> is found, its position is saved as <code>restart</code>; any state mismatch resets the scan to that position.</p>
+<p>7-state machine (states 0–6), scanning from <strong>right to left</strong>. Each time a <code>+</code> is found, its position is saved as <code>restart</code>; any state mismatch resets the scan to that position.</p>
 <pre class="mermaid"><code>stateDiagram-v2
     direction LR
 
@@ -596,6 +797,16 @@
     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>
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DevDoc/implementation/kmer/index.html

@@ -182,6 +182,33 @@
   
   
   
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+      <a href="../../installation/" class="md-nav__link">
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@@ -191,10 +218,10 @@
       
         
         
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@@ -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 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <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">
             
   
   
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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="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">
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@@ -514,10 +569,21 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#memory-layout" class="md-nav__link">
+  <a href="#types-and-layout" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Memory layout
+        Types and layout
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#global-parameters" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Global parameters
       
     </span>
   </a>
@@ -558,10 +624,32 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#canonical-form" class="md-nav__link">
+  <a href="#canonical-form-and-canonicalkmerof" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Canonical form
+        Canonical form and CanonicalKmerOf
+      
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+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#sliding-window-helpers" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sliding window helpers
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+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#hashing" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Hashing
       
     </span>
   </a>
@@ -752,14 +840,42 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../evidence_elimination/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    Evidence elimination (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../layer_tier/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obikindex layer tier
   
 
     
@@ -829,6 +945,202 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    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">
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+  
+    Benchmark: query-path testing
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+    Partition and layer caching (discussion)
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+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
           </ul>
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-        <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">
             
   
   
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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_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>
             
   
@@ -939,6 +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>
       
@@ -973,10 +1369,21 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#memory-layout" class="md-nav__link">
+  <a href="#types-and-layout" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Memory layout
+        Types and layout
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#global-parameters" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Global parameters
       
     </span>
   </a>
@@ -1017,10 +1424,32 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#canonical-form" class="md-nav__link">
+  <a href="#canonical-form-and-canonicalkmerof" class="md-nav__link">
     <span class="md-ellipsis">
       
-        Canonical form
+        Canonical form and CanonicalKmerOf
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#sliding-window-helpers" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Sliding window helpers
+      
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#hashing" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Hashing
       
     </span>
   </a>
@@ -1045,12 +1474,43 @@
 
 
 <h1 id="kmer-implementation">Kmer — implementation</h1>
-<h2 id="memory-layout">Memory layout</h2>
-<p><code>Kmer</code> is a <code>#[repr(transparent)]</code> newtype over <code>u64</code>:</p>
+<h2 id="types-and-layout">Types and layout</h2>
+<p><code>KmerOf&lt;L&gt;</code> is a <code>#[repr(transparent)]</code> newtype over <code>u64</code> parameterized by a <code>KmerLength</code> marker:</p>
 <div class="highlight"><pre><span></span><code><span class="cp">#[repr(transparent)]</span>
-<span class="k">pub</span><span class="w"> </span><span class="k">struct</span><span class="w"> </span><span class="nc">Kmer</span><span class="p">(</span><span class="kt">u64</span><span class="p">);</span>
+<span class="k">pub</span><span class="w"> </span><span class="k">struct</span><span class="w"> </span><span class="nc">KmerOf</span><span class="o">&lt;</span><span class="n">L</span><span class="p">:</span><span class="w"> </span><span class="nc">KmerLength</span><span class="o">&gt;</span><span class="p">(</span><span class="kt">u64</span><span class="p">,</span><span class="w"> </span><span class="n">PhantomData</span><span class="o">&lt;</span><span class="n">L</span><span class="o">&gt;</span><span class="p">);</span>
 </code></pre></div>
-<p>Nucleotides are packed 2 bits each, <strong>left-aligned</strong>, MSB-first. Nucleotide 0 occupies bits 63–62; nucleotide i occupies bits 63−2i and 62−2i. The low 64−2k bits are always zero. k is <strong>not stored</strong> — it is a parameter of every operation that needs it, and will be owned by the future collection-level indexer.</p>
+<p>Three marker types implement <code>KmerLength</code>:</p>
+<table>
+<thead>
+<tr>
+<th>Marker</th>
+<th><code>len()</code> source</th>
+<th>Used for</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>KLen</code></td>
+<td><code>params::k()</code></td>
+<td>k-mers</td>
+</tr>
+<tr>
+<td><code>MLen</code></td>
+<td><code>params::m()</code></td>
+<td>minimizers</td>
+</tr>
+<tr>
+<td><code>ConstLen&lt;N&gt;</code></td>
+<td>const generic <code>N</code></td>
+<td>tests</td>
+</tr>
+</tbody>
+</table>
+<p>Public aliases:</p>
+<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">type</span><span class="w"> </span><span class="nc">Kmer</span><span class="w">     </span><span class="o">=</span><span class="w"> </span><span class="n">KmerOf</span><span class="o">&lt;</span><span class="n">KLen</span><span class="o">&gt;</span><span class="p">;</span><span class="w">         </span><span class="c1">// k-mer, global k</span>
+<span class="k">pub</span><span class="w"> </span><span class="k">type</span><span class="w"> </span><span class="nc">Minimizer</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">CanonicalKmerOf</span><span class="o">&lt;</span><span class="n">MLen</span><span class="o">&gt;</span><span class="p">;</span><span class="w"> </span><span class="c1">// canonical m-mer, global m</span>
+</code></pre></div>
+<p>Nucleotides are packed 2 bits each, <strong>left-aligned</strong>, MSB-first. Nucleotide 0 occupies bits 63–62; nucleotide i occupies bits 63−2i and 62−2i. The low 64−2·len bits are always zero. The length is <strong>not stored</strong> — every operation reads it from <code>L::len()</code>.</p>
 <table>
 <thead>
 <tr>
@@ -1071,33 +1531,41 @@
 </tr>
 </tbody>
 </table>
+<h2 id="global-parameters">Global parameters</h2>
+<p><code>params::set_k(k)</code> / <code>params::k()</code> and <code>params::set_m(m)</code> / <code>params::m()</code> are backed by <code>OnceLock&lt;usize&gt;</code> in production (write-once, panic on conflict) and by <code>thread_local! { Cell&lt;usize&gt; }</code> in test builds (per-thread, freely writable). <code>params::init(k, m)</code> sets both in one call.</p>
 <h2 id="encoding">Encoding</h2>
-<p><code>Kmer::from_ascii(ascii, k)</code> encodes the first k bytes of an ASCII slice using the shared <code>ENC</code> table (see <a href="../superkmer/#ascii-encoding-and-decoding">SuperKmer — ASCII encoding</a>):</p>
+<p><code>KmerOf::&lt;L&gt;::from_ascii(ascii)</code> encodes the first <code>L::len()</code> bytes using the shared <code>ENC</code> table (see <a href="../superkmer/#ascii-encoding-and-decoding">SuperKmer — ASCII encoding</a>):</p>
 <div class="highlight"><pre><span></span><code><span class="k">for</span><span class="w"> </span><span class="n">i</span><span class="w"> </span><span class="k">in</span><span class="w"> </span><span class="mi">0</span><span class="o">..</span><span class="n">k</span><span class="w"> </span><span class="p">{</span>
 <span class="w">    </span><span class="n">val</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">(</span><span class="n">val</span><span class="w"> </span><span class="o">&lt;&lt;</span><span class="w"> </span><span class="mi">2</span><span class="p">)</span><span class="w"> </span><span class="o">|</span><span class="w"> </span><span class="n">encode_base</span><span class="p">(</span><span class="n">ascii</span><span class="p">[</span><span class="n">i</span><span class="p">])</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="kt">u64</span><span class="p">;</span>
 <span class="p">}</span>
-<span class="n">Kmer</span><span class="p">(</span><span class="n">val</span><span class="w"> </span><span class="o">&lt;&lt;</span><span class="w"> </span><span class="p">(</span><span class="mi">64</span><span class="w"> </span><span class="o">-</span><span class="w"> </span><span class="mi">2</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">k</span><span class="p">))</span>
+<span class="n">KmerOf</span><span class="p">(</span><span class="n">val</span><span class="w"> </span><span class="o">&lt;&lt;</span><span class="w"> </span><span class="p">(</span><span class="mi">64</span><span class="w"> </span><span class="o">-</span><span class="w"> </span><span class="mi">2</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">k</span><span class="p">),</span><span class="w"> </span><span class="n">PhantomData</span><span class="p">)</span>
 </code></pre></div>
 <p>Zero allocation — result lives on the stack.</p>
 <h2 id="decoding">Decoding</h2>
-<p><code>write_ascii(k, buf)</code> appends k ASCII characters to a caller-supplied <code>Vec&lt;u8&gt;</code> using the shared <code>DEC4</code> table: one lookup per 4 nucleotides, two partial-byte lookups for the remainder. No allocation in the hot path.</p>
-<p><code>to_ascii(k)</code> is a convenience wrapper that allocates and returns a <code>Vec&lt;u8&gt;</code>; intended for tests and display only.</p>
+<p><code>write_ascii(writer)</code> writes k ASCII characters to any <code>W: Write</code> using the shared <code>DEC4</code> table: one lookup per 4 nucleotides, one partial lookup for the remainder. No allocation in the hot path.</p>
+<p><code>to_ascii()</code> is a convenience wrapper that allocates and returns a <code>Vec&lt;u8&gt;</code>; intended for tests and display only.</p>
 <h2 id="reverse-complement">Reverse complement</h2>
 <p>Computed as pure arithmetic — no lookup table, no memory access:</p>
 <div class="highlight"><pre><span></span><code><span class="kd">let</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="o">!</span><span class="bp">self</span><span class="p">.</span><span class="mi">0</span><span class="p">;</span><span class="w">                                                               </span><span class="c1">// complement</span>
 <span class="kd">let</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">x</span><span class="p">.</span><span class="n">swap_bytes</span><span class="p">();</span><span class="w">                                                        </span><span class="c1">// reverse bytes</span>
 <span class="kd">let</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">((</span><span class="n">x</span><span class="w"> </span><span class="o">&gt;&gt;</span><span class="w"> </span><span class="mi">4</span><span class="p">)</span><span class="w"> </span><span class="o">&amp;</span><span class="w"> </span><span class="mh">0x0F0F0F0F0F0F0F0F</span><span class="p">)</span><span class="w"> </span><span class="o">|</span><span class="w"> </span><span class="p">((</span><span class="n">x</span><span class="w"> </span><span class="o">&amp;</span><span class="w"> </span><span class="mh">0x0F0F0F0F0F0F0F0F</span><span class="p">)</span><span class="w"> </span><span class="o">&lt;&lt;</span><span class="w"> </span><span class="mi">4</span><span class="p">);</span><span class="w"> </span><span class="c1">// swap nibbles</span>
 <span class="kd">let</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">((</span><span class="n">x</span><span class="w"> </span><span class="o">&gt;&gt;</span><span class="w"> </span><span class="mi">2</span><span class="p">)</span><span class="w"> </span><span class="o">&amp;</span><span class="w"> </span><span class="mh">0x3333333333333333</span><span class="p">)</span><span class="w"> </span><span class="o">|</span><span class="w"> </span><span class="p">((</span><span class="n">x</span><span class="w"> </span><span class="o">&amp;</span><span class="w"> </span><span class="mh">0x3333333333333333</span><span class="p">)</span><span class="w"> </span><span class="o">&lt;&lt;</span><span class="w"> </span><span class="mi">2</span><span class="p">);</span><span class="w">   </span><span class="c1">// swap 2-bit groups</span>
-<span class="n">Kmer</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">&lt;&lt;</span><span class="w"> </span><span class="p">(</span><span class="mi">64</span><span class="w"> </span><span class="o">-</span><span class="w"> </span><span class="mi">2</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">k</span><span class="p">))</span>
+<span class="n">KmerOf</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">&lt;&lt;</span><span class="w"> </span><span class="p">(</span><span class="mi">64</span><span class="w"> </span><span class="o">-</span><span class="w"> </span><span class="mi">2</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">k</span><span class="p">),</span><span class="w"> </span><span class="n">PhantomData</span><span class="p">)</span>
 </code></pre></div>
 <p>After complementing, bytes are reversed (<code>swap_bytes</code>), then nibbles, then 2-bit groups — restoring 2-bit nucleotides to their correct positions in reverse order. A final left-shift realigns to MSB. Zero allocation — result lives on the stack.</p>
-<h2 id="canonical-form">Canonical form</h2>
-<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">canonical</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">k</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">Self</span><span class="w"> </span><span class="p">{</span>
-<span class="w">    </span><span class="kd">let</span><span class="w"> </span><span class="n">rc</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">revcomp</span><span class="p">(</span><span class="n">k</span><span class="p">);</span>
-<span class="w">    </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="mi">0</span><span class="w"> </span><span class="o">&lt;=</span><span class="w"> </span><span class="n">rc</span><span class="p">.</span><span class="mi">0</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="o">*</span><span class="bp">self</span><span class="w"> </span><span class="p">}</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="n">rc</span><span class="w"> </span><span class="p">}</span>
+<h2 id="canonical-form-and-canonicalkmerof">Canonical form and <code>CanonicalKmerOf</code></h2>
+<p><code>canonical()</code> returns a <code>CanonicalKmerOf&lt;L&gt;</code> — a distinct newtype that carries the same <code>u64</code> layout but enforces the invariant that the stored value equals <code>min(kmer, revcomp)</code>:</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">canonical</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">CanonicalKmerOf</span><span class="o">&lt;</span><span class="n">L</span><span class="o">&gt;</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="kd">let</span><span class="w"> </span><span class="n">rc</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">revcomp</span><span class="p">();</span>
+<span class="w">    </span><span class="n">CanonicalKmerOf</span><span class="p">(</span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="mi">0</span><span class="w"> </span><span class="o">&lt;=</span><span class="w"> </span><span class="n">rc</span><span class="p">.</span><span class="mi">0</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="mi">0</span><span class="w"> </span><span class="p">}</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="n">rc</span><span class="p">.</span><span class="mi">0</span><span class="w"> </span><span class="p">},</span><span class="w"> </span><span class="n">PhantomData</span><span class="p">)</span>
 <span class="p">}</span>
 </code></pre></div>
 <p>Lexicographic minimum of forward and reverse-complement, comparing the raw <code>u64</code> values directly (left-aligned encoding makes this equivalent to nucleotide-wise comparison). Zero allocation — result lives on the stack.</p>
+<p><code>CanonicalKmerOf::from_raw_unchecked(raw)</code> is the only other public constructor, for trusted paths such as deserialisation.</p>
+<h2 id="sliding-window-helpers">Sliding window helpers</h2>
+<p><code>push_right(nuc)</code> / <code>push_left(nuc)</code> shift the window by one base in O(1). <code>is_overlapping(other)</code> checks whether the last k−1 nucleotides of <code>self</code> equal the first k−1 of <code>other</code>.</p>
+<h2 id="hashing">Hashing</h2>
+<p><code>hash_kmer(raw: u64) -&gt; u64</code> computes <code>mix64(raw ^ 0x9e3779b97f4a7c15)</code>, the seeded splitmix64 finalizer. <code>CanonicalKmerOf::seq_hash()</code> delegates to <code>hash_kmer</code>.</p>
 
 
 

DevDoc/implementation/mphf/index.html

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+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
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+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
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+</li>
+        
+          <li class="md-nav__item">
+  <a href="#evidence-modes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Evidence modes
+      
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+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#build-functions" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Build functions
+      
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+  </a>
+  
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+      <a href="../evidence_elimination/" class="md-nav__link">
         
   
   
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-    obilayeredmap crate
+    Evidence elimination (discussion)
+  
+
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+  </span>
+  
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+    </li>
+  
+
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+      <a href="../layer_tier/" class="md-nav__link">
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+  
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+    
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+    obikindex layer tier
   
 
     
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+  
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+  
+    <li class="md-nav__item">
+      <a href="../merge/" class="md-nav__link">
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+  </span>
+  
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+
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+      <a href="../merge_parallelism/" class="md-nav__link">
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+  <span class="md-ellipsis">
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+  
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+      <a href="../filtering/" class="md-nav__link">
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+  
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+    
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+  
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+
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+      <a href="../select/" class="md-nav__link">
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+      <a href="../obitaxonomy/" class="md-nav__link">
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+    obitaxonomy crate
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+      <a href="../benchmark_query_testing/" class="md-nav__link">
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+      <a href="../partition_layer_cache/" class="md-nav__link">
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+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
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+    NUMA-aware worker pools
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+</li>
+        
+          <li class="md-nav__item">
+  <a href="#evidence-modes" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Evidence modes
+      
+    </span>
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+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#build-functions" class="md-nav__link">
+    <span class="md-ellipsis">
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+        Build functions
+      
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+  
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@@ -1226,26 +1633,26 @@
 <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>.</p>
+<p>Implemented in <code>obikindex::partition::KmerPartition::count_kmer()</code> → <code>count_partition()</code>.</p>
 <ol>
-<li><strong>Pass 1</strong>: read the dereplicated superkmer file; enumerate all unique canonical kmers into a <code>HashSet</code>. Exact count known after this pass.</li>
-<li><strong>Build a provisional MPHF</strong> (<code>GOFunction</code> from the <code>ph</code> crate) over the exact kmer set. Produces <code>mphf1.bin</code>.</li>
-<li><strong>Create <code>counts1.bin</code></strong>: one zero-initialised <code>u32</code> per MPHF slot (mmap'd).</li>
-<li><strong>Pass 2</strong>: re-read the dereplicated file; for each kmer, query <code>mphf1.get(kmer)</code> and atomically accumulate the superkmer count into <code>counts1[slot]</code>.</li>
+<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>
+<li><strong>Create <code>counts1.bin</code></strong>: <code>PersistentCompactIntVec</code> with f0 slots, zero-initialised.</li>
+<li><strong>Accumulation pass</strong>: re-read the dereplicated superkmer file; for each kmer in each superkmer, compute <code>slot = mphf.index(kmer.raw())</code> and increment <code>counts1[slot]</code> by the superkmer's COUNT.</li>
 <li><strong>Build kmer frequency spectrum</strong> from <code>counts1</code>: histogram <code>{count → n_kmers}</code>, totals f0 (distinct kmers) and f1 (total abundance). Written to <code>kmer_spectrum_raw.json</code> per partition, then merged globally.</li>
 </ol>
 <p>Files produced per partition:</p>
 <div class="highlight"><pre><span></span><code>part_XXXXX/
-  mphf1.bin               — GOFunction (provisional MPHF, discarded after phase 2)
-  counts1.bin             — [u32; n_kmers] kmer counts, mmap&#39;d
+  mphf1.bin               — ptr_hash provisional MPHF (discarded after phase 2)
+  counts1.bin             — PersistentCompactIntVec, f0 × u32 kmer counts
   kmer_spectrum_raw.json  — local frequency spectrum
 </code></pre></div>
 <h3 id="phase-2-definitive-mphf">Phase 2 — definitive MPHF</h3>
 <p>After filtering (applying a min-count threshold derived from the spectrum) and building the local De Bruijn graph + unitigs (see <a href="../pipeline/">Construction pipeline</a>), the exact filtered kmer set is available via <code>unitigs.bin</code>.</p>
-<p><code>MphfLayer::build</code> is called on the unitig file:</p>
+<p><code>MphfLayer::build(dir, block_bits, mode: &amp;IndexMode, fill_slot)</code> is called on the unitig directory:</p>
 <ol>
-<li><strong>Pass 1</strong>: iterate all canonical kmers from <code>unitigs.bin</code> in parallel, build and store <code>mphf.bin</code> (ptr_hash).</li>
-<li><strong>Pass 2</strong>: iterate sequentially, fill <code>evidence.bin</code>, call the mode-specific <code>fill_slot</code> callback.</li>
+<li><strong>Pass 1</strong> (parallel): a <code>CanonicalKmerIter</code> — clonable via <code>Arc&lt;Mmap&gt;</code>, no file reopening — is passed directly to <code>new_from_par_iter</code> via <code>par_bridge()</code>. No <code>.idx</code> is read or created at this stage; parallelism is at partition/layer level, not within a single MPHF. Produces <code>mphf.bin</code>.</li>
+<li><strong>Pass 2</strong> (sequential): iterate with <code>iter_indexed_canonical_kmers</code>; fill evidence files; call <code>fill_slot(slot, kmer)</code> callback per kmer. For Exact/Hybrid, <code>.idx</code> is written at the end of this pass — never earlier.</li>
 </ol>
 <p><code>mphf1.bin</code> and <code>counts1.bin</code> are no longer needed after phase 2 and can be deleted.</p>
 <hr />
@@ -1265,13 +1672,11 @@
 <p><strong>FMPH/FMPHGO</strong> (<code>ph</code> crate, Beling, ACM JEA 2023):</p>
 <ul>
 <li>~2.1 bits/key — most compact; good query speed; deterministic construction</li>
-<li>Works well from an exact or slightly overestimated count</li>
-<li><code>GOFunction</code> (group-oriented variant) is the specific type used</li>
+<li><code>GOFunction</code> (group-oriented variant) was the original phase-1 choice; eliminated when the external sort made the exact count available at phase 1 as well</li>
 </ul>
 <h2 id="mphf-choice-per-phase">MPHF choice per phase</h2>
-<p><strong>Phase 1</strong> (provisional, discarded after spectrum computation): <code>ph::fmph::GOFunction</code>. Compact, fast to build from the exact post-dedup kmer set. Query speed is secondary — the structure is only used during pass 2 of <code>count_kmer</code>.</p>
-<p><strong>Phase 2</strong> (persistent, queried repeatedly): <strong>ptr_hash</strong>. Exact key count is available from the unitig index; ptr_hash query speed (≥2.1×) and construction speed (≥3.1× over FMPH) are the decisive factors. The 2.4 bits/key overhead is acceptable.</p>
-<p>boomphf is eliminated: largest space overhead, streaming advantage does not apply.</p>
+<p><strong>Both phases</strong>: <strong>ptr_hash</strong>, same type alias and construction parameters. The external sort (phase 1) and the unitig index (phase 2) both provide the exact key count before MPHF construction, so ptr_hash's requirement is satisfied in both cases. Using a single MPHF implementation removes the <code>ph</code> crate dependency.</p>
+<p>boomphf: eliminated — largest space overhead, streaming advantage no longer needed. FMPH/GOFunction: eliminated — exact count available, ptr_hash is faster at equivalent compactness.</p>
 <hr />
 <h2 id="space-at-scale">Space at scale</h2>
 <p>For 1 024 partitions × 100 M kmers/partition (phase 2 index, after filtering):</p>
@@ -1318,11 +1723,14 @@
 <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)
+  unitigs.bin      — packed 2-bit nucleotide sequences (kmer evidence source)
+  unitigs.bin.idx  — random-access block index (block_bits controls granularity)
   mphf.bin         — ptr_hash phase-2 MPHF
-  evidence.bin     — n × u32: (chunk_id: 25 bits | rank: 7 bits) per slot
+  evidence.bin     — n × (chunk_id: 25 bits | rank: 7 bits) per slot  [exact mode]
+  fingerprint.bin  — n × b-bit fingerprints per slot                  [approx mode]
+  [no layer_meta.json — mode stored once in partition-level meta.json]
 </code></pre></div>
 <p>Layers are <strong>disjoint</strong>: a canonical kmer belongs to exactly one layer. Layer 0 is built from dataset A. Adding dataset B:</p>
 <ol>
@@ -1330,17 +1738,43 @@
 <li>Collect kmers of B not present in any layer → set <code>B \ A</code>.</li>
 <li>Build layer 1 from <code>B \ A</code> (dereplicate → count → De Bruijn → unitigs → <code>MphfLayer::build</code>).</li>
 </ol>
+<h3 id="evidence-modes">Evidence modes</h3>
+<p>Three evidence modes are supported via <code>IndexMode</code>, stored once in <code>PartitionMeta</code> at partition root. There is no <code>layer_meta.json</code>.</p>
+<p><strong>Exact</strong> (<code>IndexMode::Exact</code>): <code>evidence.bin</code> stores one <code>(chunk_id, rank)</code> pair per MPHF slot. Verification reconstructs the kmer and compares to the query. Zero false positives. <code>.idx</code> required at query time.</p>
+<p><strong>Approx</strong> (<code>IndexMode::Approx { b, z }</code>): <code>fingerprint.bin</code> stores a b-bit hash per slot. False-positive rate 1/2^b per query; Findere z-parameter reduces window FP to ≈ 1/2^(b·z). No <code>.idx</code> written or needed.</p>
+<p><strong>Hybrid</strong> (<code>IndexMode::Hybrid { b, z }</code>): both <code>fingerprint.bin</code> and <code>evidence.bin</code> + <code>.idx</code>. <code>find()</code> uses the fingerprint (O(1)); <code>find_strict()</code> uses exact evidence (O(1)).</p>
+<h3 id="build-functions">Build functions</h3>
+<div class="highlight"><pre><span></span><code>MphfLayer::build(dir, block_bits, mode: &amp;IndexMode, fill_slot)
+    Pass 1: CanonicalKmerIter + par_bridge() → build mphf.bin  (no .idx used)
+    Pass 2: sequential iter → fill evidence files + call fill_slot
+            .idx written last for Exact/Hybrid (query-time only)
+
+MphfLayer::build_exact_evidence(dir, block_bits)
+    Post-hoc: builds evidence.bin + .idx from existing mphf.bin + unitigs.bin
+    Uses open_sequential(); no .idx required on entry
+
+MphfLayer::build_approx_evidence(dir, b, z)
+    Post-hoc: builds fingerprint.bin from existing mphf.bin + unitigs.bin
+    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>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: decode the kmer from <code>(chunk_id, rank)</code> and compare to the query. A mismatch means the kmer is absent from this layer; probe the next layer.</p>
+<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>
+<li><strong>Exact</strong>: decode <code>(chunk_id, rank)</code> from <code>evidence.bin</code>; reconstruct the kmer via <code>unitigs.verify_canonical_kmer</code>; compare to query.</li>
+<li><strong>Approx</strong>: compare <code>kmer.seq_hash()</code> to the b-bit fingerprint stored at the slot.</li>
+</ul>
+<p>A mismatch in either mode means the kmer is absent from this layer; probe the next layer.</p>
 <h3 id="query-algorithm">Query algorithm</h3>
 <div class="highlight"><pre><span></span><code>fn query(kmer) → Option&lt;(layer_index, slot)&gt;:
     for (i, layer) in layers.iter().enumerate():
         slot = layer.mphf.index(kmer)
-        if layer.evidence.decode(slot) matches kmer:
+        if layer.evidence.matches(slot, kmer):   // exact or approx dispatch
             return Some((i, slot))
     return None
 </code></pre></div>
-<p>Expected probe depth: 1 for kmers in layer 0. Each probe is a ptr_hash lookup (~10 ns) plus one evidence decode.</p>
+<p><code>MphfLayer::find</code> dispatches on <code>LayerEvidence</code> at O(1) — no panicking <code>find_exact</code>/<code>find_approx</code> methods. <code>find_strict</code> always performs an exact check: O(1) for Exact/Hybrid, O(n) sequential scan for Approx. Expected probe depth: 1 for kmers in layer 0. Each probe is a ptr_hash lookup (~10 ns) plus one evidence check.</p>
 <h3 id="merging-layers">Merging layers</h3>
 <p>Two layer chains can be merged by re-indexing their union through the full pipeline. This is expensive (full rebuild) but produces an optimal single-layer index. Merge is a maintenance operation, not a query-path requirement.</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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-        <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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-        <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">
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@@ -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>
       
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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>
             
   
@@ -662,6 +717,17 @@
     </span>
   </a>
   
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#make_pipe-dsl" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        make_pipe! DSL
+      
+    </span>
+  </a>
+  
 </li>
         
       </ul>
@@ -802,14 +868,42 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../evidence_elimination/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    Evidence elimination (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../layer_tier/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obikindex layer tier
   
 
     
@@ -879,6 +973,202 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    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)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
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-        <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">
             
   
   
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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>
             
   
@@ -989,6 +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>
       
@@ -1087,6 +1461,17 @@
     </span>
   </a>
   
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#make_pipe-dsl" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        make_pipe! DSL
+      
+    </span>
+  </a>
+  
 </li>
         
       </ul>
@@ -1145,7 +1530,7 @@
 
 
 <h1 id="obipipeline-parallel-pipeline-library">obipipeline — parallel pipeline library</h1>
-<p><code>obipipeline</code> is a generic, multi-threaded data pipeline crate. It connects a <strong>source</strong>, a chain of <strong>transforms</strong>, and a <strong>sink</strong> via crossbeam channels, running each stage with a shared worker pool and a biased scheduler.</p>
+<p><code>obipipeline</code> is a generic, multi-threaded data pipeline crate. It connects a <strong>source</strong>, a chain of <strong>stages</strong>, and a <strong>sink</strong> via crossbeam channels, running each stage with a shared worker pool and a biased scheduler.</p>
 <h2 id="core-types">Core types</h2>
 <table>
 <thead>
@@ -1158,22 +1543,33 @@
 <tbody>
 <tr>
 <td><code>SourceFn&lt;D&gt;</code></td>
-<td><code>Box&lt;dyn FnMut() -&gt; Result&lt;D, PipelineError&gt; + Send+Sync&gt;</code></td>
+<td><code>Box&lt;dyn FnMut() -&gt; Result&lt;D, PipelineError&gt; + Send&gt;</code></td>
 <td>Called repeatedly; <code>FnMut</code> because it holds iterator state</td>
 </tr>
 <tr>
 <td><code>SharedFn&lt;D&gt;</code></td>
-<td><code>Arc&lt;dyn Fn(D) -&gt; Result&lt;D, PipelineError&gt; + Send+Sync&gt;</code></td>
-<td>Shared across workers via <code>Arc::clone</code> (no copy of the closure)</td>
+<td><code>Arc&lt;dyn Fn(D) -&gt; Result&lt;D, PipelineError&gt; + Send + Sync&gt;</code></td>
+<td>1→1 transform shared across workers via <code>Arc::clone</code></td>
+</tr>
+<tr>
+<td><code>SharedFlatFn&lt;D&gt;</code></td>
+<td><code>Arc&lt;dyn Fn(D, &amp;Sender&lt;Result&lt;D, _&gt;&gt;, &amp;Sender&lt;isize&gt;) + Send + Sync&gt;</code></td>
+<td>1→N transform; pushes items into channel, sends delta</td>
 </tr>
 <tr>
 <td><code>SinkFn&lt;D&gt;</code></td>
-<td><code>Box&lt;dyn Fn(D) -&gt; Result&lt;(), PipelineError&gt; + Send+Sync&gt;</code></td>
+<td><code>Box&lt;dyn Fn(D) -&gt; Result&lt;(), PipelineError&gt; + Send&gt;</code></td>
 <td>Final consumer; returns <code>Result</code> so errors propagate back</td>
 </tr>
 </tbody>
 </table>
-<p><code>Pipeline&lt;D&gt;</code> holds one <code>SourceFn</code>, a <code>Vec&lt;SharedFn&gt;</code>, and one <code>SinkFn</code>.<br />
+<p>Stages come in two variants:</p>
+<div class="highlight"><pre><span></span><code><span class="k">pub</span><span class="w"> </span><span class="k">enum</span><span class="w"> </span><span class="nc">Stage</span><span class="o">&lt;</span><span class="n">D</span><span class="o">&gt;</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="n">Transform</span><span class="p">(</span><span class="n">SharedFn</span><span class="o">&lt;</span><span class="n">D</span><span class="o">&gt;</span><span class="p">),</span><span class="w">   </span><span class="c1">// 1→1</span>
+<span class="w">    </span><span class="n">Flat</span><span class="p">(</span><span class="n">SharedFlatFn</span><span class="o">&lt;</span><span class="n">D</span><span class="o">&gt;</span><span class="p">),</span><span class="w">    </span><span class="c1">// 1→N</span>
+<span class="p">}</span>
+</code></pre></div>
+<p><code>Pipeline&lt;D&gt;</code> holds one <code>SourceFn</code>, a <code>Vec&lt;Stage&gt;</code>, and one <code>SinkFn</code>.<br />
 <code>WorkerPool&lt;D&gt;</code> wraps a <code>Pipeline</code> with <code>n_workers</code> and channel <code>capacity</code>.</p>
 <h2 id="workerpool">WorkerPool</h2>
 <div class="highlight"><pre><span></span><code><span class="n">WorkerPool</span><span class="p">::</span><span class="n">new</span><span class="p">(</span><span class="n">pipeline</span><span class="p">:</span><span class="w"> </span><span class="nc">Pipeline</span><span class="o">&lt;</span><span class="n">D</span><span class="o">&gt;</span><span class="p">,</span><span class="w"> </span><span class="n">n_workers</span><span class="p">:</span><span class="w"> </span><span class="kt">usize</span><span class="p">,</span><span class="w"> </span><span class="n">capacity</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">Self</span>
@@ -1193,7 +1589,7 @@
 </tr>
 <tr>
 <td><code>capacity</code></td>
-<td>Bound on every crossbeam channel in the pipeline (source output, inter-stage channels, worker input, sink input, sink error). Controls memory and back-pressure: a full channel blocks the sender until a slot frees.</td>
+<td>Bound on every crossbeam channel in the pipeline. Controls memory and back-pressure: a full channel blocks the sender until a slot frees.</td>
 </tr>
 </tbody>
 </table>
@@ -1208,7 +1604,7 @@
 </code></pre></div>
 <p>Each variant carries the concrete type for one stage's output. The macros pattern-match on this enum to route values between stages.</p>
 <h2 id="macros">Macros</h2>
-<p>Six low-level macros build individual stages; one high-level macro (<code>make_pipeline!</code>) composes them.</p>
+<p>Eight low-level macros build individual stages; one high-level macro (<code>make_pipeline!</code>) composes them.</p>
 <h3 id="low-level">Low-level</h3>
 <div class="highlight"><pre><span></span><code><span class="n">make_source</span><span class="o">!</span><span class="p">(</span><span class="n">Enum</span><span class="p">,</span><span class="w"> </span><span class="n">iterator</span><span class="p">,</span><span class="w"> </span><span class="n">OutputVariant</span><span class="p">)</span><span class="w">          </span><span class="c1">// iterator yields T</span>
 <span class="n">make_source_fallible</span><span class="o">!</span><span class="p">(</span><span class="n">Enum</span><span class="p">,</span><span class="w"> </span><span class="n">iterator</span><span class="p">,</span><span class="w"> </span><span class="n">OutputVariant</span><span class="p">)</span><span class="w"> </span><span class="c1">// iterator yields Result&lt;T, E&gt;</span>
@@ -1216,6 +1612,9 @@
 <span class="n">make_transform</span><span class="o">!</span><span class="p">(</span><span class="n">Enum</span><span class="p">,</span><span class="w"> </span><span class="n">func</span><span class="p">,</span><span class="w"> </span><span class="n">InputVariant</span><span class="p">,</span><span class="w"> </span><span class="n">OutputVariant</span><span class="p">)</span><span class="w">          </span><span class="c1">// func: T -&gt; U</span>
 <span class="n">make_transform_fallible</span><span class="o">!</span><span class="p">(</span><span class="n">Enum</span><span class="p">,</span><span class="w"> </span><span class="n">func</span><span class="p">,</span><span class="w"> </span><span class="n">InputVariant</span><span class="p">,</span><span class="w"> </span><span class="n">OutputVariant</span><span class="p">)</span><span class="w"> </span><span class="c1">// func: T -&gt; Result&lt;U, E&gt;</span>
 
+<span class="n">make_flat_transform</span><span class="o">!</span><span class="p">(</span><span class="n">Enum</span><span class="p">,</span><span class="w"> </span><span class="n">func</span><span class="p">,</span><span class="w"> </span><span class="n">InputVariant</span><span class="p">,</span><span class="w"> </span><span class="n">OutputVariant</span><span class="p">)</span><span class="w">          </span><span class="c1">// func: T -&gt; impl IntoIterator&lt;Item=U&gt;</span>
+<span class="n">make_flat_transform_fallible</span><span class="o">!</span><span class="p">(</span><span class="n">Enum</span><span class="p">,</span><span class="w"> </span><span class="n">func</span><span class="p">,</span><span class="w"> </span><span class="n">InputVariant</span><span class="p">,</span><span class="w"> </span><span class="n">OutputVariant</span><span class="p">)</span><span class="w"> </span><span class="c1">// func: T -&gt; Result&lt;impl IntoIterator&lt;Item=U&gt;, E&gt;</span>
+
 <span class="n">make_sink</span><span class="o">!</span><span class="p">(</span><span class="n">Enum</span><span class="p">,</span><span class="w"> </span><span class="n">func</span><span class="p">,</span><span class="w"> </span><span class="n">InputVariant</span><span class="p">)</span><span class="w">           </span><span class="c1">// func: T -&gt; ()</span>
 <span class="n">make_sink_fallible</span><span class="o">!</span><span class="p">(</span><span class="n">Enum</span><span class="p">,</span><span class="w"> </span><span class="n">func</span><span class="p">,</span><span class="w"> </span><span class="n">InputVariant</span><span class="p">)</span><span class="w">  </span><span class="c1">// func: T -&gt; Result&lt;(), E&gt;</span>
 </code></pre></div>
@@ -1224,17 +1623,31 @@
 <div class="highlight"><pre><span></span><code>make_pipeline! {
     DataEnum,
     source   iterator     =&gt; OutputVariant,   // or source?  for fallible
-    | func:  In =&gt; Out,                        // non-fallible transform
-    |? func: In =&gt; Out,                        // fallible transform
+    |   func: In =&gt; Out,                       // 1→1 non-fallible transform
+    |?  func: In =&gt; Out,                       // 1→1 fallible transform
+    ||  func: In =&gt; Out,                       // 1→N non-fallible flat transform
+    ||? func: In =&gt; Out,                       // 1→N fallible flat transform
     sink     func         @ InputVariant,      // or sink?    for fallible
 }
 </code></pre></div>
 <p><code>?</code> marks fallibility on source, individual transforms, or sink independently.<br />
 Implemented as a <strong>TT muncher</strong>: the internal rule <code>@build</code> recurses over transform tokens one at a time, accumulating them into a <code>vec![]</code>, then terminates on <code>sink</code>/<code>sink?</code>.</p>
+<h3 id="make_pipe-dsl">make_pipe! DSL</h3>
+<p><code>make_pipe!</code> builds a sourceless/sinkless <code>Pipe&lt;D, In, Out&gt;</code> — a reusable, composable stage sequence:</p>
+<div class="highlight"><pre><span></span><code>make_pipe! {
+    DataEnum : InType =&gt; OutType,
+    |   func: InVariant =&gt; OutVariant,
+    |?  func: InVariant =&gt; OutVariant,
+    ||  func: InVariant =&gt; OutVariant,
+    ||? func: InVariant =&gt; OutVariant,
+}
+</code></pre></div>
+<p>Two pipes compose with <code>.then(other)</code>. Apply to an iterator with <code>.apply(iter, n_workers, capacity)</code> to get a <code>PipeIter&lt;Out&gt;</code> — an iterator over the pipeline output, backed by a background <code>WorkerPool</code>. The scatter step in <code>obikmer</code> uses <code>make_pipe!</code> and <code>.apply()</code> rather than the full <code>make_pipeline!</code> / <code>WorkerPool</code> pattern.</p>
 <h2 id="scheduler-architecture">Scheduler architecture</h2>
 <div class="highlight"><pre><span></span><code>Source thread ──► [source_rx] ──► Scheduler ──► [worker_tx] ──► Workers (×N)
                                       ▲                               │
                   [stage_rxs] ────────┘◄──────────────────────────────┘
+                  [flat_delta_rx] ──► Scheduler  (in_flight adjustment)
                                       │
                               [sink_err_rx]  ← errors from sink (highest priority)
                                       │
@@ -1242,20 +1655,20 @@ Implemented as a <strong>TT muncher</strong>: the internal rule <code>@build</co
 </code></pre></div>
 <p>The scheduler is a single thread running a biased <code>Select</code> over all input channels. Priority order (highest first):</p>
 <div class="highlight"><pre><span></span><code>index 0       sink_err_rx          abort on sink error
-index 1       stage_rxs[N-1]       drain last stage first
-...
-index N       stage_rxs[0]
-index N+1     source_rx            pull new data last
+index 1       flat_delta_rx        adjust in_flight before dispatching
+index 2..=n+1 stage_rxs[n-1..0]   drain last stage first
+index n+2     source_rx            pull new data last
 </code></pre></div>
 <p>This back-pressure-friendly ordering ensures downstream stages are drained before new items enter the pipeline.</p>
-<p><strong>Workers</strong> are generic: each receives <code>(data, SharedFn, result_tx)</code> and calls <code>f(data)</code>, sending the result to the provided channel. The scheduler decides which transform to apply and where to route the result.</p>
-<p><strong>Termination</strong> uses an <code>in_flight</code> counter:</p>
+<p><strong>Workers</strong> are generic: each receives a <code>WorkerTask</code> — either <code>Transform(data, stage_idx)</code> or <code>Flat(data, stage_idx)</code>. For <code>Transform</code>, the worker calls <code>f(data)</code> and sends the result to <code>stage_txs[stage_idx]</code>. For <code>Flat</code>, the worker calls <code>f(data, &amp;push_tx, &amp;delta_tx)</code>: the closure pushes N items into <code>push_tx</code> then sends <code>N-1</code> to <code>delta_tx</code>. The scheduler uses the delta to adjust <code>in_flight</code> without knowing N in advance.</p>
+<p><strong>Termination</strong> uses an <code>in_flight: isize</code> counter and a <code>flat_workers_active: usize</code> counter:</p>
 <ul>
-<li>incremented when an item is dispatched from source to workers</li>
-<li>decremented when the item exits the last stage</li>
-<li>the loop exits only when <code>source_done &amp;&amp; in_flight == 0</code></li>
+<li><code>in_flight</code> incremented when an item is dispatched from source to workers</li>
+<li><code>in_flight</code> decremented when the item exits the last stage to the sink</li>
+<li><code>flat_workers_active</code> incremented when a <code>Flat</code> task is dispatched, decremented when the delta arrives</li>
+<li>the loop exits only when <code>source_done &amp;&amp; in_flight == 0 &amp;&amp; flat_workers_active == 0</code></li>
 </ul>
-<p>This guarantees all in-flight items complete before <code>join()</code>.</p>
+<p>This guarantees all in-flight items complete (including all N outputs of a flat stage) before <code>join()</code>.</p>
 <h2 id="error-handling">Error handling</h2>
 <p><code>PipelineError</code> has four variants:</p>
 <table>
@@ -1279,7 +1692,7 @@ index N+1     source_rx            pull new data last
 <td>Internal routing error</td>
 </tr>
 <tr>
-<td><code>StepError(Box&lt;dyn Error&gt;)</code></td>
+<td><code>StepError(Box&lt;dyn Error + Send + Sync&gt;)</code></td>
 <td>Error from user code (wrapped by <code>make_*_fallible!</code>)</td>
 </tr>
 </tbody>

DevDoc/implementation/persistent_bit_vec/index.html

@@ -12,7 +12,7 @@
         <link rel="prev" href="../persistent_compact_int_vec/">
       
       
-        <link rel="next" href="../../architecture/sequences/invariant/">
+        <link rel="next" href="../merge/">
       
       
         
@@ -182,6 +182,33 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+
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+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
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@@ -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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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
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             <span class="md-nav__icon md-icon"></span>
             
   
@@ -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">
+    
+  
+    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>
         
           
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@@ -408,8 +463,8 @@
             <span class="md-nav__icon md-icon"></span>
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             <span class="md-nav__icon md-icon"></span>
             
   
@@ -650,14 +705,42 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../evidence_elimination/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    Evidence elimination (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../layer_tier/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obikindex layer tier
   
 
     
@@ -1002,6 +1085,202 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
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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">
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+
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+  </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">
+        
+  
+  
+  <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>
       
@@ -1024,10 +1303,10 @@
       
         
         
-        <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">
             
   
   
@@ -1045,8 +1324,8 @@
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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>
             
   
@@ -1112,6 +1391,90 @@
 
               
             
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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>
+  
+  
+
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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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+  <span class="md-ellipsis">
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+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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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">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
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+  
     
     
     
@@ -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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+    <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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+  
+
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+  </span>
+  
+  
+
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+    </li>
+  
+
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+            
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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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@@ -650,14 +705,42 @@
   
   
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+      <a href="../evidence_elimination/" class="md-nav__link">
         
   
   
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-    obilayeredmap crate
+    Evidence elimination (discussion)
+  
+
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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="../layer_tier/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obikindex layer tier
   
 
     
@@ -985,6 +1068,202 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+  
+    Merge command
+  
+
+    
+  </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="../merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge parallelism & memory
+  
+
+    
+  </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="../filtering/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
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+  
+
+    
+  </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="../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>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <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>
+  
+
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+            
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         </nav>
       
@@ -1007,10 +1286,10 @@
       
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
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+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
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+  <span class="md-ellipsis">
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+    NUMA-aware worker pools
+  
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+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
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+      <a href="../evidence_elimination/" class="md-nav__link">
         
   
   
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-    obilayeredmap crate
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+  
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+    obikindex layer tier
   
 
     
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+  
+  
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+    <li class="md-nav__item">
+      <a href="../merge/" class="md-nav__link">
+        
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+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
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+    NUMA-aware worker pools
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+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
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@@ -1104,7 +1467,9 @@
 <li><strong>error valley</strong> → suggests min_count (typically the local minimum between the error peak and the coverage peak)</li>
 </ul>
 <h2 id="phase-1-scatter">Phase 1 — Scatter</h2>
-<p>Single streaming pass over raw input files (FASTA/FASTQ, gzip). FASTQ quality scores are ignored. For each read:</p>
+<p>Single streaming pass over raw input files (FASTA/FASTQ, gzip). FASTQ quality scores are ignored.</p>
+<p>Input files are read via <code>open_nuc_stream</code>, which opens and decompresses the file, auto-detects the format (FASTA / FASTQ / GenBank), and yields a sequence of <code>NucPage</code> buffers. Each <code>NucPage</code> is a flat 64 KB buffer of normalised bytes (<code>ACGT</code> + <code>\x00</code> separators), carrying a k−1 byte overlap from the preceding page so that no k-mer is lost at page boundaries. Per-record identity (sequence id, raw bytes) is not preserved; this is intentional — the scatter phase only needs normalised bases to produce superkmers.</p>
+<p>For each read fragment within a page:</p>
 <ol>
 <li><strong>Ambiguous base filter</strong>: cut at any non-ACGT base; discard fragments shorter than k.</li>
 <li><strong>Entropy filter</strong>: scan each fragment with a sliding window of size k. When the kmer <span class="arithmatex">\(K_i = S[i \mathinner{..} i+k-1]\)</span> ended by nucleotide <span class="arithmatex">\(S[j]\)</span> (with <span class="arithmatex">\(j = i+k-1\)</span>) has entropy below threshold <span class="arithmatex">\(\theta\)</span>, emit the current segment and start a new one (see algorithm below). <span class="arithmatex">\(K_i\)</span> belongs to neither segment, and no valid kmer is lost.</li>
@@ -1154,8 +1519,13 @@ B ≈ 100 is tunable; RAM needed ≈ partition_size / B.</p>
     for each kmer in sequence:
         kmer_counts[canonical(kmer)] += COUNT
 </code></pre></div>
-<p>Implemented as an external sort or a temporary HashMap, depending on partition size. At the end of this phase, each distinct canonical kmer has its exact total count.</p>
-<p>Abundance filter applied here: kmers with <code>total_count &lt; q</code> are discarded. <code>q</code> is a collection parameter (0 = keep all, including singletons for ≤1x data).</p>
+<p>Implemented as a three-step pipeline in <code>count_partition()</code>:</p>
+<ol>
+<li><strong>External sort</strong> (<code>kmer_sort::sort_unique_kmers</code>): read dereplicated superkmers, extract canonical kmer raw <code>u64</code> values, sort in RAM-bounded chunks (adaptive: 40% of available RAM ÷ n_threads, min 1 M kmers/chunk), k-way merge with inline dedup → <code>sorted_unique.bin</code>. f0 is now known exactly.</li>
+<li><strong>Provisional MPHF</strong> (ptr_hash): built from <code>sorted_unique.bin</code> via <code>new_from_par_iter(f0, ...)</code>. Stored to <code>mphf1.bin</code>; <code>sorted_unique.bin</code> deleted immediately.</li>
+<li><strong>Accumulation pass</strong>: re-read dereplicated superkmers; for each kmer, <code>slot = mphf.index(kmer.raw())</code>, increment <code>counts1[slot]</code> by the superkmer COUNT. Stored in a <code>PersistentCompactIntVec</code> (<code>counts1.bin</code>).</li>
+</ol>
+<p>At the end of this phase, each distinct canonical kmer has its exact total count, and the frequency spectrum (<code>spectrums/{label}.json</code>) is written to the index root.</p>
 <p>No pre-filter on super-kmer COUNT is possible at phase 2: a super-kmer with COUNT=1 may contain only high-abundance kmers, each present in many other super-kmers across the partition.</p>
 <h2 id="phase-4-super-kmer-compaction">Phase 4 — Super-kmer compaction</h2>
 <p>The valid kmer set from phase 3 is used as a mask to rewrite the super-kmer files:</p>
@@ -1188,14 +1558,52 @@ branching / dead-end → unitig start or end
 <p>Output: <code>unitigs.bin</code> — the permanent evidence structure for the partition. Each kmer in the partition appears at exactly one (unitig_id, offset) location.</p>
 <p><strong>Scope of local unitigs:</strong> these are unitigs of the partition's local de Bruijn graph, not global unitigs. A kmer whose k-1 successor or predecessor falls in another partition appears as a dead end locally and terminates the unitig. This does not affect correctness of verification but means partition-local unitigs cannot be directly reused for global assembly.</p>
 <h2 id="phase-6-mphf-construction-and-index-finalisation">Phase 6 — MPHF construction and index finalisation</h2>
-<p>Built once on the definitive kmer set (all kmers in all unitigs of the partition). See <a href="../obilayeredmap/">obilayeredmap</a> and <a href="../mphf/">MPHF selection</a> for the current implementation.</p>
-<div class="highlight"><pre><span></span><code>kmers from unitigs → MPHF → mphf.bin
-                   → evidence.bin : n × u32, each = (chunk_id: 25 bits | rank: 7 bits)
-                   → payload      : counts/ (mode 2) or presence/ (mode 3)
+<p><code>build_index_layer</code> is called per partition (in parallel via <code>build_layers</code>) with the following parameters sourced from <code>IndexConfig</code>:</p>
+<ul>
+<li><code>block_bits</code> — from <code>IndexConfig::block_bits</code>; controls the <code>.idx</code> block size (2^block_bits unitig chunks per block) for exact evidence</li>
+<li><code>evidence</code> — <code>EvidenceKind::Exact</code> or <code>EvidenceKind::Approx { b, z }</code>; propagated unchanged from <code>IndexConfig::evidence</code></li>
+<li><code>min_ab</code> / <code>max_ab</code> — abundance bounds applied before graph construction</li>
+<li><code>with_counts</code> — whether to store kmer counts alongside set membership</li>
+</ul>
+<p><strong>Abundance filtering:</strong> when <code>min_ab &gt; 1</code> or <code>max_ab.is_some()</code>, the provisional <code>mphf1.bin</code> and <code>counts1.bin</code> produced in phase 3 are memory-mapped. Each canonical kmer is accepted only if its count in <code>counts1</code> satisfies the bounds. If either file is absent, filtering is skipped (all kmers accepted).</p>
+<div class="highlight"><pre><span></span><code>for each kmer in dereplicated super-kmer:
+    ab = counts1[mphf1.index(kmer.raw())]
+    if ab &lt; min_ab || ab &gt; max_ab: skip
+    graph.push(kmer)
 </code></pre></div>
-<p>The MPHF is built in two passes over <code>unitigs.bin</code>: parallel pass for <code>mphf.bin</code>, sequential pass for <code>evidence.bin</code> and payload. The exact kmer count is available from the unitig index (<code>unitigs.bin.idx</code>) before the passes begin.</p>
-<p><strong>Exact verification via unitig evidence:</strong></p>
-<p><code>unitigs.bin</code> serves as the evidence structure. The MPHF maps every input to <code>[0, N)</code> including absent kmers — the unitig read-back (via <code>evidence.bin</code>) is the only correct membership test.</p>
+<p><strong>Graph build and unitig write:</strong></p>
+<p>The surviving kmers are fed into <code>GraphDeBruijn</code>, which computes degrees and yields unitigs. Unitigs are written to <code>layer_0/unitigs.bin</code> via a <code>UnitigFileWriter</code>.</p>
+<p><strong>MPHF and evidence build:</strong></p>
+<p><code>Layer::build</code> (membership-only) or <code>Layer::&lt;PersistentCompactIntMatrix&gt;::build</code> (with counts) is called next. Internally, <code>MphfLayer::build</code> performs two passes:</p>
+<ol>
+<li><strong>Pass 1 (parallel):</strong> build <code>unitigs.bin.idx</code> (block size = 2^<code>block_bits</code>) then construct the MPHF from all canonical kmers in <code>unitigs.bin</code>; store to <code>mphf.bin</code>.</li>
+<li><strong>Pass 2 (sequential):</strong> for each kmer in <code>unitigs.bin</code>, compute its slot and write <code>evidence.bin</code> (<code>chunk_id: 25 bits | rank: 7 bits</code> packed into a <code>u32</code>); also invoke the payload callback (<code>fill_slot</code>) to populate <code>counts/</code> if <code>with_counts</code>.</li>
+</ol>
+<p>After <code>Layer::build</code> completes, <code>layer_meta.json</code> records <code>EvidenceKind::Exact</code>.</p>
+<p><strong>Approximate evidence override:</strong></p>
+<p>If <code>evidence</code> is <code>EvidenceKind::Approx { b, z }</code>, <code>build_approx_evidence</code> is called immediately after <code>Layer::build</code>. It overwrites the exact evidence bundle with <code>fingerprint.bin</code> (b-bit hash per slot) and rewrites <code>layer_meta.json</code> with <code>EvidenceKind::Approx { b, z }</code>. No <code>.idx</code> file is needed at query time in this mode.</p>
+<div class="highlight"><pre><span></span><code>// Exact path  →  evidence.bin + unitigs.bin.idx + layer_meta.json(Exact)
+// Approx path →  fingerprint.bin + layer_meta.json(Approx{b,z})
+//               (evidence.bin left on disk but not used)
+</code></pre></div>
+<p><strong>Partition metadata:</strong></p>
+<p>After all layer files are written, <code>PartitionMeta { n_layers: 1 }</code> is serialised to <code>index/meta.json</code> inside the partition directory. This file is required by <code>LayeredMap::open</code> for subsequent merge operations.</p>
+<p><strong>File layout per partition after phase 6:</strong></p>
+<div class="highlight"><pre><span></span><code>part_XXXXX/
+  index/
+    meta.json                ← PartitionMeta { n_layers: 1 }
+    layer_0/
+      unitigs.bin            ← permanent evidence (all modes)
+      unitigs.bin.idx        ← block index (exact mode only)
+      mphf.bin               ← MPHF
+      evidence.bin           ← exact evidence (exact mode)
+      fingerprint.bin        ← b-bit fingerprints (approx mode)
+      layer_meta.json        ← EvidenceKind tag
+      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="../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/
   → MPHF(q) → slot s
@@ -1204,7 +1612,13 @@ branching / dead-end → unitig start or end
   → match   : return payload[s]   ← exact hit
   → no match: kmer absent         ← MPHF collision on absent kmer
 </code></pre></div>
-<p><code>superkmers.bin.gz</code> is no longer needed at this point and can be deleted.</p>
+<p><strong>Query path (approximate evidence):</strong></p>
+<div class="highlight"><pre><span></span><code>query kmer q
+  → MPHF(q) → slot s
+  → fingerprint[s] matches seq_hash(q)?
+  → yes : probable hit (FP rate = 1/2^b per kmer, 1/2^(b·z) per z-window)
+  → no  : kmer absent
+</code></pre></div>
 <div class="footnote">
 <hr />
 <ol>

DevDoc/implementation/superkmer/index.html

@@ -9,7 +9,7 @@
       
       
       
-        <link rel="prev" href="../../theory/indexing/">
+        <link rel="prev" href="../../theory/evolutionary_distances/">
       
       
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@@ -182,6 +182,33 @@
   
   
   
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@@ -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 @@
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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>
             
   
@@ -752,14 +807,42 @@
   
   
     <li class="md-nav__item">
-      <a href="../obilayeredmap/" class="md-nav__link">
+      <a href="../evidence_elimination/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    obilayeredmap crate
+    Evidence elimination (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../layer_tier/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obikindex layer tier
   
 
     
@@ -829,6 +912,202 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge command
+  
+
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+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
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+    Kmer filtering
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+  </span>
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+  
+
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+
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+      <a href="../select/" class="md-nav__link">
+        
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+  
+
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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">
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+  
+    obitaxonomy crate
+  
+
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+  
+  
+
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+    </li>
+  
+
+              
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+              
+                
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+  
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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">
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+  
+    Benchmark: query-path testing
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+
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+  
+  
+
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+    </li>
+  
+
+              
+            
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+  
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+  
+    <li class="md-nav__item">
+      <a href="../partition_layer_cache/" class="md-nav__link">
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+    Partition and layer caching (discussion)
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+  
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+
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@@ -851,10 +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" >
         
           
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@@ -872,8 +1151,8 @@
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-        <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>
             
   
@@ -939,6 +1218,90 @@
 
               
             
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+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
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+  
+  
+
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+    </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>
+  
+  
+
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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_partition_runner/" class="md-nav__link">
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+  
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+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
           </ul>
         </nav>
       
@@ -1046,61 +1409,49 @@
 
 <h1 id="superkmer-implementation">SuperKmer — implementation</h1>
 <h2 id="memory-layout">Memory layout</h2>
-<p>A super-kmer is stored as a <strong>32-bit header</strong> followed by a <strong>byte-aligned nucleotide sequence</strong> (2 bits/base, nucleotide 0 at the MSB of the first byte):</p>
+<p><code>SuperKmer</code> holds two separate fields:</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">SuperKmer</span><span class="w"> </span><span class="p">{</span>
+<span class="w">    </span><span class="k">pub</span><span class="p">(</span><span class="k">crate</span><span class="p">)</span><span class="w"> </span><span class="n">count</span><span class="p">:</span><span class="w"> </span><span class="kt">u32</span><span class="p">,</span>
+<span class="w">    </span><span class="k">pub</span><span class="p">(</span><span class="k">crate</span><span class="p">)</span><span class="w"> </span><span class="n">inner</span><span class="p">:</span><span class="w"> </span><span class="nc">PackedSeq</span><span class="p">,</span>
+<span class="p">}</span>
+</code></pre></div>
+<p><code>PackedSeq</code> stores a 2-bit packed DNA sequence as a heap-allocated <code>Box&lt;[u8]&gt;</code> plus a <code>tail: u8</code> field:</p>
 <table>
 <thead>
 <tr>
 <th>Field</th>
-<th>Bits</th>
+<th>Type</th>
 <th>Role</th>
 </tr>
 </thead>
 <tbody>
 <tr>
-<td>COUNT</td>
-<td>24</td>
-<td>Occurrence count (≤ 16 M)</td>
+<td><code>tail</code></td>
+<td><code>u8</code></td>
+<td>Number of valid nucleotides in the last byte: 0 encodes 4, 1–3 are identity</td>
 </tr>
 <tr>
-<td>NKMERS</td>
-<td>8</td>
-<td>Number of kmers (= seq_length − k + 1, range 1–255)</td>
+<td><code>seq</code></td>
+<td><code>Box&lt;[u8]&gt;</code></td>
+<td>2-bit packed bytes, nucleotide 0 at bits 7–6 of <code>seq[0]</code></td>
 </tr>
 </tbody>
 </table>
-<p>Bit layout (MSB to LSB): <code>[31:8] COUNT  [7:0] NKMERS</code></p>
-<p>NKMERS is stored as a raw <code>u8</code> in <strong>kmer units</strong>, not nucleotides. The nucleotide length is recovered as <code>NKMERS + k − 1</code>. This avoids the awkward wrapping convention (<code>0 = 256</code>) that would be needed if nucleotide length were stored directly, and gains k−1 = 30 units of headroom:</p>
-<table>
-<thead>
-<tr>
-<th>unit</th>
-<th>u8 covers</th>
-<th>max nucleotides</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-<td>nucleotides</td>
-<td>255 nt</td>
-<td>225 kmers</td>
-</tr>
-<tr>
-<td><strong>kmers</strong></td>
-<td><strong>255 kmers</strong></td>
-<td><strong>285 nt</strong></td>
-</tr>
-</tbody>
-</table>
-<p>The public accessors:</p>
-<div class="highlight"><pre><span></span><code><span class="k">fn</span><span class="w"> </span><span class="nf">n_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="kt">usize</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="p">(</span><span class="bp">self</span><span class="p">.</span><span class="mi">0</span><span class="w"> </span><span class="o">&amp;</span><span class="w"> </span><span class="mh">0xFF</span><span class="p">)</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="kt">usize</span><span class="w"> </span><span class="p">}</span>
-<span class="k">fn</span><span class="w"> </span><span class="nf">seql</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="kt">usize</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">n_kmers</span><span class="p">()</span><span class="w"> </span><span class="o">+</span><span class="w"> </span><span class="n">K</span><span class="w"> </span><span class="o">-</span><span class="w"> </span><span class="mi">1</span><span class="w"> </span><span class="p">}</span>
-<span class="k">fn</span><span class="w"> </span><span class="nf">count</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="kt">u32</span><span class="w">   </span><span class="p">{</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="mi">0</span><span class="w"> </span><span class="o">&gt;&gt;</span><span class="w"> </span><span class="mi">8</span><span class="w"> </span><span class="p">}</span>
-<span class="k">fn</span><span class="w"> </span><span class="nf">increment</span><span class="p">(</span><span class="o">&amp;</span><span class="k">mut</span><span class="w"> </span><span class="bp">self</span><span class="p">)</span><span class="w">               </span><span class="p">{</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="mi">0</span><span class="w"> </span><span class="o">+=</span><span class="w"> </span><span class="mi">1</span><span class="w"> </span><span class="o">&lt;&lt;</span><span class="w"> </span><span class="mi">8</span><span class="p">;</span><span class="w"> </span><span class="p">}</span>
-<span class="k">fn</span><span class="w"> </span><span class="nf">add</span><span class="p">(</span><span class="o">&amp;</span><span class="k">mut</span><span class="w"> </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">u32</span><span class="p">)</span><span class="w">             </span><span class="p">{</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="mi">0</span><span class="w"> </span><span class="o">+=</span><span class="w"> </span><span class="n">n</span><span class="w"> </span><span class="o">&lt;&lt;</span><span class="w"> </span><span class="mi">8</span><span class="p">;</span><span class="w"> </span><span class="p">}</span>
-<span class="k">fn</span><span class="w"> </span><span class="nf">set_count</span><span class="p">(</span><span class="o">&amp;</span><span class="k">mut</span><span class="w"> </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">u32</span><span class="p">)</span><span class="w">       </span><span class="p">{</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="mi">0</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="p">(</span><span class="bp">self</span><span class="p">.</span><span class="mi">0</span><span class="w"> </span><span class="o">&amp;</span><span class="w"> </span><span class="mh">0xFF</span><span class="p">)</span><span class="w"> </span><span class="o">|</span><span class="w"> </span><span class="p">(</span><span class="n">n</span><span class="w"> </span><span class="o">&lt;&lt;</span><span class="w"> </span><span class="mi">8</span><span class="p">);</span><span class="w"> </span><span class="p">}</span>
+<p>Nucleotide length is recovered without storing it explicitly:</p>
+<div class="highlight"><pre><span></span><code>seql = (seq.len() - 1) * 4 + tail_count(tail)
+</code></pre></div>
+<p>There is no packed header word — <code>count</code> and the sequence live in separate fields.</p>
+<p>The on-disk binary format (produced by <code>write_to_binary</code>) is:</p>
+<div class="highlight"><pre><span></span><code>[varint(count)] [u8: seql − k] [packed bytes…]
+</code></pre></div>
+<p><code>seql − k</code> fits in a <code>u8</code> when <code>n_kmers = seql − k + 1 ≤ MAX_KMERS_PER_CHUNK (= 256)</code>. If a super-kmer exceeds 256 kmers, <code>write_to_binary</code> splits it into overlapping chunks (k−1 nucleotide overlap, same count per chunk), each a self-contained record readable by <code>read_from_binary</code>.</p>
+<p>The public accessors operate on the struct fields directly:</p>
+<div class="highlight"><pre><span></span><code><span class="k">fn</span><span class="w"> </span><span class="nf">seql</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="kt">usize</span><span class="w"> </span><span class="p">{</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">inner</span><span class="p">.</span><span class="n">seql</span><span class="p">()</span><span class="w"> </span><span class="p">}</span>
+<span class="k">fn</span><span class="w"> </span><span class="nf">count</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="kt">u32</span><span class="w">   </span><span class="p">{</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">count</span><span class="w"> </span><span class="p">}</span>
+<span class="k">fn</span><span class="w"> </span><span class="nf">increment</span><span class="p">(</span><span class="o">&amp;</span><span class="k">mut</span><span class="w"> </span><span class="bp">self</span><span class="p">)</span><span class="w">            </span><span class="p">{</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">count</span><span class="w"> </span><span class="o">+=</span><span class="w"> </span><span class="mi">1</span><span class="p">;</span><span class="w"> </span><span class="p">}</span>
+<span class="k">fn</span><span class="w"> </span><span class="nf">add</span><span class="p">(</span><span class="o">&amp;</span><span class="k">mut</span><span class="w"> </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">u32</span><span class="p">)</span><span class="w">          </span><span class="p">{</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">count</span><span class="w"> </span><span class="o">+=</span><span class="w"> </span><span class="n">n</span><span class="p">;</span><span class="w"> </span><span class="p">}</span>
+<span class="k">fn</span><span class="w"> </span><span class="nf">set_count</span><span class="p">(</span><span class="o">&amp;</span><span class="k">mut</span><span class="w"> </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">u32</span><span class="p">)</span><span class="w">    </span><span class="p">{</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">count</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">n</span><span class="p">;</span><span class="w"> </span><span class="p">}</span>
 </code></pre></div>
-<p>In practice, observed super-kmer lengths on metagenomic data (k=31) are below 55 nucleotides (≤ 25 kmers) — far from the 255-kmer cap. If a super-kmer ever exceeds 255 kmers, it is split with a k−1 nucleotide overlap, preserving all kmers without duplication (identical mechanism to partition-boundary splits).</p>
-<p>The sequence is always stored in canonical form (lexicographic minimum of forward and reverse complement), with nucleotide 0 at the MSB of the first byte. The byte array can be hashed directly without any adjustment.</p>
 <h2 id="ascii-encoding-and-decoding">ASCII encoding and decoding</h2>
 <p>Two lookup tables handle ASCII ↔ 2-bit conversion:</p>
 <ul>
@@ -1125,7 +1476,7 @@
 </code></pre></div>
 <p><code>REVCOMP4</code> is 256 bytes (fits in L1 cache), computed at compile time. No endianness dependency — all operations are pure arithmetic on byte values.</p>
 <p><strong>Step 2 — realignment.</strong>  After step 1, <code>padding = n × 8 − seql × 2</code> spurious bits (complements of the original padding A's) appear at the start of the array. They are flushed left using <code>BitSlice&lt;u8, Msb0&gt;::rotate_left(padding)</code> from the <code>bitvec</code> crate, which is SIMD-accelerated. The trailing <code>padding</code> bits are then zeroed:</p>
-<div class="highlight"><pre><span></span><code><span class="kd">let</span><span class="w"> </span><span class="n">seql</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">n_kmers</span><span class="p">()</span><span class="w"> </span><span class="o">+</span><span class="w"> </span><span class="n">k</span><span class="w"> </span><span class="o">-</span><span class="w"> </span><span class="mi">1</span><span class="p">;</span>
+<div class="highlight"><pre><span></span><code><span class="kd">let</span><span class="w"> </span><span class="n">seql</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="bp">self</span><span class="p">.</span><span class="n">seql</span><span class="p">();</span>
 <span class="n">shift</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">n</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">8</span><span class="w"> </span><span class="o">-</span><span class="w"> </span><span class="n">seql</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">2</span><span class="w">          </span><span class="c1">// number of padding bits</span>
 <span class="n">bits</span><span class="p">.</span><span class="n">rotate_left</span><span class="p">(</span><span class="n">shift</span><span class="p">)</span>
 <span class="n">bits</span><span class="p">[</span><span class="n">len</span><span class="w"> </span><span class="o">-</span><span class="w"> </span><span class="n">shift</span><span class="o">..</span><span class="p">].</span><span class="n">fill</span><span class="p">(</span><span class="kc">false</span><span class="p">)</span>
@@ -1143,7 +1494,7 @@
 </code></pre></div>
 </div>
 <h2 id="minimizer-sliding-window">Minimizer sliding window</h2>
-<p>Super-kmers are built by <code>SuperKmerIter</code> (crate <code>obiskbuilder</code>), which maintains the current minimizer with a <strong>monotonic deque</strong> over a sliding window of W = k − m + 1 m-mer positions.</p>
+<p>Super-kmers are built by <code>SuperKmerIter</code> (crate <code>obiskbuilder</code>), which tracks the current minimizer with a <strong>monotonic deque</strong> (<code>Ring&lt;MmerItem, 32&gt;</code>) inside <code>RollingStat</code>, a rolling-window entropy and minimizer tracker.</p>
 <p>Each deque entry stores:</p>
 <table>
 <thead>
@@ -1167,20 +1518,11 @@
 <tr>
 <td><code>hash</code></td>
 <td>u64</td>
-<td><span class="arithmatex">\(H(\text{canonical})\)</span> — ordering key for random minimizer selection</td>
+<td><code>hash_kmer(canonical &lt;&lt; (64 − 2m))</code> — ordering key for random minimizer selection</td>
 </tr>
 </tbody>
 </table>
-<p>The hash <span class="arithmatex">\(H\)</span> is the seeded splitmix64 finalizer (see <a href="../../theory/minimizer/">Minimizer selection</a>):</p>
-<div class="highlight"><pre><span></span><code><span class="k">fn</span><span class="w"> </span><span class="nf">hash_mmer</span><span class="p">(</span><span class="n">canonical</span><span class="p">:</span><span class="w"> </span><span class="kt">u64</span><span class="p">)</span><span class="w"> </span><span class="p">-&gt;</span><span class="w"> </span><span class="kt">u64</span><span class="w"> </span><span class="p">{</span>
-<span class="w">    </span><span class="kd">let</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">canonical</span><span class="w"> </span><span class="o">^</span><span class="w"> </span><span class="mh">0x9e3779b97f4a7c15</span><span class="p">;</span><span class="w">   </span><span class="c1">// seed: eliminates fixed point at 0</span>
-<span class="w">    </span><span class="kd">let</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="o">^</span><span class="w"> </span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">&gt;&gt;</span><span class="w"> </span><span class="mi">30</span><span class="p">);</span>
-<span class="w">    </span><span class="kd">let</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">x</span><span class="p">.</span><span class="n">wrapping_mul</span><span class="p">(</span><span class="mh">0xbf58476d1ce4e5b9</span><span class="p">);</span>
-<span class="w">    </span><span class="kd">let</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="o">^</span><span class="w"> </span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">&gt;&gt;</span><span class="w"> </span><span class="mi">27</span><span class="p">);</span>
-<span class="w">    </span><span class="kd">let</span><span class="w"> </span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">x</span><span class="p">.</span><span class="n">wrapping_mul</span><span class="p">(</span><span class="mh">0x94d049bb133111eb</span><span class="p">);</span>
-<span class="w">    </span><span class="n">x</span><span class="w"> </span><span class="o">^</span><span class="w"> </span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">&gt;&gt;</span><span class="w"> </span><span class="mi">31</span><span class="p">)</span>
-<span class="p">}</span>
-</code></pre></div>
+<p>The hash uses the seeded splitmix64 finalizer (<code>mix64(raw ^ 0x9e3779b97f4a7c15)</code>), the same function as <code>kmer::hash_kmer</code>.</p>
 <p>On each new nucleotide, once the window is full, the deque is updated:</p>
 <div class="admonition abstract">
 <p class="admonition-title">Algorithm — minimizer deque update</p>
@@ -1196,17 +1538,21 @@
 </code></pre></div>
 </div>
 <p>The front of the deque is always the current minimizer. Because the deque is maintained in strictly increasing hash order, each entry is popped at most once — O(1) amortized per nucleotide.</p>
-<p>A super-kmer boundary is emitted when the minimizer changes: <code>deque.front.hash ≠ prev_hash</code>. The <code>canonical</code> field of the front entry is <strong>not</strong> used for boundary detection — that uses the hash alone. The canonical value is stored so that the partition key <span class="arithmatex">\(H(\text{canonical})\)</span> can be recomputed independently at routing time from the stored <code>minimizer_pos</code>, without inheriting the minimum-order-statistic bias (see <a href="../../theory/minimizer/#partition-key-independence">Minimizer selection — partition key independence</a>).</p>
+<p>A super-kmer boundary is emitted when the minimizer changes: <code>current_minimizer != prev_minimizer</code>. <code>SuperKmerIter</code> also emits a boundary when:</p>
+<ul>
+<li>entropy of the current k-mer falls at or below the threshold θ (cursor retreated by k−1)</li>
+<li>super-kmer length reaches 256 nucleotides (cursor retreated by k)</li>
+</ul>
 <h2 id="kmer-extraction">Kmer extraction</h2>
-<p>A k-mer is extracted from a super-kmer with <code>SuperKmer::kmer(i, k)</code>, which returns a <code>Kmer</code> — a left-aligned <code>u64</code> newtype (see <a href="../kmer/">Kmer implementation</a>):</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">kmer</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">i</span><span class="p">:</span><span class="w"> </span><span class="kt">usize</span><span class="p">,</span><span class="w"> </span><span class="n">k</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="nb">Result</span><span class="o">&lt;</span><span class="n">Kmer</span><span class="p">,</span><span class="w"> </span><span class="n">KmerError</span><span class="o">&gt;</span>
+<p>A k-mer is extracted from a super-kmer with <code>SuperKmer::kmer(i)</code>, which delegates to <code>PackedSeq::extract::&lt;KLen&gt;(i)</code> and returns a <code>Kmer</code> — a left-aligned <code>u64</code> newtype (see <a href="../kmer/">Kmer implementation</a>):</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">kmer</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">i</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="nb">Result</span><span class="o">&lt;</span><span class="n">Kmer</span><span class="p">,</span><span class="w"> </span><span class="n">KmerError</span><span class="o">&gt;</span>
 </code></pre></div>
-<p>The bit slice <code>seq[i*2 .. (i+k)*2]</code> (Msb0 order) is loaded as a big-endian <code>u64</code> via <code>bitvec::load_be</code>, then left-shifted to produce the canonical left-aligned layout. One call — no loop, no allocation.</p>
+<p>The bit slice <code>seq[i*2 .. (i+k)*2]</code> (Msb0 order) is loaded as a <code>u64</code> via <code>bitvec::load_be</code>, then left-shifted to produce the canonical left-aligned layout. One call — no loop, no allocation.</p>
 <hr />
 <div class="admonition abstract">
 <p class="admonition-title">Algorithm — Super-kmer reverse complement</p>
 <div class="highlight"><pre><span></span><code>procedure SuperKmerRevcomp(seq, SEQL):
-    seql  ← NKMERS + k − 1               -- nucleotide length
+    seql  ← nucleotide length
     n     ← ⌈seql / 4⌉                  -- number of bytes
     shift ← n × 8 − seql × 2            -- padding bits to flush