Eric Coissac
bb7adc1154
Expands MkDocs navigation and documentation for evidence elimination, the merge command, and kmer filtering. Refactors kmer representation to a generic `KmerOf<L>` type with a bitwise reverse complement algorithm. Unifies MPHF construction, introduces approximate fingerprint-based indexing, and updates the pipeline, chunkreader, and storage layouts. Adds code coverage reports and clarifies architectural invariants for improved maintainability.
1057 lines
17 KiB
HTML
1057 lines
17 KiB
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obikmer
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Encoding.refs
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obikmer
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<span class="md-ellipsis">
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Theory
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Theory
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<a href="../../kmers/" class="md-nav__link">
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<span class="md-ellipsis">
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Kmers and super-kmers
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<a href="../encoding/" class="md-nav__link">
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<span class="md-ellipsis">
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DNA encoding
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<span class="md-ellipsis">
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Entropy filter
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<a href="../minimizer/" class="md-nav__link">
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<span class="md-ellipsis">
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Minimizer selection
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<a href="../indexing/" class="md-nav__link">
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Partitioning architecture
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</nav>
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Implementation
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Implementation
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<span class="md-ellipsis">
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SuperKmer
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</a>
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Kmer
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<span class="md-ellipsis">
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Chunk reader
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Construction pipeline
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obipipeline library
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<a href="../../implementation/storage/" class="md-nav__link">
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<span class="md-ellipsis">
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On-disk storage
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<a href="../../implementation/mphf/" class="md-nav__link">
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<span class="md-ellipsis">
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MPHF selection
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<a href="../../implementation/unitig_evidence/" class="md-nav__link">
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<span class="md-ellipsis">
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Unitig evidence encoding
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<a href="../../implementation/evidence_elimination/" class="md-nav__link">
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<span class="md-ellipsis">
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Evidence elimination (discussion)
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<a href="../../implementation/obilayeredmap/" class="md-nav__link">
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obilayeredmap crate
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PersistentCompactIntVec
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PersistentBitVec
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Merge command
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<!-- coverage sidecar — ne pas ajouter au nav mkdocs -->
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<h1 id="coverage-theoryencodingmd">Coverage: theory/encoding.md</h1>
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<h2 id="code-couvert">Code couvert</h2>
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<ul>
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<li><code>obikseq/src/kmer.rs</code> — encodage 2 bits/base, revcomp, forme canonique</li>
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<h2 id="notes">Notes</h2>
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<p>Document purement théorique. Peu de risque de dérive sauf si l'encodage interne de Kmer change.
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Vérifier que la table d'encodage A=00, C=01, G=10, T=11 est toujours celle du code.</p>
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