Eric Coissac
5c1584967f
The command now supports reopening existing indexes instead of failing when the output file exists. Control flow branches between opening an existing index and constructing a new one, moving configuration setup exclusively to the creation path. Directory existence is enforced upfront with proper I/O error propagation. The --force flag retains its original semantics by removing the target directory before proceeding with a fresh build.
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Chunk reader
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Construction pipeline
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obipipeline library
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Evidence elimination (discussion)
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obikindex layer tier
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PersistentCompactIntVec
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<!-- coverage sidecar — ne pas ajouter au nav mkdocs -->
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<h1 id="coverage-architectureindex_architecturemd">Coverage: architecture/index_architecture.md</h1>
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<h2 id="code-couvert">Code couvert</h2>
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<ul>
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<li><code>obikindex/src/layer/typed_layer.rs</code> — Layer<D>, trait LayerData, modes () / PersistentCompactIntMatrix / PersistentBitMatrix</li>
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<li><code>obikindex/src/layer/mphf_layer.rs</code> — MphfLayer, EvidenceKind (Exact / Approx), LayerEvidence enum</li>
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<li><code>obikindex/src/layer/map.rs</code> — LayeredMap<D></li>
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<li><code>obikindex/src/layer/meta.rs</code> — LayerMeta, PartitionMeta</li>
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<li><code>obikindex/src/meta.rs</code> — IndexConfig (kmer_size, n_bits, with_counts, evidence, block_bits), IndexMeta</li>
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<li><code>obikindex/src/index.rs</code> — KmerIndex, build_layers</li>
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<li><code>obicompactvec/src/</code> — PersistentCompactIntMatrix, PersistentBitMatrix (DataStore implementations)</li>
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</ul>
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<h2 id="notes">Notes</h2>
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<p>FORT RISQUE DE DÉRIVE. Nombreux changements récents :
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- Ajout de <code>EvidenceKind</code> (Exact / Approx { b, z }) dans <code>IndexConfig</code> et <code>LayerMeta</code>
|
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- Ajout de <code>block_bits</code> dans <code>IndexConfig</code>
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- <code>LayerEvidence</code> enum dans <code>mphf_layer.rs</code> remplace l'ancienne approche monolithique
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- Distinction <code>open()</code> vs <code>open_sequential()</code> dans <code>UnitigFileReader</code>
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- Commandes <code>reindex</code> et <code>estimate</code> ajoutées
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Vérifier que la hiérarchie à 3 niveaux décrite est toujours exacte et que les nouveaux paramètres sont documentés.</p>
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