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Eric Coissac 5c1584967f feat: enable index resumption and enforce directory creation

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.

2026-08-21 05:06:38 +02:00

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Coverage: implementation/pipeline.md

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obikindex/src/partition/partition.rs — estimation des paramètres (phase 0)
obiskbuilder/src/iter.rs — scatter : filtre entropie, extraction superkmers, routage partition (phase 1)
obikindex/src/partition/filter.rs — déduplication bucket-sort (phase 2)
obikindex/src/partition/kmer_sort.rs — tri externe + agrégation de comptages (phase 3)
obidebruinj/src/debruijn.rs — graphe De Bruijn, extraction des unitigs (phase 5)
obikindex/src/partition/index_layer.rs — construction MPHF + évidence (phase 6), paramètre block_bits
obikindex/src/index.rs — build_layers(), dereplicate_and_count()

Notes

RISQUE DE DÉRIVE modéré. Vérifier :

Phase 6 : la doc mentionne-t-elle le filtre d'abondance (min_ab, max_ab) ?
Phase 6 : block_bits passé à build_index_layer depuis IndexConfig
Phase 6 : dispatch exact/approx selon EvidenceKind dans build_index_layer

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Coverage: implementation/pipeline.md

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Notes

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