Add configurable sparsity flag to index finalization and merge CLI

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Extends `KmerIndex::finalize_indexed` to accept a `sparse` boolean parameter, enabling control over whether output presence matrices are packed in a compact sparse format or stored densely. The merge command now exposes a `--dense` flag to invert this setting, defaulting to the existing sparse representation. Call sites in select and rebuild modules pass `false` to preserve current behavior. A benchmark lock file is also added for dependency tracking.

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Eric Coissac

2026-08-22 17:36:50 +02:00

parent bb380d0c7d

commit cbf6893f38

6 changed files with 23 additions and 8 deletions

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benchmark/tmp/bacteria_sparse/.obikmer.lock