feat(obikmer): add index subcommand for kmer counting pipeline

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Introduce the `index` CLI subcommand, implementing a resumable, multi-stage pipeline to partition, dereplicate, and count kmers from input sequences. The command builds a layered de Bruijn graph index per partition, applies optional abundance filtering, and persists unitigs alongside an MPHF-based count matrix. Update `Cargo.toml` and `Cargo.lock` to include new dependencies (`epserde`, `ptr_hash`, `cacheline-ef`, `obicompactvec`, `obilayeredmap`) required for the index builder, and refresh the profiling data files.

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Eric Coissac

2026-05-20 14:37:30 +02:00

parent c20a1ed465

commit e66c4d81ef

9 changed files with 231 additions and 1 deletions

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