Push pnxswqpxlyso #13

2026-06-01T12:44:40Z

coissac commented

2026-06-01 12:44:40 +00:00

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coissac added 5 commits 2026-06-01 12:44:40 +00:00

feat: add iter_canonical_kmers iterator and tests 8b57c91ab7

Implements `iter_canonical_kmers` in `unitig_index` to yield canonical kmers by traversing unitig chunks. Includes unit tests to verify that the iterator exclusively yields canonical kmers and matches `iter_kmers` in count and canonical equivalence.

refactor: abstract k-mer types and fix bit alignment 657f964dda

Abstracts k-mer storage using a `RawKmer` alias and `KMER_BITS` constant to simplify bit manipulation and enable future extension to larger types. Updates bit-shifting and masking logic across `kmer.rs` and `packed_seq.rs` to prevent overflow and improve type safety. Adapts the MPHF layer to iterate over indexed canonical k-mers with explicit slot bounds validation and bit-level encoding. Fixes test suite compilation errors by correcting method names, adding tuple destructuring, and passing the required `IndexMode::Exact` parameter.

docs: Update README to reflect new indexing workflow 1e2115a1b0

Replace the documented direct combined indexing command with a two-step workflow. This involves building separate exact indexes per genome, merging them into a single multi-genome index via `obikmer merge`, and keeping the approximate index conversion unchanged.

refactor: streamline merge pipeline and MPHF indexing 0350ca855b

Replace mphf.find() with direct mphf.index() calls to eliminate absence checks and fallback vectors. Introduce a lightweight MphfOnly wrapper for faster index loading, and standardize k-mer iteration across merge and rebuild layers. Update IndexMeta configuration and n_new calculation to leverage MPHF cardinality, streamlining the overall merge pipeline.

enforce uniform index mode and optimize base index selection add6d7f873

Adds validation to ensure all input sources share the same `IndexMode`. Introduces base index selection logic that prioritizes approximate or hybrid evidence and maximizes base size to minimize newly indexed k-mers. Includes helper functions for triviality evaluation, cumulative size calculation, and mode consistency checks.

coissac merged commit 4fd0eb989f into main

2026-06-01 12:45:46 +00:00

coissac deleted branch push-pnxswqpxlyso

2026-06-01 12:45:46 +00:00

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Reference: OBIKmers/obikmer#13