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.
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.
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.
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.
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.
Eric Coissac