Introduce `MemoryBitVec` and `MemoryIntVec` for efficient in-memory storage with hybrid compression and overflow handling. Implement `BitSlice`, `BitSliceMut`, `IntSlice`, and `IntSliceMut` traits across persistent and memory-backed types to enable generic slice operations and bitwise/arithmetic overloads. Add `col_persist` and `col_as_memory` methods to `BitMatrix` and `IntMatrix` for efficient column extraction. Align with the new single-pass rebuild architecture by supporting fast kmer filtering and matrix rebuilding. Includes comprehensive tests and profiling instrumentation for the packing phase.
This commit replaces raw string genome labels with a structured `GenomeInfo` type for better metadata tracking. It adds a `--meta` flag to the index command, and implements a new `annotate` CLI subcommand to import metadata from CSV files or export it via `--dump`. Distance and shared-count matrices are now serialized to CSV, with UPGMA clustering trees exported as Newick files. Query outputs now include per-genome k-mer match counts in JSON, while fixing syntax and variable naming issues in index merging and dump generation.
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.
Introduces the `obilayeredmap` crate (v0.1.0), implementing an append-only, disk-backed k-mer index using a minimal perfect hash function (MPHF). The module features memory-mapped reads, buffered writes, custom error handling, partition metadata persistence, and comprehensive unit tests. Also adds a reverse complement benchmark for `obikseq` and updates `Cargo.lock` with the new dependencies.
Eric Coissac