Introduces `partial_jaccard_dist` to return raw intersection and union counts, improving Jaccard distance flexibility. Corrects `not()` to explicitly zero padding bits in the final word, ensuring accurate bit-counting for partially-filled words. Adds an optimized `build_from_counts` constructor.
Introduces PersistentBitVec, a dense, memory-mapped bit vector optimized for bulk u64-word operations and SIMD acceleration, complete with bitwise operators and Jaccard/Hamming distance metrics. Upgrades PersistentCompactIntVec to a unified .pciv format using 64-bit indices and offsets, consolidating the binary layout and updating builder/reader lifecycles accordingly. Adds corresponding documentation, updates MkDocs navigation, and implements a comprehensive test suite for persistence round-trips, edge cases, and metric accuracy.
Introduce the `obicompactvec` crate, featuring a two-tier, memory-mapped integer vector that uses a primary `u8` array with a sentinel for overflow dispatch and a sparse L1-resident index for fast random access. Implement builder and reader modules with zero-copy serialization and comprehensive test coverage. Update `obilayeredmap` to replace the default hash function with a cache-line-optimized `Mphf`, adding explicit bounds checking and duplicate-slot detection. Add documentation for both modules and update project configuration files accordingly.
Introduce the `obilayeredmap` specification and persistent MPHF-based index architecture for incremental multi-dataset indexing. Implement chunked binary serialization with a fixed `u8` k-mer count limit (256) and overlapping super-kmer segments. Add memory-mapped I/O and a companion `.idx` index file for allocation-free, O(1) unitig access. Update MkDocs navigation, enhance the k-mer comparison script, and add comprehensive tests for serialization, partitioning, and file I/O pipelines.
Replace raw SuperkMer routing with a new RoutableSuperKimer type that embeds canonical sequences and precomputed minimizers, enabling direct partition routing via hash. Update the build pipeline to yield RoutableSuperKmers throughout (builder, scatterer), refactor FASTA/unitig export commands to use the new type and compressed outputs (.fasta.gz, .unitigs.fasta.zst), revise SuperKmer header to store n_kmers instead of seql (avoiding 256-byte wrap), and update documentation to reflect minimizer-based theory, two evidence-encoding strategies for unitig-MPHF indexing (global offset vs. ID+rank), and the new obipipeline library architecture with parallel workers, biased scheduling, and error handling.
- Add `hash` field to MmerItem for stable, randomized minimizer ordering
- Introduce hash_mMER() using mix64 with XOR seed to avoid fixed points (e.g., poly-A/T)
- Remove is_degenerate() and minimizer_worse(), simplifying comparison to hash-only
- Update push logic: compare hashes instead of canonical values with degeneracy checks
- Introduce `obipipline` crate with multi-threaded data pipeline architecture
- Implement core types: SourceFn, SharedFun (Arc), SinkFN with biased scheduler and crossbeam channels
- Add macros: `make_source!`, `transform!/fallible`/sink!, and high-level DSL macro
- Replace old wrapper/error modules with unified scheduler module (renamed types, improved error variants)
- Update workspace: add `obipipeline` member to Cargo.toml and lockfile
- Document pipeline in docmd/implementation with full architecture, error handling & example
- Refactor sandbox_pipeline.rs to use new DSL instead of manual channel wiring
Eric Coissac