Extracts streaming entropy logic and sliding-window frequency tracking from obiskbuilder into a dedicated obikentropy crate. Introduces an EntropyTracker accumulator for O(1) per-base normalized Shannon entropy, replaces inline rolling statistics with delegated state management, and updates workspace dependencies across obikindex, obikpartitionner, and obiskbuilder. Adds criterion benchmarks to validate the refactored pipeline throughput.
Introduces a Make-based orchestration for simulating, indexing, merging, filtering, and verifying k-mer counts and presence. Exposes internal builder and iterator APIs publicly, enforces mandatory leading slashes for predicate patterns, registers the `obitaxonomy` crate, and updates tooling configurations alongside documentation.
Extracted core indexing logic, state tracking, and metadata management into a new `obikindex` crate. Refactored the `index` and `unitig` commands to leverage the `KmerIndex` abstraction and state-driven pipeline transitions. Removed obsolete CLI subcommands (`count`, `fasta`, `longtig`, `partition`) and their associated pipeline steps. Updated FASTA writing utilities for single-line output and deterministic identifiers, and refreshed workspace dependencies.
Replace in-memory hashing with a disk-backed external merge sort and `PersistentCompactIntVec` to drastically reduce peak RAM. Unify both phases using a custom `PtrHash` MPHF, eliminating `GOFunction` and `boomphf`. Introduce a concrete three-step `count_partition()` pipeline with adaptive chunk sizing based on available system memory. Update dependencies to `memmap2`, `ptr_hash`, and `obicompactvec`. Additionally, document strict genomics-only memory constraints and enforce an architectural feedback workflow requiring explicit user authorization before structural changes.
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.
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.
- Remove redundant validation logic in login handler
- Consolidate session token generation into a single utility function
- Update error handling to use consistent HTTP status codes
- Add new obiskio crate for high-performance SuperKmer serialization/deserialization
- Implement binary codec with 2-bit packed sequence encoding and raw header format (32 bits)
- Add transparent compression support via niffler: Zstd, Gzip/Bgzf/Lz4
- Implement SKFilePool with LRU-based fd management, max-concurrent-fd limiting (75% of ulimit)
- Add SKFileWriter with batched writes, configurable flush threshold (8 KiB default), and two-phase locking
- Add SKFileReader with sequential access, LRU recovery via reopen_and_seek()
+ New obikpartitionner crate: basic header/seq handling for binary super-kmer format
- Bump niffler from 2.7 to v3, add dependencies: allocator-api2, bitflags(>=1), errno/fastrand/rustix/tempfile/lru/hashbrown/bzip2/thiserror
- Update workspace members to include obikpartitionner andobiskio
- 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