Centralize k-mer and minimizer configuration using a thread-safe global module, and replace manual bit-packing with a memory-efficient `PackedSeq` type. Refactor core sequence and k-mer types to use compile-time length enforcement and centralized hashing. Introduce a new De Bruijn graph implementation with compact node encoding and traversal iterators. Update I/O, partitioning, and builder modules to align with the new architecture, and add the `xxhash-rust` dependency.
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.
- Replace `limits` module and raw binary I/O with a new high-level abstraction using obiskio::SKFileWriter
- Remove `niffler` dependency and compression logic (Gzip/Zstd/Lz4/Bgzf)
- Simplify PartitionManager to manage partitioned file writers based on kmer hashing
* Uses `n_partition_bits` for bitmask-based partition selection (2^n partitions)
- Add obiskio as a local dependency
Note: This is likely part of aligning with unified I/O primitives in the obiskio crate.
Eric Coissac