Proposes replacing the single-threaded niffler/flate2 pipeline in `obiread::xopen` with `rapidgzip-rs` for local `.gz` files. Details constraints such as path dependencies, non-seekable streams, C++ toolchain requirements, and binding maturity. Marks the optimization as parked pending throughput and correctness validation.
Replace the existing chunk and Rope-based processing pipeline with a fixed-size NucPage architecture. Introduce a new nucstream module featuring buffer-pooled, in-place parsing that auto-detects and decompresses FASTA/FASTQ/GenBank inputs into normalized ACGT streams with k-mer overlap preservation. Update obikmer scatter and superkmer stages to consume NucPage iterators and cursor-based navigation, eliminating std::io::Read dependencies and optimizing memory management. Add a configurable max_open_files CLI argument and update implementation documentation to reflect the new record vs. stream reading paths.
Refactor `Kmer`, `SuperKmer`, and chunk reader into optimized, generic representations with compile-time length parameters and bitwise operations. Update the pipeline and scheduler to support batch processing, 1→N flat transformations, and multi-source merging. Introduce an approximate evidence mode using b-bit fingerprints and `.idx` files, alongside existing exact mode. Update CLI documentation, minimizer selection, and query output schema accordingly.
Eric Coissac