Documents architectural analysis, identified performance bottlenecks including hardcoded selection flags and redundant full-index scans causing I/O-bound stalls. Details planned pipeline refactoring to unify stages around a single shared selection for a fused single-pass scan, noting future dependencies on entropy-biased family selection.
The index packing API now accepts a `sparse` parameter to generate `PersistentSparseBitMatrix` files alongside existing dense matrices. The sibling cache automatically detects this format via an `is_multi.prsb` marker file and routes queries identically to the dense variant. A new `--sparse` CLI flag exposes the option, with tests verifying end-to-end pipeline correctness and storage equivalence.
Implements a compact, row-major sparse bit matrix backed by memory-mapped components, introducing EliasFano, PersistentFixedIntVec, and PersistentRankSelectBitVec primitives for efficient storage and decoding. Adds a BinaryMatrix trait to unify row-level operations across dense and sparse implementations. Corrects edge-case behaviors for zero-width bit storage and cardinality-0 rows. Delivers reduced on-disk size and faster random row access, with column reads remaining dense-only. Test suites and benchmarks are included but currently marked as ignored.
Introduces `--subsample N` and `--shannon` CLI flags to cap retained variable families via proportional reservoir sampling and compute per-family Shannon entropy. Updates the family scanning API to support explicit selection filtering with early-exit optimization, resolving an indexing drift issue in monomorphic layers. Streams entropy metrics for 15-state and 4-nucleotide spaces directly to CSV while maintaining parallel processing across sibling layers.
Documents a proposed redesign for cross-partition batch resolution, shifting trigger logic to per-destination accumulator thresholds and introducing entropy-based pruning criteria. Adds an `n_layers_per_partition` method to the index, exposing partition metadata with consistent error handling and clarified documentation regarding build-time structural properties.
Shifts sibling annex construction from slot-indexed enumeration to iteration-order traversal by correcting cumulative k-mer offset tracking in batch enumeration. Replaces coarse per-partition parallelism with chunked work distribution to prevent thread starvation on skewed partitions. Decouples custom progress messages from ETA updates to eliminate display clobbering during high-frequency callbacks. Adds regression tests validating batch offset correctness, partial batch handling, and iterator-order consistency across layer builds.
Introduces batch retrieval and sub-matrix extraction methods across vector, view, reader, and matrix types. These implementations optimize cache locality by sorting requested indices for sequential memory access before applying an inverse permutation to restore original order. Includes allocation-free variants that populate caller-provided buffers. Updates architecture documentation to define sibling annex persistence in iteration order and clarify pipeline separation.
Eric Coissac