Push quqlpklvxsqx #18

2026-06-08T18:14:54Z

coissac commented

2026-06-08 18:14:54 +00:00

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coissac added 3 commits 2026-06-08 18:14:55 +00:00

feat: integrate tracing and enhance bit matrix operations 09d9e21744

Add the `tracing` crate to `obidebruinj`, `obisys`, and resolve it in `Cargo.lock`. Replace `eprintln!` statements with structured `debug!` and `info!` macros. Introduce a `TracedBar` wrapper for progress bars and enhance the `Stage` lifecycle to emit structured events for timing, memory metrics, and swap warnings. Add a progress spinner for unitig degree computation. Extend `PersistentBitMatrix` with columnar bit-vector operations and parallel distance methods, enabling uniform distance computations across all storage layouts while replacing previous panics with dimension-based fallbacks.

feat: implement parallel pairwise distance matrices 1ec65922df

Introduces parallelized pairwise distance matrix computation for Jaccard, Hamming, Bray-Curtis, Euclidean, and Hellinger metrics across `Columnar`, `Packed`, and `Implicit` matrix variants. Adds trait methods and convenience wrappers, safely handles normalization and zero-denominator edge cases, and updates test suites to import required traits for validation.

feat: add configurable presence threshold to kmer distance eb7805c747

Introduce a `--presence-threshold` CLI argument (default: 1) and update `KmerIndex::distance` to accept a `presence_threshold` parameter. This replaces hardcoded zero thresholds, enabling configurable filtering of low-abundance kmers during Jaccard distance calculations.

coissac merged commit 650eea43b6 into main

2026-06-08 18:15:02 +00:00

coissac deleted branch push-quqlpklvxsqx

2026-06-08 18:15:02 +00:00

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Reference: OBIKmers/obikmer#18