Push qowsvpqmoukq #61

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coissac merged 3 commits from push-qowsvpqmoukq into main 2026-07-08 18:05:43 +00:00

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3 Commits

Author	SHA1	Message	Date
Eric Coissac	fd2c23e7df	refactor: remove equivalence class folding from entropy pipeline ... Removes circular-reverse complement machinery and explicit k-mer canonicalization across the entropy pipeline. Frequency tallying and Shannon entropy computation now operate directly on raw k-mer values, eliminating prior score inflation and alignment-dependent artifacts while preserving orientation invariance. Updates build scripts to generate normalized lookup tables for k-mer lengths 1–6, restricts the public API to `EntropyTracker`, and bumps crate versions. Documentation is updated to reflect the simplified raw-value approach and revised module structure.	2026-07-08 19:36:30 +02:00
Eric Coissac	912f788f7f	feat: extract k-mer entropy computation into new obikentropy crate ... 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.	2026-07-08 18:36:16 +02:00
Eric Coissac	e725523898	feat: add entropy-driven k-mer complexity filtering ... Introduces a MinComplexity filter driven by new CLI arguments, enabling sequence-aware threshold checks during index reconstruction and partitioning. Adds the kmer_entropy module for normalized complexity scoring, updates the KmerFilter trait to evaluate per-kmer context, and refactors test modules for better organization.	2026-07-08 12:48:25 +02:00