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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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coissac commented 2026-07-08 18:05:27 +00:00
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coissac added 3 commits 2026-07-08 18:05:28 +00:00
feat: add entropy-driven k-mer complexity filtering e725523898 
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.
feat: extract k-mer entropy computation into new obikentropy crate 912f788f7f 
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.
refactor: remove equivalence class folding from entropy pipeline
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fd2c23e7df 
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.
coissac merged commit dc3392865f into main 2026-07-08 18:05:43 +00:00
coissac deleted branch push-qowsvpqmoukq 2026-07-08 18:05:43 +00:00
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Reference: OBIKmers/obikmer#61