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

..

architecture

perf: optimize k-mer queries with sparse index and run-based aggregation

2026-07-07 18:56:41 +02:00

css

first implementation but far to be optimal

2026-04-19 12:17:16 +02:00

implementation

docs: add future work section for parallel gzip decompression

2026-07-07 13:43:01 +02:00

theory

refactor: remove equivalence class folding from entropy pipeline

2026-07-08 19:36:30 +02:00

apa.csl

first implementation but far to be optimal

2026-04-19 12:17:16 +02:00

ecology-letters.csl

first implementation but far to be optimal

2026-04-19 12:17:16 +02:00

index.md

refactor: rename rebuild subcommand to filter

2026-06-09 15:26:37 +02:00

index.refs.md

docs: add coverage reference files and flag architectural drift

2026-05-23 13:44:23 +02:00

installation.md

refactor: replace rayon with NUMA-aware PartitionRunner

2026-06-15 18:53:31 +02:00

kmers.md

feat: enforce runtime validation for kmer and minimizer parameters

2026-05-29 09:10:25 +02:00

kmers.refs.md

docs: add coverage reference files and flag architectural drift

2026-05-23 13:44:23 +02:00

references.bib

first implementation but far to be optimal

2026-04-19 12:17:16 +02:00

vancouver.csl

first implementation but far to be optimal

2026-04-19 12:17:16 +02:00