Eric Coissac 49e66f16a2 docs: document architecture analysis and refactoring plans for siblings ...

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.

2026-08-16 21:54:07 +02:00

..

architecture

docs: document architecture analysis and refactoring plans for siblings

2026-08-16 21:54:07 +02:00

css

first implementation but far to be optimal

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

implementation

rename distance subcommand to phylo

2026-08-15 10:07:03 +02:00

theory

Store minorant flag in family mask to avoid costly k-mer reconstruction

2026-08-16 13:50:44 +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

rename distance subcommand to phylo

2026-08-15 10:07:03 +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

feat: add Mash distance metric and rolling entropy support

2026-07-09 11:40:48 +02:00

vancouver.csl

first implementation but far to be optimal

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