Push twnyxtspltux #76

Merged

coissac merged 5 commits from push-twnyxtspltux into main 2026-09-12 05:57:26 +00:00

Conversation 0 Commits 5 Files Changed 22

+1800 -112

5 Commits

Author	SHA1	Message	Date
Eric Coissac	2693a6af09	Implement session persistence and checkpointing ... Introduces session persistence via the `--session` option, allowing sampled sets to be restored. Implements chunked dumps and shared checkpointing for alignment and tally artifacts, ensuring state restoration upon interruption. Refines sampling logic and introduces serialization mechanisms for state management.	2026-09-12 07:48:51 +02:00
Eric Coissac	7861e886e7	Introduce session persistence and artifact caching ... This change implements a robust session management system allowing users to persist distance calculation samples and parameters across invocations. It includes concurrency-safe directory locking, deterministic parameter encoding, artifact integrity checks, and caching mechanisms to skip resampling when valid data is available.	2026-09-12 07:46:55 +02:00
Eric Coissac	a8bcf5ffac	Refactor distance matrix calculation logic for consistency ... Ensures that combined distance matrix calculations use the exact same site selection by retaining sampled data within Sankoff bundles. This involves refactoring post-sampling logic into shared functions, implementing `SankoffBundle` to reuse internal tally data, and adding validation to guarantee consistent site selection across all distance calculation paths.	2026-09-12 07:45:32 +02:00
Eric Coissac	be838da256	Refine theoretical justification for alpha estimation. ... Document limitations of various $\alpha$-estimation methods, clarifying that tree-based methods require a tree for accurate heterogeneity estimation and that `PartitionDispersion` avoids violating identifiability requirements.	2026-09-12 07:44:51 +02:00
Eric Coissac	020b391636	Implement gamma shape correction for SNP distance calculation ... Introduces support for rate heterogeneity via a Poisson-Gamma mixture model. This includes new command-line options (`--gamma-shape`, `--gamma-shape auto`) to enable automatic estimation of the shape parameter $\alpha$ based on substitution counts across partitions. The correction is applied to the distance metric, with logic to disable the correction if variance checks fail.	2026-09-12 07:44:39 +02:00