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Push twnyxtspltux #76

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coissac merged 5 commits from push-twnyxtspltux into main 2026-09-12 05:57:26 +00:00
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coissac commented 2026-09-12 05:57:14 +00:00
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coissac added 5 commits 2026-09-12 05:57:15 +00:00
Implement gamma shape correction for SNP distance calculation 020b391636 
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.
Refine theoretical justification for alpha estimation. be838da256 
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.
Refactor distance matrix calculation logic for consistency a8bcf5ffac 
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.
Introduce session persistence and artifact caching 7861e886e7 
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.
Implement session persistence and checkpointing
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2693a6af09 
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.
coissac merged commit 755cf85334 into main 2026-09-12 05:57:26 +00:00
coissac deleted branch push-twnyxtspltux 2026-09-12 05:57:35 +00:00
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Reference: OBIKmers/obikmer#76