OBIKmers/obikmer
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  • 755cf85334 Merge pull request 'Push twnyxtspltux' (#76) from push-twnyxtspltux into main main coissac 2026-09-12 05:57:25 +00:00
  • 2693a6af09 Implement session persistence and checkpointing v1.3.5 Eric Coissac 2026-09-12 07:43:40 +02:00
  • 7861e886e7 Introduce session persistence and artifact caching Eric Coissac 2026-09-12 07:04:49 +02:00
  • a8bcf5ffac Refactor distance matrix calculation logic for consistency Eric Coissac 2026-09-11 17:31:45 +02:00
  • be838da256 Refine theoretical justification for alpha estimation. Eric Coissac 2026-09-11 16:38:53 +02:00
  • 020b391636 Implement gamma shape correction for SNP distance calculation Eric Coissac 2026-09-11 12:38:46 +02:00
  • e846d35adb Merge pull request 'Feat: Introduce resource profiling and monitoring APIs' (#75) from push-sktolxuyskpp into main coissac 2026-09-11 07:51:03 +00:00
  • c0e1968654 Feat: Introduce resource profiling and monitoring APIs v1.3.4 Eric Coissac 2026-09-11 09:44:41 +02:00
  • e280b6d0a3 Merge pull request 'Implement NUMA topology detection and CPU budget capping' (#74) from push-tnkxqmwztnmm into main coissac 2026-09-11 05:23:42 +00:00
  • 98dba1802d Implement NUMA topology detection and CPU budget capping v1.3.3 Eric Coissac 2026-09-11 07:22:02 +02:00
  • dd4285b269 Merge pull request 'Introduce CPU budget and dynamic thread limiting' (#73) from push-lztkokoxqpuw into main coissac 2026-09-10 15:10:19 +00:00
  • b66a488277 Introduce CPU budget and dynamic thread limiting v1.3.2 Eric Coissac 2026-09-10 17:07:14 +02:00
  • b954032faa chore: remove obsolete configuration and memory files Eric Coissac 2026-08-31 09:04:01 +02:00
  • 43d89d8f02 Merge pull request 'disable default features for obisys dependency' (#72) from push-wvkttrwzkqoo into main coissac 2026-08-29 06:18:11 +00:00
  • 8bb1d52514 disable default features for obisys dependency v1.3.1 Eric Coissac 2026-08-29 08:08:15 +02:00
  • 77d4429645 Merge pull request 'chore: bump obikmer to 1.3.0 and disable obisys default features' (#71) from push-sllyqzuztwkr into main coissac 2026-08-29 05:51:37 +00:00
  • 4d55258ada chore: bump obikmer to 1.3.0 and disable obisys default features v1.3.0 Eric Coissac 2026-08-29 07:45:33 +02:00
  • 7e28ca4853 Merge pull request 'Push zunrplorkwkt' (#70) from push-zunrplorkwkt into main coissac 2026-08-28 23:15:37 +00:00
  • 26026288de refactor(benchmark): consolidate generated artifacts under run/ directory v1.2.3 Eric Coissac 2026-08-28 18:52:01 +02:00
  • 52f26809af refactor(benchmark): consolidate generated artifacts under run/ directory Eric Coissac 2026-08-28 18:52:01 +02:00
  • 54e4600120 feat: add batched int group stats API and expand benchmark variants Eric Coissac 2026-08-28 14:33:25 +02:00
  • 579cfd8752 docs: document partition runner deadlock fix and select CLI updates Eric Coissac 2026-08-28 14:14:22 +02:00
  • 6b0c0867cc implement hybrid hard-link copy strategy for directory bootstrap Eric Coissac 2026-08-28 14:06:37 +02:00
  • 93fe838f97 Remove in-place flag, optimize presence counting, and handle NUMA panics Eric Coissac 2026-08-28 13:53:41 +02:00
  • 7363370065 feat: add --force-copy flag to copy files instead of hard-linking Eric Coissac 2026-08-28 10:42:54 +02:00
  • caf59b5658 Update documentation for CLI command renames and new commands Eric Coissac 2026-08-28 10:26:18 +02:00
  • 95fa0c93b2 Rename CLI to obikmer2, add phylo commands, and unify index caching Eric Coissac 2026-08-28 09:55:25 +02:00
  • e101f629e6 Add family overlap computation and CLI options for phylo analysis Eric Coissac 2026-08-28 09:47:58 +02:00
  • 4f34a646c5 Implement SNP distance models with gamma correction and PHYLIP output Eric Coissac 2026-08-28 09:24:35 +02:00
  • 0b40d2d0da Add phylogenetic export support for TNT, PhyG, and IQ-TREE Eric Coissac 2026-08-28 09:05:17 +02:00
  • 1536217ac1 feat: add Sankoff cost-matrix calibration CLI and serialization Eric Coissac 2026-08-27 17:01:33 +02:00
  • 9043868228 Add single-pass pairwise reduction pipeline for SNP alignment Eric Coissac 2026-08-27 16:54:42 +02:00
  • e015362ce6 Refactor sampling and reduction to use batched SurvivingFamily data Eric Coissac 2026-08-27 16:28:57 +02:00
  • 89629e118d Add sibling family size distribution statistics and CLI flags Eric Coissac 2026-08-27 15:30:17 +02:00
  • beb2951c20 feat: add phylogenetic sampling, masking, and plain FASTA writer Eric Coissac 2026-08-27 15:26:53 +02:00
  • 5a0b71d105 Add per-family Shannon entropy calculation and reporting Eric Coissac 2026-08-27 12:44:00 +02:00
  • bbb58a698f Rename SiblingAnnexBuildExt to SiblingExt and add sibling iterators Eric Coissac 2026-08-27 09:29:22 +02:00
  • 920120d20e Implement --sibling-annex flag and k-mer family annex builder Eric Coissac 2026-08-27 09:07:17 +02:00
  • d084396aba Introduce concurrency-bounded parallel processing for index cache layers Eric Coissac 2026-08-27 07:52:08 +02:00
  • 9dee6dcd08 refactor: decouple tree construction from Newick serialization Eric Coissac 2026-08-27 06:45:41 +02:00
  • 635fc830d1 feat: add phylogenetic analysis CLI command and lazy distance traits Eric Coissac 2026-08-27 06:37:48 +02:00
  • 4b6005962e Rename PersistentCompactIntMatrix to PersistentIntMatrix Eric Coissac 2026-08-26 20:57:01 +02:00
  • 6bdc9354d3 refactor: restructure obikphylo module layout and adjust visibility Eric Coissac 2026-08-26 20:34:29 +02:00
  • 4ea3cd32ba feat: add convert command for in-place index evidence modification Eric Coissac 2026-08-26 20:20:07 +02:00
  • bd7729b095 refactor: Shift KmerIndex ownership to Arc for thread-safe sharing Eric Coissac 2026-08-26 19:26:29 +02:00
  • 10a0909687 refactor: unify iterator construction in nonzero_iter Eric Coissac 2026-08-26 14:42:21 +02:00
  • b0890d1781 Add sparse storage variant to PersistentCompactIntMatrix Eric Coissac 2026-08-26 14:00:04 +02:00
  • 904d85f33b Implement pack CLI command for matrix packing and layer compaction Eric Coissac 2026-08-26 09:08:41 +02:00
  • 96dfb5300b Add unitig extraction command to obikdump and obikmer2 Eric Coissac 2026-08-26 08:26:17 +02:00
  • 768fa0183d Add dump subcommand and introduce reusable group filtering arguments Eric Coissac 2026-08-26 08:22:49 +02:00
  • 737966899f Add obikselect crate for k-mer selection and aggregation Eric Coissac 2026-08-26 08:20:58 +02:00
  • 354e6f9bf1 Add unified matrix builder abstraction and k-mer filtering CLI Eric Coissac 2026-08-26 08:11:32 +02:00
  • b7a8b5e6cf feat: add sparse compact integer matrix implementation and utilities Eric Coissac 2026-08-26 07:45:14 +02:00
  • 294f132a0a refactor: relocate partition iterator and expose graph builder API Eric Coissac 2026-08-26 07:01:55 +02:00
  • 16ade823d6 refactor: extract partition iteration and unify group selection Eric Coissac 2026-08-25 20:00:13 +02:00
  • 881b1532b5 refactor: consolidate mmap file operations into shared helper functions Eric Coissac 2026-08-25 18:17:32 +02:00
  • ad0b7173a3 Add select0 method and expand Elias-Fano query API Eric Coissac 2026-08-24 15:25:03 +02:00
  • 5dc16b0127 refactor(obikselect): implement Algorithm trait for selection Eric Coissac 2026-08-22 17:16:30 +02:00
  • cbf6893f38 Add configurable sparsity flag to index finalization and merge CLI Eric Coissac 2026-08-22 15:25:00 +02:00
  • bb380d0c7d Add sorted_slots parameter to nonzero_triples and batch build_from_dense Eric Coissac 2026-08-22 15:06:41 +02:00
  • 23812d1af8 feat: add col_weights API and refactor obikstats to use Algorithm trait Eric Coissac 2026-08-22 13:56:50 +02:00
  • fba9c65b1a feat: add annotate CLI command for applying genome metadata via CSV Eric Coissac 2026-08-22 13:39:33 +02:00
  • fb31a35c76 Add unitig streaming iterators and estimate CLI subcommand Eric Coissac 2026-08-22 12:48:49 +02:00
  • 5048f43eea Start of a huge refactoring Eric Coissac 2026-08-22 12:34:05 +02:00
  • 1261aeba86 feat: Add superkmer CLI subcommand to obikmer2 Eric Coissac 2026-08-22 10:30:15 +02:00
  • 7183e3adb4 Add directory-level locking and introduce layered index cache Eric Coissac 2026-08-22 09:59:26 +02:00
  • 2419a6c21d refactor: shift indexing algorithms to layer-centric partition APIs Eric Coissac 2026-08-22 07:06:43 +02:00
  • fc4464a0ef Extract index modules into specialized workspace subcrates Eric Coissac 2026-08-21 21:23:12 +02:00
  • c9d10d55c7 Simplify MphfLayer::open by removing explicit IndexMode parameter Eric Coissac 2026-08-21 15:22:33 +02:00
  • 00ba968628 Introduce obikalgorithm crate to unify pipeline algorithms Eric Coissac 2026-08-21 14:10:54 +02:00
  • 8d6ba6546b refactor: migrate index metadata to on-disk JSON with fallible access Eric Coissac 2026-08-21 10:36:55 +02:00
  • 02dbdd11aa Split index lifecycle into IndexBuilder trait for maintenance operations Eric Coissac 2026-08-21 10:05:38 +02:00
  • da3aa5a2cb refactor: extract index construction state tracking into extension trait Eric Coissac 2026-08-21 09:50:24 +02:00
  • 31bb324752 Rename Layer to KmerLayer across obikindex and obikphylo Eric Coissac 2026-08-21 09:23:52 +02:00
  • 4b7b3c3c1a Extract indexing stage into LayerBuilder with NUMA-aware scheduling Eric Coissac 2026-08-21 09:18:09 +02:00
  • 346095b9eb Rename index methods to hash and expose kmer iteration APIs Eric Coissac 2026-08-21 09:10:20 +02:00
  • 0299b608e2 chore: remove CLAUDE.md and update .gitignore Eric Coissac 2026-08-21 06:01:27 +02:00
  • 878b63566f Extract k-mer counting logic into a dedicated counter module Eric Coissac 2026-08-21 05:33:23 +02:00
  • 96b6517541 refactor: rename obikindex to obikindexer Eric Coissac 2026-08-21 05:28:28 +02:00
  • 5c1584967f feat: enable index resumption and enforce directory creation Eric Coissac 2026-08-20 21:55:34 +02:00
  • abc51c2add Extract dereplication logic into obikderep crate and centralize paths Eric Coissac 2026-08-20 19:45:15 +02:00
  • 616cb76af3 Refactor indexing pipeline and partition path resolution Eric Coissac 2026-08-20 19:14:39 +02:00
  • 164e879585 feat: introduce obikpartition crate for kmer partition layer lookup Eric Coissac 2026-08-20 18:58:45 +02:00
  • c4b69e1af5 Introduce lifecycle-aware Layer::Empty variant and update callers Eric Coissac 2026-08-20 14:43:10 +02:00
  • 1c54e60c9a Rename Layer<D> to TypedLayer and introduce heterogeneous Layer enum Eric Coissac 2026-08-20 14:20:24 +02:00
  • 6c860f120f refactor: merge KmerPartitions into KmerIndex and rename obikpartition Eric Coissac 2026-08-20 13:49:06 +02:00
  • b5ec0122d0 Rename obikpartition crate to obikpartitionner Eric Coissac 2026-08-20 13:33:56 +02:00
  • f64ac14f0e chore: make COUNTS_DIR constant pub(crate) Eric Coissac 2026-08-20 12:26:39 +02:00
  • 9379bbaad8 refactor: rename obikpartitionner crate to obikpartition Eric Coissac 2026-08-20 10:18:03 +02:00
  • f9ef6b8391 rename KmerPartition to KmerPartitions and update Mat enum Eric Coissac 2026-08-20 10:11:46 +02:00
  • 76cbd3a886 Centralize partition metadata access and add layer introspection APIs Eric Coissac 2026-08-20 09:58:49 +02:00
  • f7ebc7a1ab Centralize partition directory resolution and add caching design spec Eric Coissac 2026-08-20 09:10:50 +02:00
  • 7eaa8c2016 Replace manual layer path construction with obilayeredmap::layer_dir Eric Coissac 2026-08-20 08:37:30 +02:00
  • 5a91817488 centralize layer path construction and data loading Eric Coissac 2026-08-20 06:27:16 +02:00
  • 640f29725b Optimize sparse bit matrix packing to avoid intermediate copies Eric Coissac 2026-08-20 06:12:28 +02:00
  • c2e0533fa9 Refactor bit matrix operations and optimize distance computations Eric Coissac 2026-08-20 06:08:12 +02:00
  • 9abee87af3 refactor: delegate distance computations and simplify matrix logic Eric Coissac 2026-08-20 06:00:03 +02:00
  • 19f9954050 refactor: centralize nonzero slot iteration logic across views Eric Coissac 2026-08-20 05:44:33 +02:00
  • 82374deca5 refactor: simplify sub_matrix with iterator-driven column population Eric Coissac 2026-08-20 05:34:14 +02:00
  • ac38aa759b refactor: rename batch retrieval methods and update common_traits Eric Coissac 2026-08-20 05:31:22 +02:00