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• db22d20d0a Rename obisuperkmer test script to obik-super and update command references Release_4.4.14 Eric Coissac 2026-02-10 22:17:13 +01:00
• 7c05bdb01c Merge pull request #84 from metabarcoding/push-uxvowwlxkrlq coissac 2026-02-10 22:12:18 +01:00
• b6542c4523 Bump version to 4.4.13 Eric Coissac 2026-02-10 22:10:37 +01:00
• ac41dd8a22 Refactor k-mer matching pipeline with improved concurrency and memory management Release_4.4.13 Eric Coissac 2026-02-10 22:10:22 +01:00
• bebbbbfe7d Add entropy-based filtering for k-mers Eric Coissac 2026-02-10 18:19:57 +01:00
• c6e04265f1 Add sparse index support for KDI files with fast seeking Eric Coissac 2026-02-10 13:23:56 +01:00
• 9babcc0fae Refactor lowmask options and shared kmer options Eric Coissac 2026-02-10 09:52:28 +01:00
• e775f7e256 Add option to keep shorter fragments in lowmask Eric Coissac 2026-02-10 09:36:32 +01:00
• f2937af1ad Add max frequency filtering and top-kmer saving capabilities Eric Coissac 2026-02-10 09:26:46 +01:00
• 56c1f4180c Refactor k-mer index management with subcommands and enhanced metadata support Eric Coissac 2026-02-09 23:10:30 +01:00
• f78543ee75 Refactor k-mer index building to use disk-based KmerSetGroupBuilder Eric Coissac 2026-02-09 21:57:03 +01:00
• a016ad5b8a Refactor kmer index to disk-based partitioning with minimizer Eric Coissac 2026-02-09 17:50:33 +01:00
• 09d437d10f Merge pull request #83 from metabarcoding/push-xssnppvunmlq Release_4.4.12 coissac 2026-02-09 09:58:06 +01:00
• d00ab6f83a Bump version from 4.4.11 to 4.4.12 Eric Coissac 2026-02-09 09:46:11 +01:00
• 8037860518 Update version and improve release note generation Eric Coissac 2026-02-09 09:05:47 +01:00
• 43d6cbe56a Merge pull request #82 from metabarcoding/push-vkprtnlyxmkl coissac 2026-02-09 09:16:20 +01:00
• 6dadee9371 Bump version to 4.4.12 Eric Coissac 2026-02-09 09:05:47 +01:00
• 99a8e69d10 Optimize low-complexity masking algorithm Eric Coissac 2026-02-08 20:20:28 +01:00
• c0ae49ef92 Ajout d'obilowmask_ref au fichier .gitignore Eric Coissac 2026-02-08 19:31:05 +01:00
• 08490420a2 Fix whitespace in test script and add merge consistency tests Eric Coissac 2026-02-08 18:08:13 +01:00
• 1a28d5ed64 Add progress bar configuration and conditional display Eric Coissac 2026-02-08 16:13:27 +01:00
• b2d16721f0 Fix classifier cloning and reset in chunk processing Eric Coissac 2026-02-08 15:52:18 +01:00
• 7c12b1ee83 Disable progress bar when output is piped Eric Coissac 2026-02-08 14:45:53 +01:00
• db98ddb241 Fix super k-mer minimizer bijection and add validation test Eric Coissac 2026-02-08 13:44:23 +01:00
• 7a979ba77f Add obisuperkmer command implementation and tests Eric Coissac 2026-02-07 13:53:13 +01:00
• 00c8be6b48 docs: add architecture documentation for OBITools commands Eric Coissac 2026-02-07 12:26:25 +01:00
• 4ae331db36 Refactor SuperKmer extraction to use iterator pattern Eric Coissac 2026-02-07 12:22:59 +01:00
• f1e2846d2d Amélioration du processus de release avec génération automatique des notes de version Eric Coissac 2026-02-07 11:48:18 +01:00
• cd5562fb30 Merge pull request #81 from metabarcoding/push-nrylumyxtxnr coissac 2026-02-06 10:10:22 +01:00
• f79b018430 Bump version to 4.4.11 Eric Coissac 2026-02-06 10:09:54 +01:00
• aa819618c2 Enhance OBITools4 installation script with version control and documentation Release_4.4.11 Eric Coissac 2026-02-06 09:52:43 +01:00
• da8d851d4d Merge pull request #80 from metabarcoding/push-vvonlpwlnwxy coissac 2026-02-06 09:53:29 +01:00
• 9823bcb41b Remove ecoprimers submodule Eric Coissac 2026-02-06 09:52:43 +01:00
• 9c162459b0 Merge pull request #79 from metabarcoding/push-tpytwyyyostt coissac 2026-02-06 09:51:42 +01:00
• 25b494e562 Remove ecoprimers submodule Eric Coissac 2026-02-06 09:50:45 +01:00
• 0b5cadd104 Merge pull request #78 from metabarcoding/push-pwvvkzxzmlux coissac 2026-02-06 09:48:47 +01:00
• a2106e4e82 Bump version to 4.4.10 Eric Coissac 2026-02-06 09:48:26 +01:00
• a8a00ba0f7 Simplify artifact packaging and update release notes Release_4.4.10 Eric Coissac 2026-02-06 09:48:14 +01:00
• 1595a74ada Merge pull request #77 from metabarcoding/push-lwtnswxmorrq coissac 2026-02-06 09:35:05 +01:00
• 68d723ecba Bump version to 4.4.9 Eric Coissac 2026-02-06 09:34:41 +01:00
• 250d616129 Mise à jour des workflows de release pour les nouvelles versions d'OS Release_4.4.9 Eric Coissac 2026-02-06 09:34:30 +01:00
• fbf816d219 Merge pull request #76 from metabarcoding/push-tzpmmnnxkvxx coissac 2026-02-06 09:09:05 +01:00
• 7f0133a196 Bump version to 4.4.8 Eric Coissac 2026-02-06 09:08:33 +01:00
• f798f22434 Add cross-platform binary builds and release workflow improvements Release_4.4.8 Eric Coissac 2026-02-06 09:08:20 +01:00
• 248bc9f672 Merge pull request #75 from metabarcoding/push-mxxuykppzlpw coissac 2026-02-05 18:11:12 +01:00
• 7a7db703f1 Bump version to 4.4.7 Eric Coissac 2026-02-05 18:10:44 +01:00
• da195ac5cb Optimisation de la construction des binaires Release_4.4.7 Eric Coissac 2026-02-05 18:10:36 +01:00
• 20a0a09f5f Merge pull request #74 from metabarcoding/push-yqrwnpmoqllk coissac 2026-02-05 18:03:28 +01:00
• 7d8c578c57 Merge branch 'master' into push-yqrwnpmoqllk coissac 2026-02-05 18:03:18 +01:00
• d7f615108f Bump version to 4.4.6 Eric Coissac 2026-02-05 18:02:29 +01:00
• 71574f240b Update version and add CI tests Release_4.4.6 Eric Coissac 2026-02-05 17:53:52 +01:00
• c98501a898 Merge pull request #73 from metabarcoding/push-pklkwsssrkuv coissac 2026-02-05 17:54:39 +01:00
• 23f145a4c2 Bump version to 4.4.5 Eric Coissac 2026-02-05 17:53:52 +01:00
• fe6d74efbf Add automated release workflow and update tag creation Release_4.4.5 Eric Coissac 2026-02-05 17:53:43 +01:00
• cff8135468 Merge pull request #72 from metabarcoding/push-zsprzlqxurrp coissac 2026-02-05 17:42:48 +01:00
• 02ab683fa0 Bump version to 4.4.4 Eric Coissac 2026-02-05 17:42:00 +01:00
• de88e7eecd Fix typo in variable name Eric Coissac 2026-02-05 17:41:59 +01:00
• e3c41fc11b Add Jaccard distance and similarity computations for KmerSet and KmerSetGroup Eric Coissac 2026-02-05 17:38:47 +01:00
• aa2e94dd6f Refactor k-mer normalization functions and add quorum operations Eric Coissac 2026-02-05 17:11:14 +01:00
• a43e6258be docs: translate comments to English Eric Coissac 2026-02-05 16:35:38 +01:00
• 12ca62b06a Implémentation complète de la persistance pour FrequencyFilter Eric Coissac 2026-02-05 16:26:00 +01:00
• 09ac15a76b Refactor k-mer encoding functions to use 'canonical' terminology Eric Coissac 2026-02-05 16:14:24 +01:00
• 16f72e6305 refactoring of obikmer Eric Coissac 2026-02-05 15:56:22 +01:00
• 6c6c369ee2 Add k-mer encoding and decoding functions with normalized k-mer support Eric Coissac 2026-02-05 15:51:44 +01:00
• c5dd477675 Refactor KmerSet and FrequencyFilter to use immutable K parameter and consistent Copy/Clone methods Eric Coissac 2026-02-05 15:32:19 +01:00
• afcb43b352 Ajout de la gestion des métadonnées utilisateur dans KmerSet et KmerSetGroup Eric Coissac 2026-02-05 15:02:27 +01:00
• b26b76cbf8 Add TOML persistence support for KmerSet and KmerSetGroup Eric Coissac 2026-02-05 14:57:12 +01:00
• aa468ec462 Refactor FrequencyFilter to use KmerSetGroup Eric Coissac 2026-02-05 14:46:52 +01:00
• 00dcd78e84 Refactor k-mer encoding and frequency filtering with KmerSet Eric Coissac 2026-02-05 14:41:41 +01:00
• 60f27c1dc8 Add error handling for ambiguous bases in k-mer encoding Eric Coissac 2026-02-04 21:44:52 +01:00
• 28162ac36f Ajout du filtre de fréquence avec v niveaux Roaring Bitmaps Eric Coissac 2026-02-04 21:20:27 +01:00
• 1a1adb83ac Add error marker support for k-mers with enhanced documentation Eric Coissac 2026-02-04 16:13:13 +01:00
• 05de9ca58e Add SuperKmer extraction functionality Eric Coissac 2026-02-04 16:03:51 +01:00
• 500144051a Add jj Makefile targets and k-mer encoding utilities Eric Coissac 2026-01-25 18:43:30 +01:00
• 740f66b4c7 Merge pull request #71 from metabarcoding/push-onwzsyuooozn coissac 2026-01-14 19:19:27 +01:00
• b49aba9c09 Implémentation du filtrage unique basé sur séquence et catégories Eric Coissac 2026-01-14 19:18:08 +01:00
• 52244cdb64 Merge pull request #70 from metabarcoding/push-kuwnszsxmxpn coissac 2026-01-14 18:47:17 +01:00
• 0678181023 Refactor chunk processing and update version commit Eric Coissac 2026-01-14 17:46:26 +01:00
• f55dd553c7 Merge pull request #68 from metabarcoding/push-rrulynolpprl coissac 2026-01-14 17:44:36 +01:00
• 4a383ac6c9 Merge branch 'master' into push-rrulynolpprl coissac 2025-12-18 14:12:56 +01:00
• 371e702423 obiannotate --cut bug Eric Coissac 2025-12-18 14:10:56 +01:00
• ac0d3f3fe4 Update obiuniq for very large dataset Eric Coissac 2025-12-03 11:48:50 +01:00
• 547135c747 End of obilowmask Eric Coissac 2025-11-24 14:28:21 +01:00
• f4a919732e Merge pull request #65 from metabarcoding/push-yurwulsmpxkq coissac 2025-11-26 12:13:08 +01:00
• e681666aaa End of obilowmask Eric Coissac 2025-11-24 14:28:21 +01:00
• adf2486295 Merge pull request #64 from metabarcoding/push-yurwulsmpxkq coissac 2025-11-24 15:36:20 +01:00
• 272f5c9c35 End of obilowmask Eric Coissac 2025-11-24 14:28:21 +01:00
• c1b9503ca6 Merge pull request #63 from metabarcoding/push-vypwrurrsxuk coissac 2025-11-21 14:04:34 +01:00
• 86e60aedd0 obicsv bug with stat on value map fields Eric Coissac 2025-11-21 13:29:19 +01:00
• 961abcea7b Merge pull request #61 from metabarcoding/push-mvxssvnysyxn coissac 2025-11-21 13:25:19 +01:00
• 57c65f9d50 obimatrix bug Eric Coissac 2025-11-21 13:24:24 +01:00
• e65b2a5efe obimatrix bugs Eric Coissac 2025-11-21 13:09:24 +01:00
• 3e5f3f76b0 Merge pull request #60 from metabarcoding/push-qpnzxskwpoxo coissac 2025-11-18 15:35:41 +01:00
• ccc827afd3 finalise obilowmask Eric Coissac 2025-11-11 21:41:09 +01:00
• cef29005a5 debug url reading Eric Coissac 2025-11-18 15:30:06 +01:00
• 4603d7973e implementation de obilowmask Eric Coissac 2025-10-20 17:43:25 +02:00
• 8bc47c13d3 Merge pull request #58 from metabarcoding/push-vxkqkkrokwuz coissac 2025-11-06 15:44:31 +01:00
• 07cdd6f758 debug obimultiplex Eric Coissac 2025-11-06 15:43:13 +01:00
• 432da366e2 Merge pull request #57 from metabarcoding/push-ywktmvpvtvmv coissac 2025-11-05 19:07:41 +01:00
• 2d7dc7d09d debug taxonomy core dump Eric Coissac 2025-11-05 18:59:05 +01:00