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• f92f285417 Merge pull request #101 from metabarcoding/push-klzowrsmmnyv master coissac 2026-03-16 22:29:29 +01:00
• a786b58ed3 Dynamic Batch Flushing and Build Improvements Release_4.4.29 Eric Coissac 2026-03-16 22:06:51 +01:00
• a2b26712b2 refactor: replace fixed batch size with dynamic flushing based on count and memory Eric Coissac 2026-03-16 22:06:14 +01:00
• 1599abc9ad Merge pull request #99 from metabarcoding/push-urlyqwkrqypt coissac 2026-03-14 12:21:34 +01:00
• af213ab446 4.4.28: Static Linux Builds, Memory-Aware Batching, and Build Stability Release_4.4.28 Eric Coissac 2026-03-14 11:59:15 +01:00
• a60184c115 chore: bump version to 4.4.27 and add zlib-static dependency Eric Coissac 2026-03-14 11:43:42 +01:00
• f519c0ef7f 4.4.27: Static Linux builds, memory-aware batching, and build toolchain upgrades Release_4.4.27 push-wpwqvsqsrpwz Eric Coissac 2026-03-14 11:43:42 +01:00
• 585b024bf0 chore: update to Go 1.26 and refactor release workflow Eric Coissac 2026-03-13 19:30:37 +01:00
• 78e7933c6f 4.4.26: Static Linux Builds, Memory-Aware Batching & Cross-Compilation Fixes Release_4.4.26 push-yxknulsuqnvz Eric Coissac 2026-03-13 19:30:37 +01:00
• afc9ffda85 chore: bump version to 4.4.25 and fix CGO_CFLAGS for cross-compilation Eric Coissac 2026-03-13 19:24:26 +01:00
• 3cd4944fd8 4.4.25: Static Linux Builds, Memory-Aware Batching, and Build Stability Release_4.4.25 push-pvunnvzrzslw Eric Coissac 2026-03-13 19:24:26 +01:00
• fdd972bbd2 fix: add CGO_CFLAGS for static Linux builds and update go.work.sum Eric Coissac 2026-03-13 19:24:15 +01:00
• 76f595e1fe Merge pull request #95 from metabarcoding/push-kzmrqmplznrn coissac 2026-03-13 19:13:02 +01:00
• 1e1e5443e3 Merge branch 'master' into push-kzmrqmplznrn push-kzmrqmplznrn coissac 2026-03-13 19:12:49 +01:00
• 15d1f1fd80 Version 4.4.24 Release_4.4.24 Eric Coissac 2026-03-13 19:11:58 +01:00
• 8df2cbe22f Bump version to 4.4.23 and update release workflow Eric Coissac 2026-03-13 19:03:50 +01:00
• 58d685926b Merge pull request #94 from metabarcoding/push-lxxxlurqmqrt coissac 2026-03-13 19:04:15 +01:00
• e9f24426df 4.4.23: Memory-aware batching, static Linux builds, and build improvements Eric Coissac 2026-03-13 19:03:50 +01:00
• 2f7be10b5d Build improvements and Go version update Release_4.4.23 Eric Coissac 2026-03-13 19:03:22 +01:00
• 43125f9f5e feat: add progress bar to curl downloads in install script Eric Coissac 2026-03-13 16:40:53 +01:00
• c23368e929 update dependencies and Go toolchain to 1.25.0 Eric Coissac 2026-03-13 16:09:22 +01:00
• 6cb5a81685 Merge pull request #93 from metabarcoding/push-snmwxkwkqxrm coissac 2026-03-13 15:18:29 +01:00
• 94b0887069 Memory-aware Batching and Static Linux Builds push-snmwxkwkqxrm Eric Coissac 2026-03-13 15:16:41 +01:00
• c188580aac Replace Rebatch with RebatchBySize using default batch parameters Release_4.4.22 Eric Coissac 2026-03-13 15:13:56 +01:00
• 1e1f575d1c refactor: replace single batch size with min/max bounds and memory limits Eric Coissac 2026-03-13 15:07:31 +01:00
• 40769bf827 Add memory-based batching support Eric Coissac 2026-03-13 14:54:14 +01:00
• 74e6fcaf83 feat: add static linking for Linux builds using musl Eric Coissac 2026-03-13 14:26:17 +01:00
• 30ec8b1b63 Merge pull request #92 from metabarcoding/push-mvpuxnxoyypu coissac 2026-03-13 12:00:32 +01:00
• cdc72c5346 4.4.21: Parallel builds, robust installation, and rope-based parsing enhancements push-mvpuxnxoyypu Eric Coissac 2026-03-13 11:59:32 +01:00
• 82a9972be7 Add parallel compilation support and improve Makefile/install script robustness Release_4.4.21 Eric Coissac 2026-03-13 11:59:00 +01:00
• ff6e515b2a Merge pull request #91 from metabarcoding/push-uotrstkymowq coissac 2026-03-12 20:15:33 +01:00
• cd0c525f50 4.4.20: Rope-based parsing, improved release tooling, and bug fixes push-uotrstkymowq Eric Coissac 2026-03-12 20:06:24 +01:00
• abe935aa18 Add help target, colorize output, and improve release workflow Release_4.4.20 Eric Coissac 2026-03-12 19:20:45 +01:00
• 8dd32dc1bf Fix CompressStream call to use compressed variable Eric Coissac 2026-03-12 18:48:20 +01:00
• 6ee8750635 Replace SplitInTwo with LeftSplitInTwo/RightSplitInTwo for precise splitting Eric Coissac 2026-03-12 18:41:03 +01:00
• 8c318c480e replace fixed-size carry buffer with dynamic slice Eric Coissac 2026-03-11 17:05:34 +01:00
• 09fbc217d3 Add EMBL rope parsing support and improve sequence extraction Eric Coissac 2026-03-10 17:02:05 +01:00
• 3d2e205722 Refactor rope scanner and add FASTQ rope parser Eric Coissac 2026-03-10 16:46:53 +01:00
• 623116ab13 Add rope-based FASTA parsing and improve sequence handling Eric Coissac 2026-03-10 16:34:25 +01:00
• 1e4509cb63 Merge pull request #90 from metabarcoding/push-uzpqqoqvpnxw coissac 2026-03-10 15:53:08 +01:00
• b33d7705a8 Bump version to 4.4.19 push-uzpqqoqvpnxw Eric Coissac 2026-03-10 15:51:35 +01:00
• 1342c83db6 Use NewBioSequenceOwning to avoid unnecessary sequence copying Release_4.4.19 Eric Coissac 2026-03-10 15:51:28 +01:00
• b246025907 Optimize Fasta batch formatting Eric Coissac 2026-03-10 15:43:53 +01:00
• 761e0dbed3 Implémentation d'un parseur GenBank utilisant rope pour réduire l'usage de mémoire Eric Coissac 2026-03-10 15:35:23 +01:00
• a7ea47624b Optimisation du parsing des grandes séquences Eric Coissac 2026-03-10 14:20:10 +01:00
• 61e346658e Refactor jjpush workflow and enhance release notes generation Eric Coissac 2026-02-20 11:52:34 +01:00
• 1ba1294b11 Merge pull request #89 from metabarcoding/push-uoqxkozlonwx coissac 2026-02-20 11:42:40 +01:00
• b2476fffcb Bump version to 4.4.18 Eric Coissac 2026-02-20 11:40:41 +01:00
• b05404721e Bump version to 4.4.16 Release_4.4.18 Eric Coissac 2026-02-20 11:37:51 +01:00
• c57e788459 Fix GenBank parsing and add release notes script Eric Coissac 2026-02-20 10:39:14 +01:00
• c332d3ddc9 Automated Release 4.4.16 Release_4.4.17 Eric Coissac 2026-02-19 18:30:55 +01:00
• 0580611031 Implémentation des superkmers canoniques et nettoyage du parsing GenBank Release_4.4.16 Eric Coissac 2026-02-19 18:30:46 +01:00
• c30a22d356 Refactor build workflow and update version Eric Coissac 2026-02-11 06:31:10 +01:00
• 1cecf23978 Merge pull request #86 from metabarcoding/push-oulwykrpwxuz coissac 2026-02-11 06:34:05 +01:00
• 4c824ef9b7 Bump version to 4.4.15 Eric Coissac 2026-02-11 06:31:10 +01:00
• 1ce5da9bee Support new sequence file formats and improve error handling Release_4.4.15 Eric Coissac 2026-02-11 06:31:03 +01:00
• dc23d9de9a Merge pull request #85 from metabarcoding/push-smturnsrozkp coissac 2026-02-10 22:19:22 +01:00
• aa9d7bbf72 Bump version to 4.4.14 Eric Coissac 2026-02-10 22:17:22 +01:00
• 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