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• 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
• 5e12ed5400 Merge pull request #56 from metabarcoding/push-tnrvpwvqtzyo coissac 2025-11-04 18:11:21 +01:00
• 7500ee1d15 update install script Eric Coissac 2025-11-04 18:08:39 +01:00
• 5a1d66bf06 Merge pull request #53 from metabarcoding/push-skmxzrzulvtq coissac 2025-10-28 14:27:19 +01:00
• 0844dcc607 bug obimatrix Eric Coissac 2025-10-28 13:50:38 +01:00
• 7f4ebe757e Bug obiuniq - don't clean the chunks Eric Coissac 2025-10-28 13:34:18 +01:00
• 5150947e23 Merge pull request #51 from metabarcoding/push-urtwmwktsrru coissac 2025-10-20 17:41:33 +02:00
• d17a9520b9 work on obiclean chimera detection Eric Coissac 2025-10-20 16:35:19 +02:00
• 29bf4ce871 add a feature to obimatrix adding obicsv option to obimatrix Eric Coissac 2025-10-17 10:24:25 +02:00
• d7ed9d343e Update install_obitools.sh for missing directory coissac 2025-10-15 08:32:06 +02:00
• 82b6bb1ab6 correct a bug in func (worker SeqWorker) ChainWorkers(next SeqWorker) SeqWorker Eric Coissac 2025-08-11 15:09:49 +02:00
• 6d204f6281 Patch the fastq detector Eric Coissac 2025-08-08 10:23:03 -04:00
• 7a6d552450 Changes to be committed: modified: pkg/obioptions/version.go Eric Coissac 2025-08-07 17:01:48 -04:00
• 412b54822c Patch a bug in obliclean for d>1 leading to some instability in the result Eric Coissac 2025-08-07 17:01:38 -04:00
• 730d448fc3 Allows for only one cpu and it should work Eric Coissac 2025-08-06 16:09:25 -04:00
• 04f3af3e60 some renaming of functions Eric Coissac 2025-08-06 15:54:50 -04:00
• 997b6e8c01 correct the fastq detector for distinguish with a csv ngsfilter Eric Coissac 2025-08-06 15:52:54 -04:00
• f239e8da92 Rename ISequenceChunk Eric Coissac 2025-08-05 08:49:45 -04:00
• ed28d3fb5b Adds a --u-to-t option Eric Coissac 2025-07-07 15:35:26 +02:00
• 43b285587e Debug on taxonomy extraction and CSV conversion Eric Coissac 2025-07-07 15:29:40 +02:00
• 8d53d253d4 Add a reading option on readers to convet U to T Eric Coissac 2025-07-07 15:29:07 +02:00
• 8c26fc9884 Add a new test on obisummary Eric Coissac 2025-07-07 15:28:29 +02:00
• 235a7e202a Update obisummary to account new obiseq.StatsOnValues type Eric Coissac 2025-06-19 17:21:30 +02:00
• 27fa984a63 Patch obimatrix accoring to the new type obiseq.StatsOnValues Eric Coissac 2025-06-19 16:51:53 +02:00
• add9d89ccc Patch the Min and Max values of the expression language Eric Coissac 2025-06-19 16:43:26 +02:00
• 9965370d85 Manage a lock on StatsOnValues Eric Coissac 2025-06-17 16:46:11 +02:00
• 8a2bb1fe82 Changes to be committed: modified: pkg/obioptions/version.go modified: pkg/obiseq/merge.go Eric Coissac 2025-06-17 12:11:35 +02:00
• efc3f3af29 Patch a concurrent access problem Eric Coissac 2025-06-17 12:05:42 +02:00
• 1c6ab1c559 Changes to be committed: modified: pkg/obingslibrary/multimatch.go modified: pkg/obioptions/version.go Eric Coissac 2025-06-17 09:06:42 +02:00
• 38dcd98d4a Patch the genbank parser automata Eric Coissac 2025-06-17 08:52:45 +02:00
• 7b23985693 Add _ to allowed in taxid Eric Coissac 2025-06-06 14:37:57 +02:00
• d31e677304 Patch a bug in obitag Eric Coissac 2025-06-04 14:47:28 +02:00
• 6cb7a5a352 Changes to be committed: modified: cmd/obitools/obitag/main.go modified: cmd/obitools/obitaxonomy/main.go modified: pkg/obiformats/csvtaxdump_read.go modified: pkg/obiformats/ecopcr_read.go modified: pkg/obiformats/ncbitaxdump_read.go modified: pkg/obiformats/ncbitaxdump_readtar.go modified: pkg/obiformats/newick_write.go modified: pkg/obiformats/options.go modified: pkg/obiformats/taxonomy_read.go modified: pkg/obiformats/universal_read.go modified: pkg/obiiter/extract_taxonomy.go modified: pkg/obioptions/options.go modified: pkg/obioptions/version.go new file: pkg/obiphylo/tree.go modified: pkg/obiseq/biosequenceslice.go modified: pkg/obiseq/taxonomy_methods.go modified: pkg/obitax/taxonomy.go modified: pkg/obitax/taxonset.go modified: pkg/obitools/obiconvert/sequence_reader.go modified: pkg/obitools/obitag/obitag.go modified: pkg/obitools/obitaxonomy/obitaxonomy.go modified: pkg/obitools/obitaxonomy/options.go deleted: sample/.DS_Store Eric Coissac 2025-06-04 09:48:10 +02:00
• 3424d3057f Changes to be committed: modified: pkg/obiformats/ngsfilter_read.go modified: pkg/obioptions/version.go modified: pkg/obiutils/mimetypes.go Eric Coissac 2025-05-14 14:53:25 +02:00
• f9324dd8f4 add min and max to the obitools expression language Eric Coissac 2025-05-13 16:03:03 +02:00
• f1b9ac4a13 Update the expression language Eric Coissac 2025-05-07 20:45:05 +02:00
• e065e2963b Update the install script Eric Coissac 2025-05-01 11:45:46 +02:00
• 13ff892ac9 Patch type mismatch in apat C library Eric Coissac 2025-04-23 16:14:10 +02:00
• c0ecaf90ab Add the --number option to obiannotate Eric Coissac 2025-04-22 18:35:51 +02:00
• a57cfda675 Make the replace function of the eval language accepting regex Eric Coissac 2025-04-10 15:17:15 +02:00
• c2f38e737b Update of the packages Eric Coissac 2025-04-10 15:16:36 +02:00
• 0aec5ba4df change the tests according to the corrections in obipairing Eric Coissac 2025-04-04 17:10:17 +02:00
• 67e5b6ef24 Changes to be committed: modified: pkg/obioptions/version.go Eric Coissac 2025-04-04 17:02:45 +02:00