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  • 235a7e202a Update obisummary to account new obiseq.StatsOnValues type master 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
  • 3b1aa2869e Changes to be committed: modified: pkg/obioptions/version.go Eric Coissac 2025-04-04 17:01:20 +02:00
  • 7542e33010 Several bugs dicoverd during the doc writing Eric Coissac 2025-04-04 16:59:27 +02:00
  • 03b5ce9397 Patch a bug in obitag when some reference sequences have taxid absent from the taxonomy Eric Coissac 2025-03-27 16:45:02 +01:00
  • 2d52322876 Patch a bug in the obi2 annotation parser on map indexed by integers Eric Coissac 2025-03-27 14:54:13 +01:00
  • fd80249b85 Patch a bug in obitag when a taxon from the reference library is unknown in the taxonomy Eric Coissac 2025-03-27 14:28:15 +01:00
  • 5a3705b6bb Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands. Eric Coissac 2025-03-25 16:44:46 +01:00
  • 2ab6f67d58 Add a progress bar to chimera detection Eric Coissac 2025-03-25 08:37:27 +01:00
  • 8b379d30da Adds the --newick-output option to the obitaxonomy command Eric Coissac 2025-03-14 14:24:12 +01:00
  • 8448783499 Make sequence files recognized as a taxonomy Eric Coissac 2025-03-14 14:22:22 +01:00
  • d1c31c54de add a first version of the inline documentation Eric Coissac 2025-03-12 14:40:42 +01:00
  • 7a9dc1ab3b update release notes Eric Coissac 2025-03-12 14:06:20 +01:00
  • 3a1cf4fe97 Accelerate the speed of very long fasta sequences, and more generaly of every format Eric Coissac 2025-03-12 13:29:41 +01:00
  • 83926c91e1 Patch the install script to desactivate the CSV check Eric Coissac 2025-03-12 13:28:52 +01:00
  • 937a483aa6 Changes to be committed: modified: Makefile Eric Coissac 2025-03-12 12:55:41 +01:00
  • dada70e6b1 Changes to be committed: modified: Makefile Eric Coissac 2025-03-12 12:49:34 +01:00
  • 62e5a93492 update the compress option name Eric Coissac 2025-03-11 17:14:40 +01:00
  • f21f51ae62 Correct the logic of --update-taxid and --fail-on-taxonomy Eric Coissac 2025-03-11 16:56:02 +01:00
  • 3b5d4ba455 patch a bug in obiannotate Eric Coissac 2025-03-11 16:35:38 +01:00
  • 50d11ce374 Add a pre-push git-hook to run tests on obitools commands before pushing on master Eric Coissac 2025-03-08 18:56:02 +01:00
  • 52d5f6fe11 make makefile crashing on test error Eric Coissac 2025-03-08 16:54:24 +01:00
  • 78caabd2fd Add basic test on -h for all the commands Eric Coissac 2025-03-08 16:28:06 +01:00
  • 65bd29b955 normalize the usage of obitaxonomy Eric Coissac 2025-03-08 13:00:55 +01:00
  • b18c9b7ac6 add the --raw-taxid option Eric Coissac 2025-03-08 09:40:06 +01:00
  • 78df7db18d typos Eric Coissac 2025-03-08 07:44:41 +01:00
  • fc08c12ab0 update release notes Eric Coissac 2025-03-08 07:42:20 +01:00
  • 0339e4dffa Patch size limite of the filetype guesser Eric Coissac 2025-03-08 07:34:02 +01:00
  • 706b44c37f Add option for csv input format Eric Coissac 2025-03-08 07:21:24 +01:00
  • fbe7d15dc3 Changes to be committed: modified: pkg/obioptions/version.go modified: pkg/obitools/obicleandb/obicleandb.go modified: pkg/obitools/obicleandb/options.go Eric Coissac 2025-03-06 13:38:38 +01:00
  • b5cf586f17 patch a duplicate --taxonomy option in obirefidxdb Eric Coissac 2025-03-06 11:36:20 +01:00
  • 286e27d6ba patch the scienctific_name tag name to "scientific_name" Eric Coissac 2025-03-05 14:22:12 +01:00
  • 996ec69bd9 update the release notes for version 4.4.0 Release_4.4.0 Eric Coissac 2025-03-01 12:56:39 +01:00
  • 5f9182d25b Changes to be committed: modified: pkg/obioptions/version.go Eric Coissac 2025-03-01 09:20:39 +01:00
  • 9913fa8354 Changes to be committed: modified: pkg/obioptions/version.go Eric Coissac 2025-03-01 09:14:56 +01:00
  • 7b23314651 Some typos V4.3 Eric Coissac 2025-03-01 08:29:27 +01:00
  • 1e541eac4c Last commit version Eric Coissac 2025-03-01 08:24:26 +01:00
  • 13cd4c86ac Patch the bug on --out with paired sequence files Eric Coissac 2025-02-27 18:13:21 +01:00
  • 75dd535201 Add a --valid-taxid option to obigrep Eric Coissac 2025-02-27 18:12:55 +01:00
  • 573acafafc Patch bug on ecotag with too short sequences Eric Coissac 2025-02-27 15:09:07 +01:00
  • 0067152c2b Patch the production of the ratio file Eric Coissac 2025-02-27 10:19:39 +01:00
  • 791d253edc Generate the ratio file as compressed if -Z option enabled. Eric Coissac 2025-02-27 09:06:07 +01:00
  • 6245d7f684 Changes to be committed: modified: .gitignore Eric Coissac 2025-02-24 15:47:45 +01:00
  • 13d610aff7 Changes to be committed: modified: pkg/obioptions/version.go modified: pkg/obitools/obiclean/chimera.go Eric Coissac 2025-02-24 15:25:45 +01:00
  • db284f1d44 Add an experimental chimera detection... Eric Coissac 2025-02-24 15:02:49 +01:00
  • 51b3e83d32 some cleaning Eric Coissac 2025-02-24 11:31:49 +01:00
  • 8671285d02 add the --min-sample-count option to obiclean. Eric Coissac 2025-02-24 08:48:31 +01:00
  • 51d11aa36d Changes to be committed: modified: pkg/obialign/alignment.go modified: pkg/obialign/pairedendalign.go modified: pkg/obioptions/version.go modified: pkg/obitools/obipairing/pairing.go Eric Coissac 2025-02-23 17:37:56 +01:00
  • fb6f857d8c Update the computation of the consensus quality score Eric Coissac 2025-02-23 15:16:31 +01:00
  • d4209b4549 Add a basic test for obiparing Eric Coissac 2025-02-22 09:57:44 +01:00
  • ef05d4975f Upadte the scoring schema of obipairing Eric Coissac 2025-02-21 22:41:34 +01:00
  • 4588bf8b5d Patch the make file to fail on error Eric Coissac 2025-02-19 15:55:07 +01:00
  • 090633850d Changes to be committed: modified: obitests/obitools/obicount/test.sh Eric Coissac 2025-02-19 15:28:42 +01:00
  • 15a058cf63 with all the sample files for tests Eric Coissac 2025-02-19 15:27:38 +01:00
  • 2f5f7634d6 Changes to be committed: modified: obitests/obitools/obicount/test.sh Eric Coissac 2025-02-19 14:50:10 +01:00
  • 48138b605c Changes to be committed: modified: .github/workflows/obitest.yml modified: Makefile modified: obitests/obitools/obicount/test.sh Eric Coissac 2025-02-19 14:37:05 +01:00
  • aed22c12a6 Changes to be committed: modified: obitests/obitools/obicount/test.sh Eric Coissac 2025-02-19 14:34:22 +01:00
  • 443a9b3ce3 Changes to be committed: modified: Makefile modified: obitests/obitools/obicount/test.sh Eric Coissac 2025-02-19 14:28:49 +01:00
  • 7e90537379 For run of test using bash in makefile Eric Coissac 2025-02-19 13:58:52 +01:00
  • d3d15acc6c Changes to be committed: modified: obitests/obitools/obicount/test.sh modified: pkg/obioptions/version.go Eric Coissac 2025-02-19 13:54:01 +01:00
  • bd4a0b5ca5 Essais d'une google action pour lancer les tests des obitools Eric Coissac 2025-02-19 13:45:43 +01:00
  • 952f85f312 A first trial of a test for obicount Eric Coissac 2025-02-19 13:17:36 +01:00
  • d70b0a5b42 A first version of obimicroasm... microasm Eric Coissac 2025-02-16 21:47:49 +01:00
  • 4774438644 Changes to be committed: modified: pkg/obiformats/universal_read.go modified: pkg/obioptions/version.go modified: pkg/obiseq/taxonomy_methods.go Eric Coissac 2025-02-12 08:40:38 +01:00
  • 6a8061cc4f Add managment of the taxonomy alias politic Eric Coissac 2025-02-10 14:05:47 +01:00
  • e2563cd8df Patch a bug in registering merged taxa Eric Coissac 2025-02-10 11:42:46 +01:00
  • f2e81adf95 Changes to be committed: modified: .gitignore deleted: xxx.csv Eric Coissac 2025-02-05 19:28:19 +01:00
  • f27e9bc91e patch a bug related to csv and qualities Eric Coissac 2025-02-05 19:27:00 +01:00
  • 773e54965d Patch a bug on compressed output Eric Coissac 2025-02-05 14:18:24 +01:00
  • ceca33998b add extensions fq in directory scanning Eric Coissac 2025-02-04 20:34:58 +01:00
  • b9bee5f426 Changes to be committed: modified: go.mod modified: go.sum modified: pkg/obilua/obilib.go modified: pkg/obilua/obiseq.go modified: pkg/obilua/obiseqslice.go new file: pkg/obilua/obitaxon.go new file: pkg/obilua/obitaxonomy.go modified: pkg/obioptions/version.go Eric Coissac 2025-02-02 16:52:52 +01:00
  • c10df073a7 Changes to be committed: modified: pkg/obioptions/version.go modified: pkg/obitax/iterator.go Eric Coissac 2025-02-01 12:06:19 +01:00
  • d3dac1b21f Make obitag able to use the taxonomic path included in reference database as taxonomy Eric Coissac 2025-01-30 11:50:03 +01:00
  • 0df082da06 Adds possibility to extract a taxonomy from taxonomic path included in sequence files Eric Coissac 2025-01-30 11:18:21 +01:00
  • 2452aef7a9 patch multiple -Z options Eric Coissac 2025-01-29 21:35:28 +01:00
  • 337954592d add the --out option to the obitaxonomy Eric Coissac 2025-01-29 13:22:35 +01:00
  • 8a28c9ae7c add the --download-ncbi option to obitaxonomy Eric Coissac 2025-01-29 12:38:39 +01:00
  • b6b18c0fa1 Changes to be committed: modified: pkg/obioptions/version.go Eric Coissac 2025-01-29 11:34:01 +01:00
  • 67e2758d63 Switch to realease number 4.3.0 Eric Coissac 2025-01-29 11:33:30 +01:00
  • 00f2dc2697 Rename obifind obitaxonomy and introduce the new CSV format for taxonomy. taxonomy Eric Coissac 2025-01-29 10:45:26 +01:00
  • c50a0f409d break the import cyccle Eric Coissac 2025-01-27 17:23:07 +01:00