Commit Graph

Select branches

Hide Pull Requests

V4.3

blackboard

master

microasm

push-kzmrqmplznrn

push-mvpuxnxoyypu

push-pvunnvzrzslw

push-snmwxkwkqxrm

push-uotrstkymowq

push-uzpqqoqvpnxw

push-wpwqvsqsrpwz

push-yxknulsuqnvz

taxonomy

#101

#50

#51

#53

#54

#56

#57

#58

#60

#61

#62

#63

#64

#65

#68

#70

#71

#72

#73

#74

#75

#76

#77

#78

#79

#80

#81

#82

#83

#84

#85

#86

#88

#89

#90

#91

#92

#93

#94

#95

#96

#97

#98

#99

Release_4.3.0

Release_4.4.0

Release_4.4.10

Release_4.4.11

Release_4.4.12

Release_4.4.13

Release_4.4.14

Release_4.4.15

Release_4.4.16

Release_4.4.17

Release_4.4.18

Release_4.4.19

Release_4.4.20

Release_4.4.21

Release_4.4.22

Release_4.4.23

Release_4.4.24

Release_4.4.25

Release_4.4.26

Release_4.4.27

Release_4.4.28

Release_4.4.29

Release_4.4.5

Release_4.4.6

Release_4.4.7

Release_4.4.8

Release_4.4.9

Mono Color

• 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
• 7c4042df6b introduce obidefault Eric Coissac 2025-01-27 17:12:45 +01:00
• 0a567f621c small changes Eric Coissac 2025-01-24 18:12:37 +01:00
• 9acb4a85a8 Refactoring of the default values Eric Coissac 2025-01-24 18:09:59 +01:00
• 3137c1f841 Adds the ability to read gzip-tar file for the taxonomy dump Eric Coissac 2025-01-24 11:47:59 +01:00
• ffd67252c3 patch a bug in obimultiplex: change option -t into -s Eric Coissac 2025-01-23 13:50:24 +01:00
• 757448cb1e debug obigrep taxonomy options Eric Coissac 2025-01-15 20:48:34 +01:00
• 4ae3336135 obidemerge: set demerge on sample the default Eric Coissac 2025-01-10 17:09:44 +01:00
• d066bb6878 Changes to be committed: modified: .gitignore modified: cmd/test/main.go modified: pkg/obioptions/version.go Eric Coissac 2025-01-09 07:24:41 +01:00
• becb995e3d misspellings penality -> pelnalty Eric Coissac 2025-01-09 07:22:23 +01:00
• c58d9772ac Two small corrections on options Eric Coissac 2025-01-07 11:51:37 +01:00
• 67c0d00a4d remove the obitag2 command Eric Coissac 2025-01-07 11:50:28 +01:00
• 4fe0db63ff Patch CSV reader to use the new taxonomy system Eric Coissac 2024-12-20 21:30:00 +01:00
• ccd3b06532 Merge branch 'master' into taxonomy Eric Coissac 2024-12-20 20:06:57 +01:00
• 5d0f996625 Patch a small bug on json write Eric Coissac 2024-12-20 19:42:03 +01:00
• abfa8f357a patch a bug in Taxid parsing Eric Coissac 2024-12-19 13:54:23 +01:00
• 795df34d1a Changes to be committed: modified: cmd/obitools/obitag/main.go modified: cmd/obitools/obitag2/main.go modified: go.mod modified: go.sum modified: pkg/obiformats/ncbitaxdump/read.go modified: pkg/obioptions/version.go modified: pkg/obiseq/attributes.go modified: pkg/obiseq/taxonomy_lca.go modified: pkg/obiseq/taxonomy_methods.go modified: pkg/obiseq/taxonomy_predicate.go modified: pkg/obitax/inner.go modified: pkg/obitax/lca.go new file: pkg/obitax/taxid.go modified: pkg/obitax/taxon.go modified: pkg/obitax/taxonomy.go modified: pkg/obitax/taxonslice.go modified: pkg/obitools/obicleandb/obicleandb.go modified: pkg/obitools/obigrep/options.go modified: pkg/obitools/obilandmark/obilandmark.go modified: pkg/obitools/obilandmark/options.go modified: pkg/obitools/obirefidx/famlilyindexing.go modified: pkg/obitools/obirefidx/geomindexing.go modified: pkg/obitools/obirefidx/obirefidx.go modified: pkg/obitools/obirefidx/options.go modified: pkg/obitools/obitag/obigeomtag.go modified: pkg/obitools/obitag/obitag.go modified: pkg/obitools/obitag/options.go modified: pkg/obiutils/strings.go Eric Coissac 2024-12-19 13:36:59 +01:00
• f2525d7b07 Changes to be committed: modified: pkg/obilua/lua.go modified: pkg/obioptions/version.go Eric Coissac 2024-12-04 11:42:05 +01:00
• 39dd3e3ce8 Add management of []interface{} to the LUA API. Eric Coissac 2024-12-04 10:58:17 +01:00
• f41a6fbb60 Patch a small bug on json write Eric Coissac 2024-11-29 18:39:18 +01:00
• 00b0edc15a refactoring of the file chunck writing Eric Coissac 2024-11-29 18:15:03 +01:00
• ad2461a656 some minor improvements Eric Coissac 2024-11-27 13:36:06 +01:00