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efc3f3af29
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Patch a concurrent access problem
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2025-06-17 12:05:42 +02:00 |
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1c6ab1c559
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Changes to be committed:
modified: pkg/obingslibrary/multimatch.go
modified: pkg/obioptions/version.go
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2025-06-17 09:06:42 +02:00 |
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38dcd98d4a
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Patch the genbank parser automata
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2025-06-17 08:52:45 +02:00 |
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7b23985693
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Add _ to allowed in taxid
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2025-06-06 14:37:57 +02:00 |
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d31e677304
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Patch a bug in obitag
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2025-06-04 14:47:28 +02:00 |
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6cb7a5a352
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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
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2025-06-04 09:48:10 +02:00 |
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3424d3057f
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Changes to be committed:
modified: pkg/obiformats/ngsfilter_read.go
modified: pkg/obioptions/version.go
modified: pkg/obiutils/mimetypes.go
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2025-05-14 14:53:25 +02:00 |
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f9324dd8f4
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add min and max to the obitools expression language
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2025-05-13 16:03:03 +02:00 |
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f1b9ac4a13
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Update the expression language
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2025-05-07 20:45:05 +02:00 |
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e065e2963b
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Update the install script
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2025-05-01 11:45:46 +02:00 |
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13ff892ac9
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Patch type mismatch in apat C library
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2025-04-23 16:14:10 +02:00 |
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c0ecaf90ab
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Add the --number option to obiannotate
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2025-04-22 18:35:51 +02:00 |
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a57cfda675
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Make the replace function of the eval language accepting regex
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2025-04-10 15:17:15 +02:00 |
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c2f38e737b
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Update of the packages
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2025-04-10 15:16:36 +02:00 |
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0aec5ba4df
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change the tests according to the corrections in obipairing
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2025-04-04 17:10:17 +02:00 |
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67e5b6ef24
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Changes to be committed:
modified: pkg/obioptions/version.go
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2025-04-04 17:02:45 +02:00 |
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3b1aa2869e
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Changes to be committed:
modified: pkg/obioptions/version.go
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2025-04-04 17:01:20 +02:00 |
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7542e33010
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Several bugs dicoverd during the doc writing
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2025-04-04 16:59:27 +02:00 |
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03b5ce9397
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Patch a bug in obitag when some reference sequences have taxid absent from the taxonomy
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2025-03-27 16:45:02 +01:00 |
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2d52322876
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Patch a bug in the obi2 annotation parser on map indexed by integers
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2025-03-27 14:54:13 +01:00 |
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fd80249b85
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Patch a bug in obitag when a taxon from the reference library is unknown in the taxonomy
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2025-03-27 14:28:15 +01:00 |
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5a3705b6bb
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Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.
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2025-03-25 16:44:46 +01:00 |
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2ab6f67d58
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Add a progress bar to chimera detection
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2025-03-25 08:37:27 +01:00 |
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8b379d30da
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Adds the --newick-output option to the obitaxonomy command
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2025-03-14 14:24:12 +01:00 |
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8448783499
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Make sequence files recognized as a taxonomy
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2025-03-14 14:22:22 +01:00 |
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d1c31c54de
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add a first version of the inline documentation
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2025-03-12 14:40:42 +01:00 |
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7a9dc1ab3b
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update release notes
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2025-03-12 14:06:20 +01:00 |
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3a1cf4fe97
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Accelerate the speed of very long fasta sequences, and more generaly of every format
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2025-03-12 13:29:41 +01:00 |
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83926c91e1
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Patch the install script to desactivate the CSV check
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2025-03-12 13:28:52 +01:00 |
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937a483aa6
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Changes to be committed:
modified: Makefile
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2025-03-12 12:55:41 +01:00 |
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dada70e6b1
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Changes to be committed:
modified: Makefile
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2025-03-12 12:49:34 +01:00 |
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62e5a93492
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update the compress option name
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2025-03-11 17:14:40 +01:00 |
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f21f51ae62
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Correct the logic of --update-taxid and --fail-on-taxonomy
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2025-03-11 16:56:02 +01:00 |
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3b5d4ba455
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patch a bug in obiannotate
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2025-03-11 16:35:38 +01:00 |
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50d11ce374
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Add a pre-push git-hook to run tests on obitools commands before pushing on master
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2025-03-08 18:56:02 +01:00 |
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52d5f6fe11
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make makefile crashing on test error
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2025-03-08 16:54:24 +01:00 |
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78caabd2fd
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Add basic test on -h for all the commands
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2025-03-08 16:28:06 +01:00 |
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65bd29b955
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normalize the usage of obitaxonomy
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2025-03-08 13:00:55 +01:00 |
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b18c9b7ac6
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add the --raw-taxid option
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2025-03-08 09:40:06 +01:00 |
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78df7db18d
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typos
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2025-03-08 07:44:41 +01:00 |
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fc08c12ab0
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update release notes
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2025-03-08 07:42:20 +01:00 |
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0339e4dffa
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Patch size limite of the filetype guesser
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2025-03-08 07:34:02 +01:00 |
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706b44c37f
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Add option for csv input format
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2025-03-08 07:21:24 +01:00 |
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fbe7d15dc3
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Changes to be committed:
modified: pkg/obioptions/version.go
modified: pkg/obitools/obicleandb/obicleandb.go
modified: pkg/obitools/obicleandb/options.go
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2025-03-06 13:38:38 +01:00 |
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b5cf586f17
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patch a duplicate --taxonomy option in obirefidxdb
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2025-03-06 11:36:20 +01:00 |
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286e27d6ba
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patch the scienctific_name tag name to "scientific_name"
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2025-03-05 14:22:12 +01:00 |
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996ec69bd9
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update the release notes for version 4.4.0
Release_4.4.0
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2025-03-01 12:56:39 +01:00 |
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5f9182d25b
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Changes to be committed:
modified: pkg/obioptions/version.go
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2025-03-01 09:20:39 +01:00 |
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9913fa8354
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Changes to be committed:
modified: pkg/obioptions/version.go
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2025-03-01 09:14:56 +01:00 |
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7b23314651
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Some typos
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2025-03-01 08:29:27 +01:00 |
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