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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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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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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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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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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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13cd4c86ac
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Patch the bug on --out with paired sequence files
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2025-02-27 18:13:21 +01:00 |
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573acafafc
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Patch bug on ecotag with too short sequences
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2025-02-27 15:09:07 +01:00 |
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0067152c2b
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Patch the production of the ratio file
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2025-02-27 10:19:39 +01:00 |
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791d253edc
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Generate the ratio file as compressed if -Z option enabled.
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2025-02-27 09:06:07 +01:00 |
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13d610aff7
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Changes to be committed:
modified: pkg/obioptions/version.go
modified: pkg/obitools/obiclean/chimera.go
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2025-02-24 15:25:45 +01:00 |
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db284f1d44
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Add an experimental chimera detection...
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2025-02-24 15:02:49 +01:00 |
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51b3e83d32
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some cleaning
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2025-02-24 11:31:49 +01:00 |
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8671285d02
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add the --min-sample-count option to obiclean.
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2025-02-24 08:48:31 +01:00 |
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51d11aa36d
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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
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2025-02-23 17:37:56 +01:00 |
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fb6f857d8c
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Update the computation of the consensus quality score
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2025-02-23 15:16:31 +01:00 |
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ef05d4975f
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Upadte the scoring schema of obipairing
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2025-02-21 22:41:34 +01:00 |
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7e90537379
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For run of test using bash in makefile
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2025-02-19 13:58:52 +01:00 |
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d3d15acc6c
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Changes to be committed:
modified: obitests/obitools/obicount/test.sh
modified: pkg/obioptions/version.go
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2025-02-19 13:54:01 +01:00 |
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bd4a0b5ca5
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Essais d'une google action pour lancer les tests des obitools
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2025-02-19 13:45:43 +01:00 |
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952f85f312
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A first trial of a test for obicount
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2025-02-19 13:17:36 +01:00 |
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4774438644
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Changes to be committed:
modified: pkg/obiformats/universal_read.go
modified: pkg/obioptions/version.go
modified: pkg/obiseq/taxonomy_methods.go
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2025-02-12 08:40:38 +01:00 |
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6a8061cc4f
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Add managment of the taxonomy alias politic
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2025-02-10 14:05:47 +01:00 |
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e2563cd8df
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Patch a bug in registering merged taxa
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2025-02-10 11:42:46 +01:00 |
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f27e9bc91e
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patch a bug related to csv and qualities
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2025-02-05 19:27:00 +01:00 |
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773e54965d
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Patch a bug on compressed output
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2025-02-05 14:18:24 +01:00 |
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ceca33998b
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add extensions fq in directory scanning
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2025-02-04 20:34:58 +01:00 |
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b9bee5f426
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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
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2025-02-02 16:52:52 +01:00 |
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c10df073a7
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Changes to be committed:
modified: pkg/obioptions/version.go
modified: pkg/obitax/iterator.go
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2025-02-01 12:06:19 +01:00 |
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d3dac1b21f
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Make obitag able to use the taxonomic path included in reference database as taxonomy
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2025-01-30 11:50:03 +01:00 |
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0df082da06
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Adds possibility to extract a taxonomy from taxonomic path included in sequence files
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2025-01-30 11:18:21 +01:00 |
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