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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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2452aef7a9
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patch multiple -Z options
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2025-01-29 21:35:28 +01:00 |
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337954592d
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add the --out option to the obitaxonomy
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2025-01-29 13:22:35 +01:00 |
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8a28c9ae7c
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add the --download-ncbi option to obitaxonomy
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2025-01-29 12:38:39 +01:00 |
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b6b18c0fa1
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Changes to be committed:
modified: pkg/obioptions/version.go
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2025-01-29 11:34:01 +01:00 |
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67e2758d63
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Switch to realease number 4.3.0
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2025-01-29 11:33:30 +01:00 |
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00f2dc2697
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Rename obifind obitaxonomy and introduce the new CSV format for taxonomy.
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2025-01-29 10:45:26 +01:00 |
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c50a0f409d
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break the import cyccle
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2025-01-27 17:23:07 +01:00 |
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7c4042df6b
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introduce obidefault
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2025-01-27 17:12:45 +01:00 |
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0a567f621c
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small changes
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2025-01-24 18:12:37 +01:00 |
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9acb4a85a8
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Refactoring of the default values
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2025-01-24 18:09:59 +01:00 |
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3137c1f841
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Adds the ability to read gzip-tar file for the taxonomy dump
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2025-01-24 11:47:59 +01:00 |
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ffd67252c3
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patch a bug in obimultiplex: change option -t into -s
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2025-01-23 13:50:24 +01:00 |
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757448cb1e
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debug obigrep taxonomy options
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2025-01-15 20:48:34 +01:00 |
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4ae3336135
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obidemerge: set demerge on sample the default
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2025-01-10 17:09:44 +01:00 |
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