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Author SHA1 Message Date
Eric Coissac 27fa984a63 Patch obimatrix accoring to the new type obiseq.StatsOnValues 2025-06-19 16:51:53 +02:00
Eric Coissac add9d89ccc Patch the Min and Max values of the expression language 2025-06-19 16:43:26 +02:00
Eric Coissac 9965370d85 Manage a lock on StatsOnValues 2025-06-17 16:46:11 +02:00
Eric Coissac 8a2bb1fe82 Changes to be committed: 
modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/merge.go
 2025-06-17 12:11:35 +02:00
Eric Coissac efc3f3af29 Patch a concurrent access problem 2025-06-17 12:05:42 +02:00
Eric Coissac 1c6ab1c559 Changes to be committed: 
modified:   pkg/obingslibrary/multimatch.go
	modified:   pkg/obioptions/version.go
 2025-06-17 09:06:42 +02:00
Eric Coissac 38dcd98d4a Patch the genbank parser automata 2025-06-17 08:52:45 +02:00
Eric Coissac 7b23985693 Add _ to allowed in taxid 2025-06-06 14:37:57 +02:00
Eric Coissac d31e677304 Patch a bug in obitag 2025-06-04 14:47:28 +02:00
Eric Coissac 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
 2025-06-04 09:48:10 +02:00
Eric Coissac 3424d3057f Changes to be committed: 
modified:   pkg/obiformats/ngsfilter_read.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiutils/mimetypes.go
 2025-05-14 14:53:25 +02:00
Eric Coissac f9324dd8f4 add min and max to the obitools expression language 2025-05-13 16:03:03 +02:00
Eric Coissac f1b9ac4a13 Update the expression language 2025-05-07 20:45:05 +02:00
Eric Coissac e065e2963b Update the install script 2025-05-01 11:45:46 +02:00
Eric Coissac 13ff892ac9 Patch type mismatch in apat C library 2025-04-23 16:14:10 +02:00
Eric Coissac c0ecaf90ab Add the --number option to obiannotate 2025-04-22 18:35:51 +02:00
Eric Coissac a57cfda675 Make the replace function of the eval language accepting regex 2025-04-10 15:17:15 +02:00
Eric Coissac c2f38e737b Update of the packages 2025-04-10 15:16:36 +02:00
Eric Coissac 0aec5ba4df change the tests according to the corrections in obipairing 2025-04-04 17:10:17 +02:00
Eric Coissac 67e5b6ef24 Changes to be committed: 
modified:   pkg/obioptions/version.go
 2025-04-04 17:02:45 +02:00
Eric Coissac 3b1aa2869e Changes to be committed: 
modified:   pkg/obioptions/version.go
 2025-04-04 17:01:20 +02:00
Eric Coissac 7542e33010 Several bugs dicoverd during the doc writing 2025-04-04 16:59:27 +02:00
Eric Coissac 03b5ce9397 Patch a bug in obitag when some reference sequences have taxid absent from the taxonomy 2025-03-27 16:45:02 +01:00
Eric Coissac 2d52322876 Patch a bug in the obi2 annotation parser on map indexed by integers 2025-03-27 14:54:13 +01:00
Eric Coissac fd80249b85 Patch a bug in obitag when a taxon from the reference library is unknown in the taxonomy 2025-03-27 14:28:15 +01:00
Eric Coissac 5a3705b6bb Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands. 2025-03-25 16:44:46 +01:00
Eric Coissac 2ab6f67d58 Add a progress bar to chimera detection 2025-03-25 08:37:27 +01:00
Eric Coissac 8b379d30da Adds the --newick-output option to the obitaxonomy command 2025-03-14 14:24:12 +01:00
Eric Coissac 8448783499 Make sequence files recognized as a taxonomy 2025-03-14 14:22:22 +01:00
Eric Coissac d1c31c54de add a first version of the inline documentation 2025-03-12 14:40:42 +01:00
Eric Coissac 7a9dc1ab3b update release notes 2025-03-12 14:06:20 +01:00
Eric Coissac 3a1cf4fe97 Accelerate the speed of very long fasta sequences, and more generaly of every format 2025-03-12 13:29:41 +01:00
Eric Coissac 83926c91e1 Patch the install script to desactivate the CSV check 2025-03-12 13:28:52 +01:00
Eric Coissac 937a483aa6 Changes to be committed: 
modified:   Makefile
 2025-03-12 12:55:41 +01:00
Eric Coissac dada70e6b1 Changes to be committed: 
modified:   Makefile
 2025-03-12 12:49:34 +01:00
Eric Coissac 62e5a93492 update the compress option name 2025-03-11 17:14:40 +01:00
Eric Coissac f21f51ae62 Correct the logic of --update-taxid and --fail-on-taxonomy 2025-03-11 16:56:02 +01:00
Eric Coissac 3b5d4ba455 patch a bug in obiannotate 2025-03-11 16:35:38 +01:00
Eric Coissac 50d11ce374 Add a pre-push git-hook to run tests on obitools commands before pushing on master 2025-03-08 18:56:02 +01:00
Eric Coissac 52d5f6fe11 make makefile crashing on test error 2025-03-08 16:54:24 +01:00
Eric Coissac 78caabd2fd Add basic test on -h for all the commands 2025-03-08 16:28:06 +01:00
Eric Coissac 65bd29b955 normalize the usage of obitaxonomy 2025-03-08 13:00:55 +01:00
Eric Coissac b18c9b7ac6 add the --raw-taxid option 2025-03-08 09:40:06 +01:00
Eric Coissac 78df7db18d typos 2025-03-08 07:44:41 +01:00
Eric Coissac fc08c12ab0 update release notes 2025-03-08 07:42:20 +01:00
Eric Coissac 0339e4dffa Patch size limite of the filetype guesser 2025-03-08 07:34:02 +01:00
Eric Coissac 706b44c37f Add option for csv input format 2025-03-08 07:21:24 +01:00
Eric Coissac fbe7d15dc3 Changes to be committed: 
modified:   pkg/obioptions/version.go
	modified:   pkg/obitools/obicleandb/obicleandb.go
	modified:   pkg/obitools/obicleandb/options.go
 2025-03-06 13:38:38 +01:00
Eric Coissac b5cf586f17 patch a duplicate --taxonomy option in obirefidxdb 2025-03-06 11:36:20 +01:00
Eric Coissac 286e27d6ba patch the scienctific_name tag name to "scientific_name" 2025-03-05 14:22:12 +01:00
Eric Coissac 996ec69bd9 update the release notes for version 4.4.0 2025-03-01 12:56:39 +01:00
Eric Coissac 5f9182d25b Changes to be committed: 
modified:   pkg/obioptions/version.go
 2025-03-01 09:20:39 +01:00
Eric Coissac 9913fa8354 Changes to be committed: 
modified:   pkg/obioptions/version.go
 2025-03-01 09:14:56 +01:00
Eric Coissac 7b23314651 Some typos 2025-03-01 08:29:27 +01:00
Eric Coissac 1e541eac4c Last commit version 2025-03-01 08:24:26 +01:00
Eric Coissac 13cd4c86ac Patch the bug on --out with paired sequence files 2025-02-27 18:13:21 +01:00
Eric Coissac 75dd535201 Add a --valid-taxid option to obigrep 2025-02-27 18:12:55 +01:00
Eric Coissac 573acafafc Patch bug on ecotag with too short sequences 2025-02-27 15:09:07 +01:00
Eric Coissac 0067152c2b Patch the production of the ratio file 2025-02-27 10:19:39 +01:00
Eric Coissac 791d253edc Generate the ratio file as compressed if -Z option enabled. 2025-02-27 09:06:07 +01:00
Eric Coissac 6245d7f684 Changes to be committed: 
modified:   .gitignore
 2025-02-24 15:47:45 +01:00
Eric Coissac 13d610aff7 Changes to be committed: 
modified:   pkg/obioptions/version.go
	modified:   pkg/obitools/obiclean/chimera.go
 2025-02-24 15:25:45 +01:00
Eric Coissac db284f1d44 Add an experimental chimera detection... 2025-02-24 15:02:49 +01:00
Eric Coissac 51b3e83d32 some cleaning 2025-02-24 11:31:49 +01:00
Eric Coissac 8671285d02 add the --min-sample-count option to obiclean. 2025-02-24 08:48:31 +01:00
Eric Coissac 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
 2025-02-23 17:37:56 +01:00
Eric Coissac fb6f857d8c Update the computation of the consensus quality score 2025-02-23 15:16:31 +01:00
Eric Coissac d4209b4549 Add a basic test for obiparing 2025-02-22 09:57:44 +01:00
Eric Coissac ef05d4975f Upadte the scoring schema of obipairing 2025-02-21 22:41:34 +01:00
Eric Coissac 4588bf8b5d Patch the make file to fail on error 2025-02-19 15:55:07 +01:00
Eric Coissac 090633850d Changes to be committed: 
modified:   obitests/obitools/obicount/test.sh
 2025-02-19 15:28:42 +01:00
Eric Coissac 15a058cf63 with all the sample files for tests 2025-02-19 15:27:38 +01:00
Eric Coissac 2f5f7634d6 Changes to be committed: 
modified:   obitests/obitools/obicount/test.sh
 2025-02-19 14:50:10 +01:00
Eric Coissac 48138b605c Changes to be committed: 
modified:   .github/workflows/obitest.yml
	modified:   Makefile
	modified:   obitests/obitools/obicount/test.sh
 2025-02-19 14:37:05 +01:00
Eric Coissac aed22c12a6 Changes to be committed: 
modified:   obitests/obitools/obicount/test.sh
 2025-02-19 14:34:22 +01:00
Eric Coissac 443a9b3ce3 Changes to be committed: 
modified:   Makefile
	modified:   obitests/obitools/obicount/test.sh
 2025-02-19 14:28:49 +01:00
Eric Coissac 7e90537379 For run of test using bash in makefile 2025-02-19 13:58:52 +01:00
Eric Coissac d3d15acc6c Changes to be committed: 
modified:   obitests/obitools/obicount/test.sh
	modified:   pkg/obioptions/version.go
 2025-02-19 13:54:01 +01:00
Eric Coissac bd4a0b5ca5 Essais d'une google action pour lancer les tests des obitools 2025-02-19 13:45:43 +01:00
Eric Coissac 952f85f312 A first trial of a test for obicount 2025-02-19 13:17:36 +01:00
Eric Coissac 4774438644 Changes to be committed: 
modified:   pkg/obiformats/universal_read.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/taxonomy_methods.go
 2025-02-12 08:40:38 +01:00
Eric Coissac 6a8061cc4f Add managment of the taxonomy alias politic 2025-02-10 14:05:47 +01:00
Eric Coissac e2563cd8df Patch a bug in registering merged taxa 2025-02-10 11:42:46 +01:00
Eric Coissac f2e81adf95 Changes to be committed: 
modified:   .gitignore
	deleted:    xxx.csv
 2025-02-05 19:28:19 +01:00
Eric Coissac f27e9bc91e patch a bug related to csv and qualities 2025-02-05 19:27:00 +01:00
Eric Coissac 773e54965d Patch a bug on compressed output 2025-02-05 14:18:24 +01:00
Eric Coissac ceca33998b add extensions fq in directory scanning 2025-02-04 20:34:58 +01:00
Eric Coissac 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
 2025-02-02 16:52:52 +01:00
Eric Coissac c10df073a7 Changes to be committed: 
modified:   pkg/obioptions/version.go
	modified:   pkg/obitax/iterator.go
 2025-02-01 12:06:19 +01:00
Eric Coissac d3dac1b21f Make obitag able to use the taxonomic path included in reference database as taxonomy 2025-01-30 11:50:03 +01:00
Eric Coissac 0df082da06 Adds possibility to extract a taxonomy from taxonomic path included in sequence files 2025-01-30 11:18:21 +01:00
Eric Coissac 2452aef7a9 patch multiple -Z options 2025-01-29 21:35:28 +01:00
Eric Coissac 337954592d add the --out option to the obitaxonomy 2025-01-29 13:22:35 +01:00
Eric Coissac 8a28c9ae7c add the --download-ncbi option to obitaxonomy 2025-01-29 12:38:39 +01:00
Eric Coissac b6b18c0fa1 Changes to be committed: 
modified:   pkg/obioptions/version.go
 2025-01-29 11:34:01 +01:00
Eric Coissac 67e2758d63 Switch to realease number 4.3.0 2025-01-29 11:33:30 +01:00
Eric Coissac 00f2dc2697 Rename obifind obitaxonomy and introduce the new CSV format for taxonomy. 2025-01-29 10:45:26 +01:00
Eric Coissac c50a0f409d break the import cyccle 2025-01-27 17:23:07 +01:00
Eric Coissac 7c4042df6b introduce obidefault 2025-01-27 17:12:45 +01:00
Eric Coissac 0a567f621c small changes 2025-01-24 18:12:37 +01:00