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765 Commits 13 Branches 35 Tags
3e349e92e11b8543f6ba5f56e8eac65cc18d854b
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213 Commits

Author SHA1 Message Date
Eric Coissac 0844dcc607 bug obimatrix 2025-10-28 13:57:31 +01:00
Eric Coissac 7f4ebe757e Bug obiuniq - don't clean the chunks 2025-10-28 13:50:22 +01:00
Eric Coissac d17a9520b9 work on obiclean chimera detection 2025-10-20 17:29:47 +02:00
Eric Coissac 29bf4ce871 add a feature to obimatrix adding obicsv option to obimatrix 2025-10-20 16:34:58 +02:00
Eric Coissac 82b6bb1ab6 correct a bug in func (worker SeqWorker) ChainWorkers(next SeqWorker) SeqWorker 2025-08-11 15:09:49 +02:00
Eric Coissac 6d204f6281 Patch the fastq detector 2025-08-08 10:23:03 -04:00
Eric Coissac 7a6d552450 Changes to be committed: 
modified:   pkg/obioptions/version.go
 2025-08-07 17:01:48 -04:00
Eric Coissac 730d448fc3 Allows for only one cpu and it should work 2025-08-06 16:09:25 -04:00
Eric Coissac 04f3af3e60 some renaming of functions 2025-08-06 15:54:50 -04:00
Eric Coissac ed28d3fb5b Adds a --u-to-t option 2025-07-07 15:35:26 +02:00
Eric Coissac 43b285587e Debug on taxonomy extraction and CSV conversion 2025-07-07 15:29:40 +02:00
Eric Coissac 235a7e202a Update obisummary to account new obiseq.StatsOnValues type 2025-06-19 17:21:30 +02:00
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 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 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 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