obitools/obitools4
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613 Commits 8 Branches 2 Tags
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469 Commits

Author SHA1 Message Date
Eric Coissac
e681666aaa End of obilowmask 2025-11-26 11:14:56 +01:00
Eric Coissac
86e60aedd0 obicsv bug with stat on value map fields 2025-11-21 14:03:31 +01:00
Eric Coissac
e65b2a5efe obimatrix bugs 2025-11-21 13:24:06 +01:00
Eric Coissac
ccc827afd3 finalise obilowmask 2025-11-18 15:33:08 +01:00
Eric Coissac
cef29005a5 debug url reading 2025-11-18 15:30:20 +01:00
Eric Coissac
4603d7973e implementation de obilowmask 2025-11-18 15:30:20 +01:00
Eric Coissac
07cdd6f758 debug obimultiplex 
bug option obimultiplex
 2025-11-06 15:43:13 +01:00
Eric Coissac
2d7dc7d09d debug taxonomy core dump 2025-11-05 19:01:15 +01:00
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
412b54822c Patch a bug in obliclean for d>1 leading to some instability in the result 2025-08-07 17:01:38 -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
997b6e8c01 correct the fastq detector for distinguish with a csv ngsfilter 2025-08-06 15:52:54 -04:00
Eric Coissac
f239e8da92 Rename ISequenceChunk 2025-08-05 08:49:45 -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
8d53d253d4 Add a reading option on readers to convet U to T 2025-07-07 15:29:07 +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