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619 Commits 11 Branches 2 Tags
06781810236df440dc62fcdfb3ae10cc2d8bee6e
Commit Graph

472 Commits

Author SHA1 Message Date
Eric Coissac
0678181023 Refactor chunk processing and update version commit 
Optimize chunk processing by moving variable declarations inside the loop and update the commit hash in version.go to reflect the latest changes.
 2026-01-14 18:46:04 +01:00
Eric Coissac
371e702423 obiannotate --cut bug 2025-12-18 14:11:11 +01:00
Eric Coissac
ac0d3f3fe4 Update obiuniq for very large dataset 2025-12-18 14:11:11 +01:00
Eric Coissac
547135c747 End of obilowmask 2025-12-03 11:49:07 +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