|
|
7b23985693
|
Add _ to allowed in taxid
|
2025-06-06 14:37:57 +02:00 |
|
|
|
d31e677304
|
Patch a bug in obitag
|
2025-06-04 14:47:28 +02:00 |
|
|
|
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 |
|
|
|
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 |
|
|
|
f9324dd8f4
|
add min and max to the obitools expression language
|
2025-05-13 16:03:03 +02:00 |
|
|
|
f1b9ac4a13
|
Update the expression language
|
2025-05-07 20:45:05 +02:00 |
|
|
|
e065e2963b
|
Update the install script
|
2025-05-01 11:45:46 +02:00 |
|
|
|
13ff892ac9
|
Patch type mismatch in apat C library
|
2025-04-23 16:14:10 +02:00 |
|
|
|
c0ecaf90ab
|
Add the --number option to obiannotate
|
2025-04-22 18:35:51 +02:00 |
|
|
|
a57cfda675
|
Make the replace function of the eval language accepting regex
|
2025-04-10 15:17:15 +02:00 |
|
|
|
c2f38e737b
|
Update of the packages
|
2025-04-10 15:16:36 +02:00 |
|
|
|
0aec5ba4df
|
change the tests according to the corrections in obipairing
|
2025-04-04 17:10:17 +02:00 |
|
|
|
67e5b6ef24
|
Changes to be committed:
modified: pkg/obioptions/version.go
|
2025-04-04 17:02:45 +02:00 |
|
|
|
3b1aa2869e
|
Changes to be committed:
modified: pkg/obioptions/version.go
|
2025-04-04 17:01:20 +02:00 |
|
|
|
7542e33010
|
Several bugs dicoverd during the doc writing
|
2025-04-04 16:59:27 +02:00 |
|
|
|
03b5ce9397
|
Patch a bug in obitag when some reference sequences have taxid absent from the taxonomy
|
2025-03-27 16:45:02 +01:00 |
|
|
|
2d52322876
|
Patch a bug in the obi2 annotation parser on map indexed by integers
|
2025-03-27 14:54:13 +01:00 |
|
|
|
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 |
|
|
|
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 |
|
|
|
2ab6f67d58
|
Add a progress bar to chimera detection
|
2025-03-25 08:37:27 +01:00 |
|
|
|
8b379d30da
|
Adds the --newick-output option to the obitaxonomy command
|
2025-03-14 14:24:12 +01:00 |
|
|
|
8448783499
|
Make sequence files recognized as a taxonomy
|
2025-03-14 14:22:22 +01:00 |
|
|
|
d1c31c54de
|
add a first version of the inline documentation
|
2025-03-12 14:40:42 +01:00 |
|
|
|
7a9dc1ab3b
|
update release notes
|
2025-03-12 14:06:20 +01:00 |
|
|
|
3a1cf4fe97
|
Accelerate the speed of very long fasta sequences, and more generaly of every format
|
2025-03-12 13:29:41 +01:00 |
|
|
|
83926c91e1
|
Patch the install script to desactivate the CSV check
|
2025-03-12 13:28:52 +01:00 |
|
|
|
937a483aa6
|
Changes to be committed:
modified: Makefile
|
2025-03-12 12:55:41 +01:00 |
|
|
|
dada70e6b1
|
Changes to be committed:
modified: Makefile
|
2025-03-12 12:49:34 +01:00 |
|
|
|
62e5a93492
|
update the compress option name
|
2025-03-11 17:14:40 +01:00 |
|
|
|
f21f51ae62
|
Correct the logic of --update-taxid and --fail-on-taxonomy
|
2025-03-11 16:56:02 +01:00 |
|
|
|
3b5d4ba455
|
patch a bug in obiannotate
|
2025-03-11 16:35:38 +01:00 |
|
|
|
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 |
|
|
|
52d5f6fe11
|
make makefile crashing on test error
|
2025-03-08 16:54:24 +01:00 |
|
|
|
78caabd2fd
|
Add basic test on -h for all the commands
|
2025-03-08 16:28:06 +01:00 |
|
|
|
65bd29b955
|
normalize the usage of obitaxonomy
|
2025-03-08 13:00:55 +01:00 |
|
|
|
b18c9b7ac6
|
add the --raw-taxid option
|
2025-03-08 09:40:06 +01:00 |
|
|
|
78df7db18d
|
typos
|
2025-03-08 07:44:41 +01:00 |
|
|
|
fc08c12ab0
|
update release notes
|
2025-03-08 07:42:20 +01:00 |
|
|
|
0339e4dffa
|
Patch size limite of the filetype guesser
|
2025-03-08 07:34:02 +01:00 |
|
|
|
706b44c37f
|
Add option for csv input format
|
2025-03-08 07:21:24 +01:00 |
|
|
|
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 |
|
|
|
b5cf586f17
|
patch a duplicate --taxonomy option in obirefidxdb
|
2025-03-06 11:36:20 +01:00 |
|
|
|
286e27d6ba
|
patch the scienctific_name tag name to "scientific_name"
|
2025-03-05 14:22:12 +01:00 |
|
|
|
996ec69bd9
|
update the release notes for version 4.4.0
Release_4.4.0
|
2025-03-01 12:56:39 +01:00 |
|
|
|
5f9182d25b
|
Changes to be committed:
modified: pkg/obioptions/version.go
|
2025-03-01 09:20:39 +01:00 |
|
|
|
9913fa8354
|
Changes to be committed:
modified: pkg/obioptions/version.go
|
2025-03-01 09:14:56 +01:00 |
|
|
|
7b23314651
|
Some typos
|
2025-03-01 08:29:27 +01:00 |
|
|
|
1e541eac4c
|
Last commit version
|
2025-03-01 08:24:26 +01:00 |
|
|
|
13cd4c86ac
|
Patch the bug on --out with paired sequence files
|
2025-02-27 18:13:21 +01:00 |
|
|
|
75dd535201
|
Add a --valid-taxid option to obigrep
|
2025-02-27 18:12:55 +01:00 |
|
