|
|
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 |
|
|
|
c0ecaf90ab
|
Add the --number option to obiannotate
|
2025-04-22 18:35:51 +02:00 |
|
|
|
7542e33010
|
Several bugs dicoverd during the doc writing
|
2025-04-04 16:59:27 +02:00 |
|
|
|
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 |
|
|
|
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 |
|
|
|
65bd29b955
|
normalize the usage of obitaxonomy
|
2025-03-08 13:00:55 +01:00 |
|
|
|
6a8061cc4f
|
Add managment of the taxonomy alias politic
|
2025-02-10 14:05:47 +01:00 |
|
|
|
d3dac1b21f
|
Make obitag able to use the taxonomic path included in reference database as taxonomy
|
2025-01-30 11:50:03 +01:00 |
|
|
|
0df082da06
|
Adds possibility to extract a taxonomy from taxonomic path included in sequence files
|
2025-01-30 11:18:21 +01:00 |
|
|
|
8a28c9ae7c
|
add the --download-ncbi option to obitaxonomy
|
2025-01-29 12:38:39 +01:00 |
|
|
|
00f2dc2697
|
Rename obifind obitaxonomy and introduce the new CSV format for taxonomy.
|
2025-01-29 10:45:26 +01:00 |
|
|
|
7c4042df6b
|
introduce obidefault
|
2025-01-27 17:12:45 +01:00 |
|
|
|
9acb4a85a8
|
Refactoring of the default values
|
2025-01-24 18:09:59 +01:00 |
|
|
|
3137c1f841
|
Adds the ability to read gzip-tar file for the taxonomy dump
|
2025-01-24 11:47:59 +01:00 |
|
|
|
ffd67252c3
|
patch a bug in obimultiplex: change option -t into -s
|
2025-01-23 13:50:24 +01:00 |
|
|
|
d066bb6878
|
Changes to be committed:
modified: .gitignore
modified: cmd/test/main.go
modified: pkg/obioptions/version.go
|
2025-01-09 07:24:41 +01:00 |
|
|
|
67c0d00a4d
|
remove the obitag2 command
|
2025-01-07 11:50:28 +01:00 |
|
|
|
ccd3b06532
|
Merge branch 'master' into taxonomy
|
2024-12-20 20:06:57 +01:00 |
|
|
|
795df34d1a
|
Changes to be committed:
modified: cmd/obitools/obitag/main.go
modified: cmd/obitools/obitag2/main.go
modified: go.mod
modified: go.sum
modified: pkg/obiformats/ncbitaxdump/read.go
modified: pkg/obioptions/version.go
modified: pkg/obiseq/attributes.go
modified: pkg/obiseq/taxonomy_lca.go
modified: pkg/obiseq/taxonomy_methods.go
modified: pkg/obiseq/taxonomy_predicate.go
modified: pkg/obitax/inner.go
modified: pkg/obitax/lca.go
new file: pkg/obitax/taxid.go
modified: pkg/obitax/taxon.go
modified: pkg/obitax/taxonomy.go
modified: pkg/obitax/taxonslice.go
modified: pkg/obitools/obicleandb/obicleandb.go
modified: pkg/obitools/obigrep/options.go
modified: pkg/obitools/obilandmark/obilandmark.go
modified: pkg/obitools/obilandmark/options.go
modified: pkg/obitools/obirefidx/famlilyindexing.go
modified: pkg/obitools/obirefidx/geomindexing.go
modified: pkg/obitools/obirefidx/obirefidx.go
modified: pkg/obitools/obirefidx/options.go
modified: pkg/obitools/obitag/obigeomtag.go
modified: pkg/obitools/obitag/obitag.go
modified: pkg/obitools/obitag/options.go
modified: pkg/obiutils/strings.go
|
2024-12-19 13:36:59 +01:00 |
|
|
|
ad2461a656
|
some minor improvements
|
2024-11-27 13:36:06 +01:00 |
|
|
|
40fb4e9767
|
reduce the memory impact of obiuniq.
|
2024-11-27 13:30:16 +01:00 |
|
|
|
3d06978808
|
a functional new version of obifind
|
2024-11-24 19:33:24 +01:00 |
|
|
|
f3d8707c08
|
Add default taxonomy
|
2024-11-16 10:01:07 +01:00 |
|
|
|
03f4e88a17
|
Fisrt functional version
|
2024-11-14 19:10:23 +01:00 |
|
|
|
7255c71576
|
commit version
|
2024-09-24 16:36:59 +02:00 |
|
|
|
373464cb06
|
On development genome skim tools
|
2024-08-30 11:17:33 +02:00 |
|
|
|
31bfc88eb9
|
Patch a bug on writing to stdout, and add clearer error on openning data files
|
2024-08-13 09:45:28 +02:00 |
|
|
|
bdb96dda94
|
Adds the obimicrosat command
|
2024-08-05 15:31:20 +02:00 |
|
|
|
1b1cd41fd3
|
Add some code refactoring from the blackboard branch
|
2024-08-02 12:35:46 +02:00 |
|
|
|
2247c3bc0a
|
obitag xprize version
Former-commit-id: 2c47d88724102b115aac5641abccb880dfbec64d
|
2024-07-25 18:11:11 -04:00 |
|
|
|
4e4fac491f
|
Fisrt versin of the two levels indexing
Former-commit-id: 4d86483bc120e27cb6f5d2c216596d410274fc69
|
2024-07-12 15:17:48 +02:00 |
|
|
|
42c5881ddc
|
some cleanning on the new tools
Former-commit-id: f265a3910d2872c56af81c9b873669f2cb627781
|
2024-07-11 10:46:11 +02:00 |
|
|
|
154753de90
|
Same bug but for fastq sequence writing only
Former-commit-id: 86d208fe66828da9943c559df80ff095b07eaf7a
|
2024-06-26 18:46:47 +02:00 |
|
|
|
e6b87ecd02
|
Reduce memory allocation events
Former-commit-id: fbdb2afc857b02adc2593e2278d3bd838e99b0b2
|
2024-06-22 21:01:53 +02:00 |
|
|
|
3a7661f324
|
obimultiplex2 in now obimultiplex
Former-commit-id: ee6f5e15a3f1729dfc2806d039c842c9c3bdd343
|
2024-06-07 09:04:37 +02:00 |
|
|
|
a0a9fb461c
|
trial on rewriting obimultiplex
Former-commit-id: d00f3353d83760dc878c6411ad344d96216096a7
|
2024-06-04 16:50:07 +02:00 |
|
|
|
38945d0a41
|
Adds the --template option to obimultiplex
Former-commit-id: 349e9f278abd6a6c258f31d99ea04853a79c62de
|
2024-05-31 11:34:06 +02:00 |
|
|
|
55ce36f329
|
Update of obipcr and homogenization of logging
Former-commit-id: 46abf47c19ace5248042c02cf1f81d9f6c12eb10
|
2024-05-16 15:18:30 +02:00 |
|
|
|
61be8a55b1
|
Merge obiminion and obiconsensus
Former-commit-id: 49d65d671e9fe4454de60c20507c3d8df6e9c51c
|
2024-05-14 17:53:32 +02:00 |
|
|
|
017030bcce
|
Add obiminion first version
Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d
|
2024-05-14 08:16:12 +02:00 |
|
|
|
b40015deb7
|
first preliminary version of obiscript.
Former-commit-id: 0d2c0fc5e33e0873ba5c04aca4cf7dd69aa83c90
|
2024-03-06 12:56:44 -03:00 |
|
|
|
7bd073ccd4
|
First version of obisplit and patch a bug in the new workers API
Former-commit-id: f28af9f104c08d68e29fd866739d8dd58241da63
|
2024-03-03 11:16:24 -04:00 |
|
|
|
0f3871d203
|
Change the API of workers
Former-commit-id: 9b07306edd8cf28266f86f95823948fa99d39ea9
|
2024-03-02 16:03:46 -04:00 |
|
|
|
37c3e16d5d
|
Adds the option --pairing-scale to obipairing
Former-commit-id: c60416708467f5e818e70e08b3c512014b6212f0
|
2023-12-07 12:28:16 +01:00 |
|
|
|
5682247ff8
|
Update main.go
Former-commit-id: f2aec0d30c0d2b31a9d00c7d4adf47421123b0fb
|
2023-12-01 16:42:12 +01:00 |
|
|
|
8d77cc4133
|
Change path of the obitools pkg
Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
|
2023-11-29 12:14:37 +01:00 |
|
|
|
b556e045e5
|
Adds option to tune the pairing of the sequences in obipairing and some stats to the results
Former-commit-id: a6cf9cb4d4ab20a433a2534fd7d11cd3ca8ebbaa
|
2023-11-24 12:29:37 +01:00 |
|
|
|
2e0c1bd801
|
Correct the number of workers
Former-commit-id: febbccfb853263e0761ecfccb0f09c8c1bf88475
|
2023-11-22 09:46:30 +01:00 |
|
