|
|
0067152c2b
|
Patch the production of the ratio file
|
2025-02-27 10:19:39 +01:00 |
|
|
|
791d253edc
|
Generate the ratio file as compressed if -Z option enabled.
|
2025-02-27 09:06:07 +01:00 |
|
|
|
13d610aff7
|
Changes to be committed:
modified: pkg/obioptions/version.go
modified: pkg/obitools/obiclean/chimera.go
|
2025-02-24 15:25:45 +01:00 |
|
|
|
db284f1d44
|
Add an experimental chimera detection...
|
2025-02-24 15:02:49 +01:00 |
|
|
|
51b3e83d32
|
some cleaning
|
2025-02-24 11:31:49 +01:00 |
|
|
|
8671285d02
|
add the --min-sample-count option to obiclean.
|
2025-02-24 08:48:31 +01:00 |
|
|
|
51d11aa36d
|
Changes to be committed:
modified: pkg/obialign/alignment.go
modified: pkg/obialign/pairedendalign.go
modified: pkg/obioptions/version.go
modified: pkg/obitools/obipairing/pairing.go
|
2025-02-23 17:37:56 +01:00 |
|
|
|
fb6f857d8c
|
Update the computation of the consensus quality score
|
2025-02-23 15:16:31 +01:00 |
|
|
|
ef05d4975f
|
Upadte the scoring schema of obipairing
|
2025-02-21 22:41:34 +01:00 |
|
|
|
7e90537379
|
For run of test using bash in makefile
|
2025-02-19 13:58:52 +01:00 |
|
|
|
d3d15acc6c
|
Changes to be committed:
modified: obitests/obitools/obicount/test.sh
modified: pkg/obioptions/version.go
|
2025-02-19 13:54:01 +01:00 |
|
|
|
bd4a0b5ca5
|
Essais d'une google action pour lancer les tests des obitools
|
2025-02-19 13:45:43 +01:00 |
|
|
|
952f85f312
|
A first trial of a test for obicount
|
2025-02-19 13:17:36 +01:00 |
|
|
|
4774438644
|
Changes to be committed:
modified: pkg/obiformats/universal_read.go
modified: pkg/obioptions/version.go
modified: pkg/obiseq/taxonomy_methods.go
|
2025-02-12 08:40:38 +01:00 |
|
|
|
6a8061cc4f
|
Add managment of the taxonomy alias politic
|
2025-02-10 14:05:47 +01:00 |
|
|
|
e2563cd8df
|
Patch a bug in registering merged taxa
|
2025-02-10 11:42:46 +01:00 |
|
|
|
f27e9bc91e
|
patch a bug related to csv and qualities
|
2025-02-05 19:27:00 +01:00 |
|
|
|
773e54965d
|
Patch a bug on compressed output
|
2025-02-05 14:18:24 +01:00 |
|
|
|
ceca33998b
|
add extensions fq in directory scanning
|
2025-02-04 20:34:58 +01:00 |
|
|
|
b9bee5f426
|
Changes to be committed:
modified: go.mod
modified: go.sum
modified: pkg/obilua/obilib.go
modified: pkg/obilua/obiseq.go
modified: pkg/obilua/obiseqslice.go
new file: pkg/obilua/obitaxon.go
new file: pkg/obilua/obitaxonomy.go
modified: pkg/obioptions/version.go
|
2025-02-02 16:52:52 +01:00 |
|
|
|
c10df073a7
|
Changes to be committed:
modified: pkg/obioptions/version.go
modified: pkg/obitax/iterator.go
|
2025-02-01 12:06:19 +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 |
|
|
|
2452aef7a9
|
patch multiple -Z options
|
2025-01-29 21:35:28 +01:00 |
|
|
|
337954592d
|
add the --out option to the obitaxonomy
|
2025-01-29 13:22:35 +01:00 |
|
|
|
8a28c9ae7c
|
add the --download-ncbi option to obitaxonomy
|
2025-01-29 12:38:39 +01:00 |
|
|
|
b6b18c0fa1
|
Changes to be committed:
modified: pkg/obioptions/version.go
|
2025-01-29 11:34:01 +01:00 |
|
|
|
67e2758d63
|
Switch to realease number 4.3.0
|
2025-01-29 11:33:30 +01:00 |
|
|
|
00f2dc2697
|
Rename obifind obitaxonomy and introduce the new CSV format for taxonomy.
|
2025-01-29 10:45:26 +01:00 |
|
|
|
c50a0f409d
|
break the import cyccle
|
2025-01-27 17:23:07 +01:00 |
|
|
|
7c4042df6b
|
introduce obidefault
|
2025-01-27 17:12:45 +01:00 |
|
|
|
0a567f621c
|
small changes
|
2025-01-24 18:12:37 +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 |
|
|
|
757448cb1e
|
debug obigrep taxonomy options
|
2025-01-15 20:48:34 +01:00 |
|
|
|
4ae3336135
|
obidemerge: set demerge on sample the default
|
2025-01-10 17:09:44 +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 |
|
|
|
c58d9772ac
|
Two small corrections on options
|
2025-01-07 11:51:37 +01:00 |
|
|
|
4fe0db63ff
|
Patch CSV reader to use the new taxonomy system
|
2024-12-20 21:30:00 +01:00 |
|
|
|
ccd3b06532
|
Merge branch 'master' into taxonomy
|
2024-12-20 20:06:57 +01:00 |
|
|
|
5d0f996625
|
Patch a small bug on json write
|
2024-12-20 19:42:03 +01:00 |
|
|
|
abfa8f357a
|
patch a bug in Taxid parsing
|
2024-12-19 13:54:23 +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 |
|
|
|
f2525d7b07
|
Changes to be committed:
modified: pkg/obilua/lua.go
modified: pkg/obioptions/version.go
|
2024-12-04 11:42:05 +01:00 |
|
|
|
39dd3e3ce8
|
Add management of []interface{} to the LUA API.
|
2024-12-04 10:58:17 +01:00 |
|
|
|
f41a6fbb60
|
Patch a small bug on json write
|
2024-11-29 18:39:18 +01:00 |
|
|
|
00b0edc15a
|
refactoring of the file chunck writing
|
2024-11-29 18:15:03 +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 |
|
