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487 Commits 8 Branches 2 Tags
b9bee5f4264af725c980bf9571f752112721362d
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209 Commits

Author SHA1 Message Date
Eric Coissac
d3dac1b21f Make obitag able to use the taxonomic path included in reference database as taxonomy 2025-01-30 11:50:03 +01:00
Eric Coissac
0df082da06 Adds possibility to extract a taxonomy from taxonomic path included in sequence files 2025-01-30 11:18:21 +01:00
Eric Coissac
2452aef7a9 patch multiple -Z options 2025-01-29 21:35:28 +01:00
Eric Coissac
337954592d add the --out option to the obitaxonomy 2025-01-29 13:22:35 +01:00
Eric Coissac
8a28c9ae7c add the --download-ncbi option to obitaxonomy 2025-01-29 12:38:39 +01:00
Eric Coissac
00f2dc2697 Rename obifind obitaxonomy and introduce the new CSV format for taxonomy. 2025-01-29 10:45:26 +01:00
Eric Coissac
c50a0f409d break the import cyccle 2025-01-27 17:23:07 +01:00
Eric Coissac
7c4042df6b introduce obidefault 2025-01-27 17:12:45 +01:00
Eric Coissac
9acb4a85a8 Refactoring of the default values 2025-01-24 18:09:59 +01:00
Eric Coissac
3137c1f841 Adds the ability to read gzip-tar file for the taxonomy dump 2025-01-24 11:47:59 +01:00
Eric Coissac
ffd67252c3 patch a bug in obimultiplex: change option -t into -s 2025-01-23 13:50:24 +01:00
Eric Coissac
757448cb1e debug obigrep taxonomy options 2025-01-15 20:48:34 +01:00
Eric Coissac
4ae3336135 obidemerge: set demerge on sample the default 2025-01-10 17:09:44 +01:00
Eric Coissac
becb995e3d misspellings penality -> pelnalty 2025-01-09 07:22:23 +01:00
Eric Coissac
c58d9772ac Two small corrections on options 2025-01-07 11:51:37 +01:00
Eric Coissac
4fe0db63ff Patch CSV reader to use the new taxonomy system 2024-12-20 21:30:00 +01:00
Eric Coissac
ccd3b06532 Merge branch 'master' into taxonomy 2024-12-20 20:06:57 +01:00
Eric Coissac
5d0f996625 Patch a small bug on json write 2024-12-20 19:42:03 +01:00
Eric Coissac
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
Eric Coissac
00b0edc15a refactoring of the file chunck writing 2024-11-29 18:15:03 +01:00
Eric Coissac
40fb4e9767 reduce the memory impact of obiuniq. 2024-11-27 13:30:16 +01:00
Eric Coissac
d29a56dcbf Changes to be committed: 
modified:   Release-notes.md
	modified:   pkg/obialign/pairedendalign.go
	modified:   pkg/obilua/obiseq.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/biosequence.go
	modified:   pkg/obitools/obipairing/pairing.go
 2024-11-27 09:56:22 +01:00
Eric Coissac
69ef1758a2 obicsv debug 2024-11-24 23:38:49 +01:00
Eric Coissac
3d06978808 a functional new version of obifind 2024-11-24 19:33:24 +01:00
Eric Coissac
7884a74f9c Patch a bug in obitagpcr 2024-11-18 21:10:47 +01:00
Eric Coissac
36327c79c8 Changes to be committed: 
modified:   .gitignore
	new file:   pkg/obitax/default_taxonomy.go
	modified:   pkg/obitax/taxon.go
	modified:   pkg/obitax/taxonnode.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonset.go
	modified:   pkg/obitax/taxonslice.go
	modified:   pkg/obitools/obifind/iterator.go
	modified:   pkg/obitools/obifind/options.go
 2024-11-16 10:01:49 +01:00
Eric Coissac
f5d79d0bc4 update api documentation 2024-11-16 05:59:41 +01:00
Eric Coissac
03f4e88a17 Fisrt functional version 2024-11-14 19:10:23 +01:00
Eric Coissac
4b65bfce84 Changes to be committed: 
modified:   pkg/obioptions/version.go
	modified:   pkg/obitools/obitagpcr/pcrtag.go
 2024-11-04 14:30:17 +01:00
Eric Coissac
fc75974c68 Changes to be committed: 
modified:   pkg/obioptions/version.go
	modified:   pkg/obitools/obitagpcr/options.go
 2024-11-04 13:25:52 +01:00
Eric Coissac
422f11cceb Changes to be committed: 
modified:   pkg/obitools/obitagpcr/pcrtag.go
 2024-10-29 16:53:10 +01:00
Eric Coissac
fefc360f80 Changes to be committed: 
modified:   pkg/obioptions/version.go
	modified:   pkg/obitools/obitagpcr/pcrtag.go
	modified:   pkg/obiutils/abs.go
	new file:   pkg/obiutils/abs_test.go
 2024-10-28 21:51:21 +01:00
Eric Coissac
241f2286f2 remove the slice pool management 2024-09-24 16:31:30 +02:00
Eric Coissac
2b4a633c30 EndGapFree alignments 2024-09-24 15:52:12 +02:00
Eric Coissac
05bf2bfd6c Add option related to agrep match on obigrep and obiannotate 2024-09-09 16:52:13 +02:00
Eric Coissac
65ae82622e correction of several small bugs 2024-09-03 06:08:07 -03:00
Eric Coissac
373464cb06 On development genome skim tools 2024-08-30 11:17:33 +02:00
Eric Coissac
cd330db672 Add option to obimicrosat to control microsat length and orientation 2024-08-30 11:16:43 +02:00
Eric Coissac
31bfc88eb9 Patch a bug on writing to stdout, and add clearer error on openning data files 2024-08-13 09:45:28 +02:00
Eric Coissac
bdb96dda94 Adds the obimicrosat command 2024-08-05 15:31:20 +02:00
Eric Coissac
1b1cd41fd3 Add some code refactoring from the blackboard branch 2024-08-02 12:35:46 +02:00
Eric Coissac
67665a6b40 Xprize update 
Former-commit-id: d38919a897961e4d40da3b844057c3fb94fdb6d7
 2024-07-25 18:09:03 -04:00
Eric Coissac
4e4fac491f Fisrt versin of the two levels indexing 
Former-commit-id: 4d86483bc120e27cb6f5d2c216596d410274fc69
 2024-07-12 15:17:48 +02:00
Eric Coissac
42c5881ddc some cleanning on the new tools 
Former-commit-id: f265a3910d2872c56af81c9b873669f2cb627781
 2024-07-11 10:46:11 +02:00
Eric Coissac
c7ed47e110 first version of obidemerge, obijoin and a new filter for obicleandb but to be finnished 
Former-commit-id: 8a1ed26e5548c30db75644c294d478ec4d753f19
 2024-07-10 15:21:42 +02:00
Eric Coissac
bd855c4965 Adds CSV as an input format 
Former-commit-id: a365bb6947064adc2709d66df05fa54c6fe47fad
 2024-07-03 21:04:27 +02:00
Eric Coissac
5d9ac261ff correct an attribute name 
Former-commit-id: 2bc540dc3863aef4f8745666047c2a7d94405343
 2024-07-01 17:44:18 +02:00
Eric Coissac
fd663357b5 First version of obicleandb... 
Former-commit-id: e60b61d015abbf029a555b51de99b4252c50ab59
 2024-07-01 17:12:42 +02:00
Eric Coissac
e40d0bfbe7 Debug fasta and fastq writer when the first sequence is hudge 
Former-commit-id: d208ff838abb7e19e117067f6243298492d60f14
 2024-06-26 18:39:42 +02:00
Eric Coissac
e6b87ecd02 Reduce memory allocation events 
Former-commit-id: fbdb2afc857b02adc2593e2278d3bd838e99b0b2
 2024-06-22 21:01:53 +02:00