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13 Commits

Author SHA1 Message Date
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
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
9471fedfa1 Fisrt step in the obitax rewriting 2024-11-08 09:48:16 +01:00
Eric Coissac
54a138196c Patch a bug in fasta and fastq reading 
Former-commit-id: bcaa264b4c4a7c67617eb909b199176bf09913db
 2024-06-21 14:28:57 +02:00
Eric Coissac
b428c48353 Obitag, allow for reference sequences with bad taxid, which are discarded with the emission of a warning 
Former-commit-id: a8781da1afa86de9c34b008959f0705ae69fc64f
 2024-03-18 19:11:41 +01:00
Eric Coissac
0f3871d203 Change the API of workers 
Former-commit-id: 9b07306edd8cf28266f86f95823948fa99d39ea9
 2024-03-02 16:03:46 -04:00
Eric Coissac
b9a7961c91 Add more error checks on taxonomy reading 
Former-commit-id: 30c848d8e61214afcc7d92f0d3a3f5a1474fc720
 2023-12-14 08:09:06 +01:00
Eric Coissac
8d77cc4133 Change path of the obitools pkg 
Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
 2023-11-29 12:14:37 +01:00
Eric Coissac
18d3eec24a Change the annotation locker to a pointer to mutex to avoid coying mutex 
Former-commit-id: d179d8753b593183312bd11184e5d8ebb301138a
 2023-08-27 16:00:35 +02:00
Eric Coissac
7b7128196a small refactoring including doc 
Former-commit-id: 6d6b527d89d77aa571831f7500f841840e280536
 2023-08-27 15:52:28 +02:00
Eric Coissac
60c187404d Restore old obisort and add LCA functionnality to obiannotate. 
Former-commit-id: aecaacc9dae49f74bd888a8eb8140822d31a42a6
 2023-05-02 10:43:22 +02:00
Eric Coissac
8aa323dad5 Add a first version of obitag the successor of ecotag 2022-10-26 13:16:56 +02:00