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7b23985693
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Add _ to allowed in taxid
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2025-06-06 14:37:57 +02:00 |
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6cb7a5a352
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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
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2025-06-04 09:48:10 +02:00 |
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03b5ce9397
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Patch a bug in obitag when some reference sequences have taxid absent from the taxonomy
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2025-03-27 16:45:02 +01:00 |
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5a3705b6bb
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Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.
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2025-03-25 16:44:46 +01:00 |
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8448783499
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Make sequence files recognized as a taxonomy
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2025-03-14 14:22:22 +01:00 |
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b18c9b7ac6
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add the --raw-taxid option
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2025-03-08 09:40:06 +01:00 |
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6a8061cc4f
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Add managment of the taxonomy alias politic
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2025-02-10 14:05:47 +01:00 |
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e2563cd8df
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Patch a bug in registering merged taxa
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2025-02-10 11:42:46 +01:00 |
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773e54965d
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Patch a bug on compressed output
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2025-02-05 14:18:24 +01:00 |
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c10df073a7
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Changes to be committed:
modified: pkg/obioptions/version.go
modified: pkg/obitax/iterator.go
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2025-02-01 12:06:19 +01:00 |
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0df082da06
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Adds possibility to extract a taxonomy from taxonomic path included in sequence files
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2025-01-30 11:18:21 +01:00 |
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2452aef7a9
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patch multiple -Z options
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2025-01-29 21:35:28 +01:00 |
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00f2dc2697
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Rename obifind obitaxonomy and introduce the new CSV format for taxonomy.
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2025-01-29 10:45:26 +01:00 |
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c50a0f409d
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break the import cyccle
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2025-01-27 17:23:07 +01:00 |
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7c4042df6b
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introduce obidefault
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2025-01-27 17:12:45 +01:00 |
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9acb4a85a8
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Refactoring of the default values
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2025-01-24 18:09:59 +01:00 |
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5d0f996625
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Patch a small bug on json write
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2024-12-20 19:42:03 +01:00 |
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abfa8f357a
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patch a bug in Taxid parsing
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2024-12-19 13:54:23 +01:00 |
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795df34d1a
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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
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2024-12-19 13:36:59 +01:00 |
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00b0edc15a
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refactoring of the file chunck writing
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2024-11-29 18:15:03 +01:00 |
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69ef1758a2
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obicsv debug
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2024-11-24 23:38:49 +01:00 |
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3d06978808
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a functional new version of obifind
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2024-11-24 19:33:24 +01:00 |
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36327c79c8
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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
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2024-11-16 10:01:49 +01:00 |
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f5d79d0bc4
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update api documentation
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2024-11-16 05:59:41 +01:00 |
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03f4e88a17
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Fisrt functional version
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2024-11-14 19:10:23 +01:00 |
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9471fedfa1
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Fisrt step in the obitax rewriting
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2024-11-08 09:48:16 +01:00 |
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67665a6b40
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Xprize update
Former-commit-id: d38919a897961e4d40da3b844057c3fb94fdb6d7
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2024-07-25 18:09:03 -04:00 |
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54a138196c
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Patch a bug in fasta and fastq reading
Former-commit-id: bcaa264b4c4a7c67617eb909b199176bf09913db
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2024-06-21 14:28:57 +02:00 |
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b428c48353
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Obitag, allow for reference sequences with bad taxid, which are discarded with the emission of a warning
Former-commit-id: a8781da1afa86de9c34b008959f0705ae69fc64f
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2024-03-18 19:11:41 +01:00 |
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0f3871d203
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Change the API of workers
Former-commit-id: 9b07306edd8cf28266f86f95823948fa99d39ea9
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2024-03-02 16:03:46 -04:00 |
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4a0b20484f
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Add the --taxonomic-path option to obiannotate
Former-commit-id: 385309a1c4bc5ed33aeaafc63eedb9fc552f78a6
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2024-02-27 20:10:26 +01:00 |
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23758b00f6
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Patch a bug in the embl reader and adds some doc
Former-commit-id: 9b5f75fb14bcc3043da1647055279987a295d271
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2024-01-31 15:43:02 +01:00 |
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b9a7961c91
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Add more error checks on taxonomy reading
Former-commit-id: 30c848d8e61214afcc7d92f0d3a3f5a1474fc720
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2023-12-14 08:09:06 +01:00 |
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8d77cc4133
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Change path of the obitools pkg
Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
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2023-11-29 12:14:37 +01:00 |
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18d3eec24a
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Change the annotation locker to a pointer to mutex to avoid coying mutex
Former-commit-id: d179d8753b593183312bd11184e5d8ebb301138a
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2023-08-27 16:00:35 +02:00 |
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7b7128196a
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small refactoring including doc
Former-commit-id: 6d6b527d89d77aa571831f7500f841840e280536
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2023-08-27 15:52:28 +02:00 |
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60c187404d
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Restore old obisort and add LCA functionnality to obiannotate.
Former-commit-id: aecaacc9dae49f74bd888a8eb8140822d31a42a6
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2023-05-02 10:43:22 +02:00 |
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d5e84ec676
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rename goutils to obiutils
Former-commit-id: 2147f53db972bba571dfdae30c51b62d3e69cec5
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2023-03-24 10:25:12 +07:00 |
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ed87f821eb
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adds the _taxid suffix to the rank taxid attributes.
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2023-02-16 16:13:55 +01:00 |
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5639a09fb9
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Add the --with-taxon-at-rank option code to obiannotate
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2023-02-02 16:36:32 +01:00 |
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2d375df94f
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move the worker class to the obiseq package
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2023-01-22 22:39:13 +01:00 |
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29563aa94e
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Rename the Length methods Len to follow GO standart
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2022-11-17 11:09:58 +01:00 |
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8aa323dad5
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Add a first version of obitag the successor of ecotag
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2022-10-26 13:16:56 +02:00 |
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6b8f4490cf
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Change obiclean algorithm for a better evaluation of ratio
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2022-08-31 20:38:03 +02:00 |
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abaede48b5
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Refactoring of some code
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2022-08-23 11:07:39 +02:00 |
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011898bd9d
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A first version of obigrep. Normally fully functionnal, but not fully tested
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2022-02-25 07:29:52 +01:00 |
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abcf02e488
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Start to use leveled log
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2022-02-24 12:14:52 +01:00 |
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2e7c1834b0
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Big change iin the data model, and a first version of obiuniq
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2022-02-21 19:00:23 +01:00 |
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98a4363d22
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obimultiplex saves unassigned sequence
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2022-02-01 23:25:19 +01:00 |
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ef66ca4972
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Code refactoring
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2022-01-14 17:32:12 +01:00 |
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