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286e27d6ba
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patch the scienctific_name tag name to "scientific_name"
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2025-03-05 14:22:12 +01:00 |
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51b3e83d32
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some cleaning
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2025-02-24 11:31:49 +01:00 |
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8671285d02
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add the --min-sample-count option to obiclean.
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2025-02-24 08:48:31 +01:00 |
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4774438644
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Changes to be committed:
modified: pkg/obiformats/universal_read.go
modified: pkg/obioptions/version.go
modified: pkg/obiseq/taxonomy_methods.go
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2025-02-12 08:40:38 +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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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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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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ccd3b06532
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Merge branch 'master' into taxonomy
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2024-12-20 20:06:57 +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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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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d29a56dcbf
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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
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2024-11-27 09:56:22 +01:00 |
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7884a74f9c
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Patch a bug in obitagpcr
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2024-11-18 21:10:47 +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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241f2286f2
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remove the slice pool management
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2024-09-24 16:31:30 +02:00 |
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05bf2bfd6c
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Add option related to agrep match on obigrep and obiannotate
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2024-09-09 16:52:13 +02:00 |
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65ae82622e
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correction of several small bugs
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2024-09-03 06:08:07 -03:00 |
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bdb96dda94
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Adds the obimicrosat command
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2024-08-05 15:31:20 +02:00 |
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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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4e4fac491f
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Fisrt versin of the two levels indexing
Former-commit-id: 4d86483bc120e27cb6f5d2c216596d410274fc69
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2024-07-12 15:17:48 +02:00 |
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c7ed47e110
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first version of obidemerge, obijoin and a new filter for obicleandb but to be finnished
Former-commit-id: 8a1ed26e5548c30db75644c294d478ec4d753f19
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2024-07-10 15:21:42 +02:00 |
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bd855c4965
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Adds CSV as an input format
Former-commit-id: a365bb6947064adc2709d66df05fa54c6fe47fad
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2024-07-03 21:04:27 +02:00 |
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fd663357b5
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First version of obicleandb...
Former-commit-id: e60b61d015abbf029a555b51de99b4252c50ab59
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2024-07-01 17:12:42 +02:00 |
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93f9dcb95f
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Reducing memory allocation events
Former-commit-id: c94e79ba116464504580fc397270ead154063971
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2024-06-22 22:32:31 +02:00 |
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e6b87ecd02
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Reduce memory allocation events
Former-commit-id: fbdb2afc857b02adc2593e2278d3bd838e99b0b2
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2024-06-22 21:01:53 +02:00 |
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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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818ce87bab
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Patch some bugs in writing files
Former-commit-id: 612868a281dc0ecf4e6c5776973735e5c71bd517
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2024-06-19 13:15:30 +02:00 |
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65f5109957
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Plenty of small bugs
Former-commit-id: 42c7fab7d65906c80ab4cd32da6867ff21842ea8
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2024-06-04 16:49:12 +02:00 |
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aa42df326a
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Correct a bug in the fastq reader affecting the quality of the last record of each chunk
Former-commit-id: b842d60af9c2f1f971946d99999d13cfc15793b3
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2024-06-04 11:57:16 +02:00 |
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dbeb44bc79
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Patch a bug in the quality string writing
Former-commit-id: 1a76d58b8648378d10e8b59d05208263e96238c9
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2024-05-31 11:07:25 +02:00 |
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55ce36f329
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Update of obipcr and homogenization of logging
Former-commit-id: 46abf47c19ace5248042c02cf1f81d9f6c12eb10
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2024-05-16 15:18:30 +02:00 |
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017030bcce
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Add obiminion first version
Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d
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2024-05-14 08:16:12 +02:00 |
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9e63013bc2
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Correction on obiformat of bug leading to partial parsing and add godocs
Former-commit-id: b27105355f1a330eedf6eaa72c8ac94f06806c28
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2024-05-07 10:54:12 +02:00 |
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f4d71d4a66
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Patch a bug in the subseq and revcomplement methods. That patchs the bug in the option -c of obipcr
Former-commit-id: 7999b917d07545271036af6e66f53aea27fc6e7b
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2024-03-11 10:54:37 +01:00 |
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7bd073ccd4
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First version of obisplit and patch a bug in the new workers API
Former-commit-id: f28af9f104c08d68e29fd866739d8dd58241da63
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2024-03-03 11:16:24 -04:00 |
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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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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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3c48bafab0
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patch a low level bug in EnsureCapacity
Former-commit-id: 2d50dc6923e7cfca9b864fb885577c1d1f936fc1
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2024-01-16 20:51:45 +01:00 |
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2caaa62485
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Implements the kmeans++ algo to select the landmarks in the geometric method
Former-commit-id: 732404a0dc6d7276e4e479dd2481aa4bd42d4ce5
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2023-12-11 16:07:03 +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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ce66b0af2f
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Patch a bug in the pair-end alignement in case of equality between scores.
Former-commit-id: bbdb761a98b76f2421d1f0a72960e72b13b6e626
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2023-11-24 09:59:29 +01:00 |
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2e0c1bd801
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Correct the number of workers
Former-commit-id: febbccfb853263e0761ecfccb0f09c8c1bf88475
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2023-11-22 09:46:30 +01:00 |
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5ea2b8afcf
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a first version of obisummary
Former-commit-id: cca1019d82a14a322f46a20890b996b5c7491d41
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2023-11-09 22:33:06 +02:00 |
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a96ecb4837
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Adds some unit test
Former-commit-id: b1a59df1c87187a1538f30c447d42bbe96402419
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2023-11-08 11:13:56 +02:00 |
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dedf125f6e
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Patch a bug in Subsequence and adds few unit tests.
Former-commit-id: caddc9ad6523e4ef02899bfe83cc8681ef674383
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2023-11-08 10:16:34 +02:00 |
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61c30f9b6a
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Patch rev complement and first implementation of --auto in obicsv
Former-commit-id: f3020e81283b1073c4d1c2d2ff0887e3998e6764
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2023-11-07 09:37:07 +02:00 |
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6acce603a1
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Patch a bug in the new version of setDefinition()
Former-commit-id: 9a382d9891e158dd3d445bfb4053691739ca9fdb
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2023-10-05 07:48:47 +02:00 |
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d23a911080
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Change the way sequence definition are managed. They are now when present stored as an attribute
Former-commit-id: 6e618377c05b42937d2eace3c9668390980ab68c
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2023-10-05 07:21:12 +02:00 |
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62b57f4ede
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A go implementation of the fasta reader
Former-commit-id: 603592c4761fb0722e9e0501d78de1bd3ba238fa
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2023-09-01 09:30:12 +02:00 |
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3f8c0d6a2f
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Replace MakeBioSequence call by NewBioSequence call,
Implements a new file format guesser
Adds some more API doc
Former-commit-id: 9837bf1c28beca6ddb599b367f93548950ba83c1
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2023-08-30 19:59:46 +02:00 |
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