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82040dbe55
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Patch a bug leading to loose taxonomical identification (set to root) when best_id = 1
Former-commit-id: 8eb4f95d4df774563f5a5fe17d2c9c8836361caa
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2023-11-30 13:07:51 +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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72ad84c2d4
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remove a forgotten debug log
Former-commit-id: 9fe06483b0dabc9d618f4f1d752ae9e472a07904
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2023-11-25 14:04:22 +01:00 |
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db6de58548
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Patch bug in ngsfilter reader
Former-commit-id: 77a1c39bf9c023bf4a3f58167e1e8a4d5d82e7c9
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2023-11-25 13:55:43 +01:00 |
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5d24522aa6
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update the release notes
Former-commit-id: 71ffb326302e5f108a52a41853e1c7dc6ee76136
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2023-11-24 17:45:13 +01:00 |
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b556e045e5
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Adds option to tune the pairing of the sequences in obipairing and some stats to the results
Former-commit-id: a6cf9cb4d4ab20a433a2534fd7d11cd3ca8ebbaa
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2023-11-24 12:29:37 +01:00 |
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ec31ae86b9
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Adds some stats in obiparing about fast align results
Former-commit-id: 44f6d6538e759dd7dc1db068a812957f6b20f50d
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2023-11-24 10:57:10 +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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72e5855ee9
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Adds changes
Former-commit-id: 85e9faa305c918618cef5d8ea5e2eca8956213d4
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2023-11-22 14:58:21 +01:00 |
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6141d404cd
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patch a bug related to --count option of obicsv
Former-commit-id: e19e8cc12a99216d24c5e0c5350c273202d84de4
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2023-11-22 14:51:56 +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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8905a16bc0
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Inverts the default on-disk / in-memory for obiuniq
Former-commit-id: efabee73be7c2abc5d63b69128a8ee3f7d01aa2e
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2023-11-22 07:10:03 +01:00 |
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ff51cc7393
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Adds a --transpose option to obimatrix
Former-commit-id: b2ee47c15441dca971b20f583003a3788a96da23
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2023-11-22 07:05:22 +01:00 |
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9384876416
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Push version 4.1.0
Former-commit-id: 87a36bc61d99557fa4539ff44417ae1cdd2b2317
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2023-11-16 07:51:43 +01:00 |
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8620ea1637
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First version of obimatrix
Former-commit-id: 6e09eb0dd75bc688a6c83ef40dd88658fb1b296e
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2023-11-12 20:40:56 +01:00 |
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677775bf04
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Patch a bug in the fasq reader allowing to read only lower case sequence files
Former-commit-id: f19f3812f48b215cdc5d0fdb8a39f0cd4bb5289b
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2023-11-10 09:10:54 +01:00 |
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4017e213e9
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release note
Former-commit-id: 55acaae2d107ab19dcd5b1765ac866030e9ea143
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2023-11-10 00:45:11 +01:00 |
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9ee45701b7
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correction of two warnings
Former-commit-id: d2d08b5d6f7511598625536f5a708db347742c20
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2023-11-09 22:37:55 +02:00 |
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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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8f96517f3c
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small changes
Former-commit-id: 1fee30445f03ff627dab1c335e75c3f278621f6e
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2023-11-07 21:20:45 +02:00 |
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aa0443e484
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correction to release notes
Former-commit-id: 424819230f26bccd6f5ef26684f50e9ff477a7de
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2023-11-07 12:20:40 +02:00 |
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f991886155
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Force json encoding to ascii
Former-commit-id: b35110f3fed5fedfc03380863ece5c95a2b9d6a7
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2023-11-07 12:10:14 +02:00 |
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185b974d13
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Adds a JSON output format
Former-commit-id: 26f07460772c0f735bf705d473f892878d3e57f0
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2023-11-07 11:56:49 +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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6a6a6f6f2c
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Correctly handle empty files
Former-commit-id: d166aa352ce4bf32739ddc2f7d1c9967918822fd
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2023-10-16 15:34:06 +02:00 |
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e8c55a2b6b
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optimize sequence readers and patch a bug in the format guesser
Former-commit-id: 9dce1e96c57ae9a88c26fac5c8e1bdcdc2c0c7a5
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2023-10-13 21:52:57 +02:00 |
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ddf0f2cede
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Add the -D (--delta) option to obipcr
Former-commit-id: 753079807faaddb23e03fd6350125bfa67f98c7f
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2023-10-13 17:04:10 +02:00 |
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157c26cdc7
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Patch a bug in the fasta and fastq readers
Former-commit-id: 4998f157a90a6b077124d87d4a5cde0dd075d1ce
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2023-10-13 14:21:27 +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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0a8f7afb2a
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Patch sequence writers to remove definition from header when json format is used.
Former-commit-id: a8a74cccb52d577d4ea1c0ad88b121a8e511149d
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2023-10-05 07:31:31 +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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5c30ec354f
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Go implementation of fasta and fastq parser
Former-commit-id: 3f4fd355c169afbef2d5fef1f5e407aabb71d031
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2023-09-03 19:16:37 +02:00 |
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6d1ac60c48
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Convert first nucleotide of sequence to lower case in fasta reader
Former-commit-id: 856bb3a39a4f1143a34b1f8b4d8d12b0151c0c3e
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2023-09-01 09:40:02 +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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c2533667b2
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Tag a Fatal bug release 4.0.5
Former-commit-id: 10b27c6d3867756d3159ef22eefd75db3fab84d0
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2023-08-29 18:32:00 +02:00 |
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8ebf368a8f
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Patch an extra mutex unlock in biosequence constructor
Former-commit-id: 87a20acb5def1c6832e114726276c638f0ca9efe
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2023-08-29 18:24:02 +02:00 |
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45ea4dacf7
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Every small changes to include into Release 4.0.4
Former-commit-id: b2a48c5b5c471f072785e02d4bb0f149a09cdf6f
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2023-08-27 17:22:51 +02:00 |
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d437fba535
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Doc change
Former-commit-id: 5cd4547147804f887ad699d4886702545584ba32
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2023-08-27 17:06:36 +02:00 |
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0303244e3c
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Adds doc and unit tests
Former-commit-id: 6f60f97947111b4fc65cc0e72d18770ba6094088
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2023-08-27 16:48:15 +02:00 |
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cd7414d471
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Unit tests for obiutils.Set
Former-commit-id: 352ec0da26184d13f74a34a1ad70ca4edef7e4a6
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2023-08-27 16:40:41 +02:00 |
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bfe6fa630a
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Adds unit tests
Former-commit-id: 33e9d9a8a370afc3d6318c6972de02a957fa3098
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2023-08-27 16:23:09 +02:00 |
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5b7d88ccc6
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Patch a bug in the Dim function
Former-commit-id: 004545e81df4dcf33294fb062de8204692035cdf
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2023-08-27 16:18:10 +02:00 |
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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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f1025f97b8
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Add a missing prototype
Former-commit-id: 6c5b476f30adba6e0eb41e11e152124090c3f04e
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2023-08-27 15:51:23 +02:00 |
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9bf006af93
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A first prototype for the space of sequences
Former-commit-id: 07dc6ef044b5b6a6fb45dc2acb01dffe71a96195
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2023-08-27 14:58:55 +02:00 |
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cbd42d5b30
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Implements a parallel version of Kmeans
Former-commit-id: 58ab24b9b274451e00eea0275249234e2c2ea09b
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2023-08-26 01:26:40 +02:00 |
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