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a36e830de3
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homogenize worker count
Former-commit-id: 4352ac6694c08023cdf0e090723fac8af655cea4
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2023-12-20 08:14:07 +01:00 |
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7a31d5b07b
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Adds some more error controle on taxonomy reading
Former-commit-id: 29c9eafd8c32a92d30611094b06e600aff2e09c6
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2023-12-14 09:17:46 +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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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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37c3e16d5d
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Adds the option --pairing-scale to obipairing
Former-commit-id: c60416708467f5e818e70e08b3c512014b6212f0
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2023-12-07 12:28:16 +01:00 |
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008f33aee4
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Adds a better detection of invalid format of ngsfilter files
Former-commit-id: 2d3c4709264b822f2750a7a159a01700ec0bf6ed
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2023-12-07 10:47:34 +01:00 |
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0f8066d367
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many changes ;-)
Former-commit-id: cb4aea844e960e4af4dc673ebc8eec49a7d12b13
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2023-12-05 15:28:29 +01:00 |
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03bef6461d
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Complement to the documentation
Former-commit-id: 89952a6f3bb261a6aaec24430906e635914ffce4
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2023-12-04 13:16:34 +01:00 |
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eb351a7530
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patch bug in worker
Former-commit-id: f83cc62fc7a85f732e871f8866f80f738f494f9e
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2023-12-03 22:44:13 +01:00 |
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d29f82a28d
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Update kmeans.go
Former-commit-id: 910a94ea5a5a0514a30ff3549c4cf71c13d4577b
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2023-12-01 16:45:47 +01:00 |
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5682247ff8
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Update main.go
Former-commit-id: f2aec0d30c0d2b31a9d00c7d4adf47421123b0fb
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2023-12-01 16:42:12 +01:00 |
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71bb5f3f89
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Update options.go
Former-commit-id: b794cb924596b069b13ac07de3291ba640289d7a
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2023-12-01 16:38:02 +01:00 |
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a0d77d8a60
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Update obilandmark.go
Former-commit-id: 6cb6da988fa8a0f87025f4da36173cfc4131e056
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2023-12-01 16:37:32 +01:00 |
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e7481f8f0f
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patch for impot bug
Former-commit-id: f01546fabfbd603519c0fcf3225c63fa5a134e99
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2023-12-01 16:31:35 +01:00 |
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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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