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b4afd784dc
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few small correction
Former-commit-id: 9319387ef5379b66e008233dbd7b6ea60b5d3b1e
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2024-03-06 12:52:22 -03:00 |
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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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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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f2f7b4574e
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update the geometric obitag
Former-commit-id: acd8fe1c8c1cf443098432d818397b0b5d02df33
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2024-01-17 23:38:51 +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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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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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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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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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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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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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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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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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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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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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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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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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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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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077f3b5bb5
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first trial of obilandmark
Former-commit-id: 00a50bdbf407b03dfdc385a848a536559f5966a5
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2023-08-25 23:23:23 +02:00 |
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be47ec909c
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add the --skip-empty option
Former-commit-id: ec9cb0ecaf90a61bf9289cf4c089b5cc2fcb65a5
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2023-07-17 14:24:02 +02:00 |
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b44fcfb2a0
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Correct a bug related to the renaming of the forward_mismatch and reverse_mismatch to forward_error and reverse_error
Former-commit-id: c0d6cfda0d8e50364616fd79313c5711ed7bb43e
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2023-06-08 16:40:03 +02:00 |
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d46f6b06c5
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several small changes
Former-commit-id: c1cdb95885e44fd6ee7d1c963860d7ab41230c96
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2023-06-07 17:50:10 +02:00 |
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e29dacc1ba
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change default of output options and add the actual printing of the column sequence
Former-commit-id: bc3adf7ddecca3683def980ffc8a8bd63410ab3a
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2023-06-07 17:47:06 +02:00 |
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7f08f58336
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several correction in obitag and adds the --save-db option
Former-commit-id: b3a15b1a1b3971388a8749faaba519028f6e976c
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2023-06-07 17:45:11 +02:00 |
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e9574bae07
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Small change to increase efficiency (a little)
Former-commit-id: fa54c9bf82b8ba60653255ab2a5f671619dcfdcb
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2023-05-05 13:33:15 +02:00 |
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3778ae9266
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Correction a a bug and transfert of the new matching rules from obirefidx to obitag
Former-commit-id: a28540f72a504ad4e7e8a8b6f7609116913445b4
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2023-05-05 07:37:19 +02:00 |
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88a9e38952
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Took better advantage of taxonomy structure and LCA upperbound base on common word. Accelleration by a factor two of obirefidx compared to previous version.
Former-commit-id: 35f40498d642058e9dbff20128d11303a314018d
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2023-05-04 09:32:47 +02:00 |
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870cb1aabb
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New refdb indexing algorithm
Former-commit-id: 7ae480cec5d277a08620a2e666b5c9b69bb6cd73
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2023-05-03 15:32:31 +02:00 |
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bffcab1096
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Complete release notes and change obiannotate options accordingly
Former-commit-id: 947db1f4606d57893cf758df57a4c954e3949e6b
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2023-05-02 11:01:26 +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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e9dcacbf24
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Correction of one base deletion in the consensus
Former-commit-id: 6aabd8bfdb5263a2285718cb2eca27628c0e717c
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2023-04-19 09:12:12 +02:00 |
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9bac7f387a
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Patch a bug in the help messages
Former-commit-id: 61ffea65db66215c072139540ec19c11c52efbbc
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2023-04-17 11:32:10 +02:00 |
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71023423e6
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Add a new command obitagpcr able to tag reads according to their corresponding pcr samples
Former-commit-id: 1f34bf0a27d55afc3556efd64f6ccee6d2329aff
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2023-04-07 17:45:22 +02:00 |
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d70bb45f3f
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Small change in parallelisation tuning
Former-commit-id: 3fe2495b7fd86a0ba47dd87907323a457bae481a
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2023-04-05 14:15:47 +02:00 |
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84b3e4d097
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Reduce memomry inprint of obipcr
Former-commit-id: bd25be2d454f083c729346a828e27f07ad1a216e
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2023-03-31 10:53:53 +02:00 |
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4bf041be62
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Add some option to the obiconsensus command
Former-commit-id: cf30a404a4943e4527106c977b01712ef454e028
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2023-03-28 21:23:27 +07:00 |
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