Eric Coissac
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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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Eric Coissac
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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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Eric Coissac
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73996bb0b7
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Small change in consensus weight
Former-commit-id: 58bcc67044b82e4e1d9e0e52be336ae02ab248e9
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2024-06-19 09:11:59 +02:00 |
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Eric Coissac
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44533fb61e
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Bugs in the non stric tag matching algorithm
Former-commit-id: efad98d6521322209ce22bc58fab54c7bddd19ec
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2024-06-10 21:19:26 +02:00 |
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Eric Coissac
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3a7661f324
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obimultiplex2 in now obimultiplex
Former-commit-id: ee6f5e15a3f1729dfc2806d039c842c9c3bdd343
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2024-06-07 09:04:37 +02:00 |
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Eric Coissac
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bc12b1aaa2
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Add a complete documented example of the new obitag format
Former-commit-id: 748a2357cc29aefd3bdee55c85c06eab31fb9fe1
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2024-06-06 23:44:23 +02:00 |
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Eric Coissac
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1b43fa4247
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First complete version of obimultiplex2
Former-commit-id: 170593bd597c7914d3f1fd3d2b865186d7f11966
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2024-06-06 23:11:13 +02:00 |
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Eric Coissac
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985c91452a
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correction of bug and format in obisplit
Former-commit-id: d600713a5f48c8d682971be9b8a09a1c021be28c
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2024-06-05 17:18:44 +02:00 |
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Eric Coissac
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c8ad96f5e6
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First fonctionnal version with fixed tag length and strict matching
Former-commit-id: 5affee2c7c66dd1da5b17c2d1ea64f44db76df50
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2024-06-04 21:46:09 +02:00 |
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Eric Coissac
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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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Eric Coissac
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38945d0a41
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Adds the --template option to obimultiplex
Former-commit-id: 349e9f278abd6a6c258f31d99ea04853a79c62de
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2024-05-31 11:34:06 +02:00 |
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Eric Coissac
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4487723d14
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Adds possibility to provide the ngsfilter configuration as a CSV file
Former-commit-id: f0fd2cb1a7b149ae2a330edc5087b21be2c4585b
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2024-05-31 11:08:20 +02:00 |
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Eric Coissac
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dd9307a4cd
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Swich to the system min and max functions and remove the version from obiutils
Former-commit-id: 8c4558921b0d0c266b070f16e83813de6e6d4a0f
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2024-05-30 08:27:24 +02:00 |
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Eric Coissac
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98b3bc2a8c
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Patch a bug on the reading of each last sequence of a chunck in the fasta reader
Former-commit-id: eacf64112582befa4751f66352999a28abf349f7
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2024-05-27 10:17:17 +02:00 |
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Eric Coissac
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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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Eric Coissac
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61be8a55b1
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Merge obiminion and obiconsensus
Former-commit-id: 49d65d671e9fe4454de60c20507c3d8df6e9c51c
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2024-05-14 17:53:32 +02:00 |
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Eric Coissac
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7fcb0538a3
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Cleaning of obiminion
Former-commit-id: 75148afd70e5006cc6855bcddc86506b099761a1
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2024-05-14 11:45:46 +02:00 |
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Eric Coissac
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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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Eric Coissac
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d30d736e48
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Simplify the workers code by removing dupplicates
Former-commit-id: 638fcf8d88dd93755d1ec89c8fe92f6ed3f733df
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2024-04-30 12:22:22 +02:00 |
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Eric Coissac
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f37477b26c
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Progress bar are automagically disabled if stderr is redirected
Former-commit-id: 20a3a22db7dcf530b9e9cad9090b46f22db0d078
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2024-04-22 12:23:59 +02:00 |
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Eric Coissac
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8f08959ebb
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Make the --no-progressbar option effective on graph building progress too.
Former-commit-id: 3fabecfc9de69ad406d6840c8f821c16eebaef46
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2024-04-22 12:01:43 +02:00 |
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Eric Coissac
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0a2ea962db
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obitag bug
Former-commit-id: e6f8750d8db74c0b175c4a93d5b58bd84f293d52
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2024-04-03 16:28:06 +02:00 |
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Eric Coissac
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3d1d9f32df
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Make obiconsensus using the count of the sequences
Former-commit-id: 7fc5292aeb225843a86cd85591a5405e35125e3d
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2024-04-03 12:58:32 +02:00 |
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Eric Coissac
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bf41d16e67
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Patch a bug in obitag on the identification of the best match
Former-commit-id: e551b3b83e79a517dd5409ea8112fb005c39c2ee
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2024-04-03 12:30:40 +02:00 |
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Eric Coissac
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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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aa07ef2127
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adds a obisplit_nfrg attribute
Former-commit-id: b8d32ba8f32a77457747f6a4616432feb5313396
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2024-03-13 10:41:53 +01:00 |
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65933ca031
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A working version of obiscript
Former-commit-id: 6652ac7dfe681e6c92a2946c34a8248bd62996b0
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2024-03-08 21:39:05 +01:00 |
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b40015deb7
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first preliminary version of obiscript.
Former-commit-id: 0d2c0fc5e33e0873ba5c04aca4cf7dd69aa83c90
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2024-03-06 12:56:44 -03:00 |
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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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