 coissac
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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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coissac
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6758ee6a8a
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Patch conversion from lua table to go slice or map
Former-commit-id: d94b879215374438a096e4b80a49b362266149ac
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2024-03-12 17:18:29 +01:00 |
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coissac
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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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coissac
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8a2bbd1c3b
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Patch a bug in the genbank reader when reading CONTIG entries
Former-commit-id: dfe1433fbb68a79d59a3ee45e7e5b58c1599dad6
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2024-03-11 10:53:25 +01:00 |
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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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4127ddb26f
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.gitignore
Former-commit-id: e1dcb41970f7a5405005cda8a1bbd90798e8020d
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2024-02-27 07:29:14 +01:00 |
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coissac
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c9fe6f6ebf
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Make some correction on genbank/embl parser
Former-commit-id: fb2ebb351f61d78432bb9648d0a509b6557651a2
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2024-02-27 07:28:56 +01:00 |
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coissac
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38c49e9f38
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Switch GOPATH to the local directory in Makefile
Former-commit-id: ae00f1136021e6fcd5047aadb4762653cf003d5d
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2024-02-27 07:22:57 +01:00 |
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coissac
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1542ce4c63
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Work on EMBL and Genbank parser efficienct
Former-commit-id: 309cc9ce4eea4c8085d7d4451a66a81710532f07
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2024-02-20 13:23:07 +01:00 |
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coissac
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95caebec8f
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update modules
Former-commit-id: 04651744d21f0db3406a0aa7bb9cdf9729140349
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2024-02-16 18:12:59 +01:00 |
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coissac
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c1d9bea6bb
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Release 4.1.2
Former-commit-id: 68a0f5c50b7a33e31b76c0c0994e17dc8321963b
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2024-02-16 18:05:08 +01:00 |
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coissac
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54ec09037e
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Patch a genbank & embl parsing error.
Former-commit-id: 060e80f42d176e6982e63d1128993fbcb4ad395f
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2024-02-16 15:20:37 +01:00 |
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coissac
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69b4d9ed20
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Patch e bug in the ngsfilter library when match with indel are at the extremities
Former-commit-id: 5a8a3100ac4b3eca104644597abe599eb7f2a5f4
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2024-02-01 09:54:34 +01:00 |
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coissac
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6cc5c44a32
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Correct the bug in embl reader
Former-commit-id: 579d397ca16e8c4cf2f8ba01e503e62b2fffa06f
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2024-01-31 15:50:14 +01:00 |
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coissac
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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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coissac
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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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coissac
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13cfebd737
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some more cleaning
Former-commit-id: e96df5e82929ceece14b0625dc5ad1ebc59899b7
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2024-01-16 21:11:38 +01:00 |
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coissac
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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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coissac
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6fca03227a
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Archive cleaning
Former-commit-id: ded6d9cb43e3ecdf6eb6965e73580ce30ab986c5
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2024-01-04 14:27:33 +01:00 |
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coissac
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5b57139450
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Reduce doc size
Former-commit-id: 6f92f375e9cf92159e769ce562071bb56a871819
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2024-01-04 14:17:44 +01:00 |
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coissac
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74854fa65c
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remove bade files
Former-commit-id: cc6c11243d25d1a9ba5acea301dd91e31f996b77
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2024-01-04 09:11:00 +01:00 |
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coissac
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344de1d494
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remove bad files
Former-commit-id: df4c80c51173d7e3f7a7d7f647ca8613c330c958
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2024-01-04 09:09:26 +01:00 |
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coissac
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ff54ef93d8
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remove bad files
Former-commit-id: 44bd45070e43c60ff37a7c579ca4ae1517ec7bcc
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2024-01-04 09:05:44 +01:00 |
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coissac
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43728146bb
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remove bad files
Former-commit-id: bb9eefd13801477ea78f1da1c5e145f6c8c8186a
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2024-01-04 09:04:12 +01:00 |
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coissac
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0a62e39ee0
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remove wrongly pushed files
Former-commit-id: 165c8984ae88893ccf181e158aaacb218dcda752
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2024-01-04 09:00:21 +01:00 |
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coissac
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e3938c7ba0
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Update release date
Former-commit-id: 773ca2e8938c10cdf24911598d56708a5a80fbc2
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2023-12-20 10:06:17 +01:00 |
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coissac
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1a0ca8c847
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Tags release 4.1.1
Former-commit-id: 31c11305f9301615bdc1c9dfd0c7270777b6a096
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2023-12-20 10:02:40 +01:00 |
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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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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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coissac
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2a11adb346
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Add some doc and switch to the parallel gzip library
Former-commit-id: 2c1187001f989ba3de5895f516d4c8b54d52a4c4
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2023-08-25 14:36:38 +02:00 |
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coissac
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8a98210103
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A small bug in logging and API documentation
Former-commit-id: 1ab4534581987586741db13d3453db52973524fe
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2023-08-14 15:21:30 +02:00 |
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coissac
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845c76abeb
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documentation updates
Former-commit-id: 39653082c9cd026299f6fcabef7446d569704e1f
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2023-08-14 15:20:02 +02:00 |
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