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5b98393a68
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Refactor sequence file reading
Former-commit-id: 3dcb96e68da648d72bb585da047e3496427d7851
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2024-05-01 00:50:23 +02:00 |
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33d4d63acd
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Adds a warning on max-cpu = 1
Former-commit-id: ed02328d7d0e36b7c6b77ea776c0bde7c0eb64f3
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2024-04-30 13:27:19 +02:00 |
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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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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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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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df74b2b2bd
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Add a basic managment of obisequenceslice to obiscript
Former-commit-id: c3d2888ebbfb237826630548b839ce93cdbf86eb
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2024-04-16 12:58:25 +02:00 |
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cb35612a6c
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new --version option and qualities method in obiscript
Former-commit-id: 7b0ce2901785d5c7494dec3a7a95d1fc5dc4a52b
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2024-04-13 12:40:43 +02:00 |
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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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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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d68210ef94
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Tag version 4.2.0
Former-commit-id: 9315e463fcf9c654ff34738d0fb93c94538600a1
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2024-04-03 12:57:00 +02:00 |
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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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e25c3b7365
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Bug in the json parsing
Former-commit-id: e652b04b9fa7e11124eb5930c7bec4613c808758
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2024-03-19 13:50:13 +01:00 |
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11a14b6dc8
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Parse correctly json header when a curly brace is included in a string.
Former-commit-id: 35225bc7db165825d4e5ef583324e54829695503
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2024-03-19 13:47:03 +01:00 |
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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