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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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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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e47b50de7f
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Patch a bug in seting of the tag delimiter with an upper case
Former-commit-id: a3962400b7ab91b25102c4c7c35cd824bf7ceaf0
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2024-06-06 23:25:16 +02:00 |
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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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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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87a7219ab4
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Adds the reading of the options through the csv formated ngsfilter configuration file
Former-commit-id: 0e9a13689da2ba45293c7de1f728d3d0d34d3238
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2024-06-04 22:57:07 +02:00 |
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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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a0a9fb461c
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trial on rewriting obimultiplex
Former-commit-id: d00f3353d83760dc878c6411ad344d96216096a7
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2024-06-04 16:50:07 +02:00 |
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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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e843d2aa5c
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Patch a tricky bug in parsing of json header and save the last sequence from files
Former-commit-id: bfe3d0e9eb8e65113699d535bd1d9a5fe0d3ce1d
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2024-06-04 13:46:23 +02:00 |
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aa42df326a
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Correct a bug in the fastq reader affecting the quality of the last record of each chunk
Former-commit-id: b842d60af9c2f1f971946d99999d13cfc15793b3
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2024-06-04 11:57:16 +02:00 |
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411124d1b3
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Add automatic rules to manage version number
Former-commit-id: f4fcc1927f4169025c1d8cc88c5f3abcdc76037c
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2024-06-01 17:26:16 +02:00 |
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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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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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dbeb44bc79
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Patch a bug in the quality string writing
Former-commit-id: 1a76d58b8648378d10e8b59d05208263e96238c9
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2024-05-31 11:07:25 +02:00 |
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3e1d9a41ec
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Adds more format checking during fasta parsing
Former-commit-id: fbc3d9c923936287a591f01f9401b710b584aa14
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2024-05-30 18:12:06 +02:00 |
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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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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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d249902073
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A lot of changes and debug... A complete first
version of the recipy in the Cookbook about
avaluating primers
Former-commit-id: 6c816f5546b3f472f6930d112abe3da04d2d5a55
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2024-05-26 12:56:29 +02:00 |
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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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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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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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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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9e63013bc2
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Correction on obiformat of bug leading to partial parsing and add godocs
Former-commit-id: b27105355f1a330eedf6eaa72c8ac94f06806c28
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2024-05-07 10:54:12 +02:00 |
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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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