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31bfc88eb9
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Patch a bug on writing to stdout, and add clearer error on openning data files
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2024-08-13 09:45:28 +02:00 |
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bdb96dda94
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Adds the obimicrosat command
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2024-08-05 15:31:20 +02:00 |
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3f57935328
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Adjust the size of the genbank and embl buffer size
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2024-08-05 11:32:37 +02:00 |
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886b5d9a96
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Optimize memory for readers and writers
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2024-08-05 10:48:28 +02:00 |
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f83032e643
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Tag version
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2024-08-02 14:30:53 +02:00 |
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242f4d8f56
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Realease notes
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2024-08-02 13:50:33 +02:00 |
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1b1cd41fd3
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Add some code refactoring from the blackboard branch
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2024-08-02 12:35:46 +02:00 |
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bc1aaaf7d9
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New install script updated for github
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2024-07-29 14:35:21 +02:00 |
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67665a6b40
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Xprize update
Former-commit-id: d38919a897961e4d40da3b844057c3fb94fdb6d7
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2024-07-25 18:09:03 -04:00 |
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4e4fac491f
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Fisrt versin of the two levels indexing
Former-commit-id: 4d86483bc120e27cb6f5d2c216596d410274fc69
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2024-07-12 15:17:48 +02:00 |
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42c5881ddc
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some cleanning on the new tools
Former-commit-id: f265a3910d2872c56af81c9b873669f2cb627781
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2024-07-11 10:46:11 +02:00 |
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c7ed47e110
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first version of obidemerge, obijoin and a new filter for obicleandb but to be finnished
Former-commit-id: 8a1ed26e5548c30db75644c294d478ec4d753f19
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2024-07-10 15:21:42 +02:00 |
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bd855c4965
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Adds CSV as an input format
Former-commit-id: a365bb6947064adc2709d66df05fa54c6fe47fad
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2024-07-03 21:04:27 +02:00 |
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5d9ac261ff
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correct an attribute name
Former-commit-id: 2bc540dc3863aef4f8745666047c2a7d94405343
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2024-07-01 17:44:18 +02:00 |
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fd663357b5
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First version of obicleandb...
Former-commit-id: e60b61d015abbf029a555b51de99b4252c50ab59
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2024-07-01 17:12:42 +02:00 |
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0187a82c5f
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Patch a bug in obimultiplex loosing sequence with primer dimer
Former-commit-id: ea14e1aa2e4670c19fe8ee7ec61565bd21cc25b0
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2024-06-30 17:42:28 +02:00 |
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154753de90
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Same bug but for fastq sequence writing only
Former-commit-id: 86d208fe66828da9943c559df80ff095b07eaf7a
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2024-06-26 18:46:47 +02:00 |
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e40d0bfbe7
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Debug fasta and fastq writer when the first sequence is hudge
Former-commit-id: d208ff838abb7e19e117067f6243298492d60f14
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2024-06-26 18:39:42 +02:00 |
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1835cb2cf3
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remove sonic which only works on AMD64
Former-commit-id: 5073957b4706b68896006ee0f7bc30e49ff72c3b
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2024-06-24 14:53:18 +02:00 |
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c1f03cb1f6
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Switch to faster json library go-json and sonic
Former-commit-id: ab9b4723f1dcf79fe5c073fff4d86f4f6969edfd
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2024-06-23 00:36:08 +02:00 |
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93f9dcb95f
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Reducing memory allocation events
Former-commit-id: c94e79ba116464504580fc397270ead154063971
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2024-06-22 22:32:31 +02:00 |
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e6b87ecd02
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Reduce memory allocation events
Former-commit-id: fbdb2afc857b02adc2593e2278d3bd838e99b0b2
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2024-06-22 21:01:53 +02:00 |
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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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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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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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a812fe8b72
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debug of obimultiplex
Former-commit-id: 1cf276840feb9d6135d96bd1bf63627d3085ae6e
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2024-06-18 23:38:33 +02:00 |
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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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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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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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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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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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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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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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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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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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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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e863dc456a
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Add an option --pprof
Former-commit-id: 3ca1280e8daddbf1075e3189f9851211ce8882ae
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2023-03-28 20:07:26 +07:00 |
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7ed567fbad
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Make the --help or -h options working when mandatory options are declared
Former-commit-id: db502ff81dcf20449d126978fcebf890edb814ae
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2023-03-21 22:01:20 +07:00 |
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d88de15cdc
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Refactoring codes for removing buffer size options. An some other changes...
Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce
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2023-03-07 11:12:13 +07:00 |
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