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• 5c30ec354f Go implementation of fasta and fastq parser Eric Coissac 2023-09-03 19:16:37 +02:00
• 6d1ac60c48 Convert first nucleotide of sequence to lower case in fasta reader Eric Coissac 2023-09-01 09:40:02 +02:00
• 62b57f4ede A go implementation of the fasta reader Eric Coissac 2023-09-01 09:30:12 +02:00
• 3f8c0d6a2f Replace MakeBioSequence call by NewBioSequence call, Implements a new file format guesser Adds some more API doc Eric Coissac 2023-08-30 19:59:46 +02:00
• c2533667b2 Tag a Fatal bug release 4.0.5 Eric Coissac 2023-08-29 18:32:00 +02:00
• 8ebf368a8f Patch an extra mutex unlock in biosequence constructor Eric Coissac 2023-08-29 18:24:02 +02:00
• 45ea4dacf7 Every small changes to include into Release 4.0.4 Eric Coissac 2023-08-27 17:22:51 +02:00
• d437fba535 Doc change Eric Coissac 2023-08-27 17:06:36 +02:00
• 0303244e3c Adds doc and unit tests Eric Coissac 2023-08-27 16:48:15 +02:00
• cd7414d471 Unit tests for obiutils.Set Eric Coissac 2023-08-27 16:40:41 +02:00
• bfe6fa630a Adds unit tests Eric Coissac 2023-08-27 16:23:09 +02:00
• 5b7d88ccc6 Patch a bug in the Dim function Eric Coissac 2023-08-27 16:18:10 +02:00
• 18d3eec24a Change the annotation locker to a pointer to mutex to avoid coying mutex Eric Coissac 2023-08-27 16:00:35 +02:00
• 7b7128196a small refactoring including doc Eric Coissac 2023-08-27 15:52:28 +02:00
• f1025f97b8 Add a missing prototype Eric Coissac 2023-08-27 15:51:23 +02:00
• 9bf006af93 A first prototype for the space of sequences Eric Coissac 2023-08-27 14:58:55 +02:00
• cbd42d5b30 Implements a parallel version of Kmeans Eric Coissac 2023-08-26 01:26:40 +02:00
• 077f3b5bb5 first trial of obilandmark Eric Coissac 2023-08-25 23:23:23 +02:00
• 2a11adb346 Add some doc and switch to the parallel gzip library Eric Coissac 2023-08-25 14:36:38 +02:00
• 8a98210103 A small bug in logging and API documentation Eric Coissac 2023-08-14 15:21:30 +02:00
• 845c76abeb documentation updates Eric Coissac 2023-08-14 15:20:02 +02:00
• 70a77c9ec6 Adds doc Eric Coissac 2023-08-14 10:04:16 +02:00
• fd4c7c2572 Adds some docs Eric Coissac 2023-08-14 00:12:17 +02:00
• be47ec909c add the --skip-empty option Eric Coissac 2023-07-17 14:24:02 +02:00
• b44fcfb2a0 Correct a bug related to the renaming of the forward_mismatch and reverse_mismatch to forward_error and reverse_error Eric Coissac 2023-06-08 16:40:03 +02:00
• 1cedc0765d update release note and the install script Eric Coissac 2023-06-07 17:54:02 +02:00
• d46f6b06c5 several small changes Eric Coissac 2023-06-07 17:50:10 +02:00
• 49fa1a76cb correction in obitag to save partially indexed reference db Eric Coissac 2023-06-07 17:48:38 +02:00
• 63dc67f344 add debuging log Eric Coissac 2023-06-07 17:47:58 +02:00
• e29dacc1ba change default of output options and add the actual printing of the column sequence Eric Coissac 2023-06-07 17:47:06 +02:00
• 7f08f58336 several correction in obitag and adds the --save-db option Eric Coissac 2023-06-07 17:45:11 +02:00
• 8895381c92 Correct a bug when sequence length is shorter than kmer size in debruijngraph Eric Coissac 2023-06-07 17:43:32 +02:00
• 68a290d564 Update install_obitools.sh Eric Coissac 2023-06-06 10:13:13 +02:00
• 3e27c1f432 Update install_obitools.sh Eric Coissac 2023-06-06 10:11:37 +02:00
• 19e43e8916 Update install_obitools.sh Eric Coissac 2023-06-06 10:02:24 +02:00
• c6b59c0c80 Update install_obitools.sh to print on stderr Eric Coissac 2023-06-06 09:21:16 +02:00
• f6628a1ba2 Update install script Eric Coissac 2023-05-23 10:09:42 +02:00
• 670876d3a4 adds info Eric Coissac 2023-05-05 14:15:05 +02:00
• e9574bae07 Small change to increase efficiency (a little) Eric Coissac 2023-05-05 13:33:15 +02:00
• 3778ae9266 Correction a a bug and transfert of the new matching rules from obirefidx to obitag Eric Coissac 2023-05-05 07:37:19 +02:00
• 88a9e38952 Took better advantage of taxonomy structure and LCA upperbound base on common word. Accelleration by a factor two of obirefidx compared to previous version. Eric Coissac 2023-05-04 09:32:47 +02:00
• 870cb1aabb New refdb indexing algorithm Eric Coissac 2023-05-03 15:32:31 +02:00
• e8bd130ffc Tagging of the 4.0.3 version. Eric Coissac 2023-05-02 11:02:58 +02:00
• bffcab1096 Complete release notes and change obiannotate options accordingly Eric Coissac 2023-05-02 11:01:26 +02:00
• 60c187404d Restore old obisort and add LCA functionnality to obiannotate. Eric Coissac 2023-05-02 10:43:22 +02:00
• e9dcacbf24 Correction of one base deletion in the consensus Eric Coissac 2023-04-19 09:12:12 +02:00
• 450e54f4aa Rename forward and reverse mitmatches tags Eric Coissac 2023-04-18 12:08:13 +02:00
• 9bac7f387a Patch a bug in the help messages Eric Coissac 2023-04-17 11:32:10 +02:00
• 71023423e6 Add a new command obitagpcr able to tag reads according to their corresponding pcr samples Eric Coissac 2023-04-07 17:45:22 +02:00
• dbf69b7da5 Patch a bug in obiseq.GetSlice Eric Coissac 2023-04-07 17:44:11 +02:00
• 74babcec55 adds the contains function to the language Eric Coissac 2023-04-07 16:54:57 +02:00
• d70bb45f3f Small change in parallelisation tuning Eric Coissac 2023-04-05 14:15:47 +02:00
• 2e7fc9a589 Release 4.0.2 Eric Coissac 2023-03-31 15:56:37 +02:00
• 3f69fa41d6 Patch a bug for multiple amplicon per sequence. Eric Coissac 2023-03-31 15:10:25 +02:00
• 84b3e4d097 Reduce memomry inprint of obipcr Eric Coissac 2023-03-31 10:53:53 +02:00
• 2c9bca5c8a realease-notes Eric Coissac 2023-03-29 11:16:25 +07:00
• e7b9ba3f30 Limit allocation during genbank parsing Eric Coissac 2023-03-28 22:42:58 +07:00
• 446ba06c63 edited .gitignore Eric Coissac 2023-03-28 21:31:31 +07:00
• 0746c95f4f Update the package dependencies Eric Coissac 2023-03-28 21:30:25 +07:00
• 4bf041be62 Add some option to the obiconsensus command Eric Coissac 2023-03-28 21:23:27 +07:00
• e863dc456a Add an option --pprof Eric Coissac 2023-03-28 20:07:26 +07:00
• 988ae79989 Optimize memory allocation of the apat algorithms Eric Coissac 2023-03-28 19:37:05 +07:00
• 21819cd41e Add some geometry data to the GML edges Eric Coissac 2023-03-28 11:43:46 +07:00
• bc82422bc5 Reduce redundante call to bytes.ToLower and substitute the last call by an home made version doing the conversion in place Eric Coissac 2023-03-28 11:43:04 +07:00
• e8a8f746d3 few bug in the graph algorithm Eric Coissac 2023-03-27 22:43:45 +07:00
• 245230ae12 A small correction Eric Coissac 2023-03-27 19:51:38 +07:00
• a33e471b39 First attempt for obiconsensus... The graph traversing algorithm is too simple Eric Coissac 2023-03-27 19:51:10 +07:00
• d5e84ec676 rename goutils to obiutils Eric Coissac 2023-03-24 10:25:12 +07:00
• 42aae88520 complete the correction related to the tag detection Eric Coissac 2023-03-23 11:52:08 +07:00
• 57474214e7 Patch excessive log in obimultiplex and an error in detecting the tag. Eric Coissac 2023-03-23 11:40:24 +07:00
• 98eac2360c adds a rule to update packages and push the corresponding updates module files Eric Coissac 2023-03-21 22:02:18 +07:00
• 7ed567fbad Make the --help or -h options working when mandatory options are declared Eric Coissac 2023-03-21 22:01:20 +07:00
• d09011fac2 Finalyse the obimultiplex with indels Eric Coissac 2023-03-21 22:01:02 +07:00
• 27d6c60e25 Add the possibility to look for patterns allowing indels. Eric Coissac 2023-03-20 15:28:24 +07:00
• 5fbe52368c Patch the empty batch bug Eric Coissac 2023-03-07 20:16:06 +07:00
• 1e7756ec91 Add comment on release notes Eric Coissac 2023-03-07 17:36:35 +07:00
• 9a48614a9b Merge branch 'master' of git.metabarcoding.org:obitools/obitools4/obitools4 Eric Coissac 2023-03-07 17:34:34 +07:00
• b3922c3896 Produce less weird crash on non existing files Eric Coissac 2023-03-07 17:34:25 +07:00
• 42cf8cea73 Update README.md Eric Coissac 2023-03-07 05:50:19 +01:00
• 7b4249b775 Update README.md Eric Coissac 2023-03-07 05:48:50 +01:00
• fbfed52508 Tag realease 4.0.1 in release notes Eric Coissac 2023-03-07 11:15:06 +07:00
• bb0282b6a1 Progress on the development Eric Coissac 2023-03-07 11:13:25 +07:00
• d4b185b716 Adds some new dependencies Eric Coissac 2023-03-07 11:12:39 +07:00
• d88de15cdc Refactoring codes for removing buffer size options. An some other changes... Eric Coissac 2023-03-07 11:12:13 +07:00
• 9811e440b8 Takes into account the option parsing errors Eric Coissac 2023-03-07 11:06:08 +07:00
• 6b52dc0700 Correct the Makefile for a default rule Eric Coissac 2023-03-02 20:48:55 +07:00
• b9bf88d4df Adds some new columns to the ratio file. Eric Coissac 2023-02-25 15:56:23 +01:00
• 6f28d2ab68 Patch a bug introduced by the new model for paired sequences Eric Coissac 2023-02-24 10:23:26 +01:00
• 6ce3053409 Merge branch 'master' of git.metabarcoding.org:obitools/obitools4/obitools4 Eric Coissac 2023-02-23 23:50:57 +01:00
• 6c5fc8f65b Save change in various files Eric Coissac 2023-02-23 23:45:41 +01:00
• 05323f960c Start writing of the man pages Eric Coissac 2023-02-23 23:43:54 +01:00
• c94b2974fb Reorganization of the documentation book directory Eric Coissac 2023-02-23 23:41:24 +01:00
• 072b85e155 change the model for representing paired reads and extend its usage to other commands Eric Coissac 2023-02-23 23:35:58 +01:00
• ebb05fcdf7 code refactoring. Prefix function name having behaviour depending on command line option by the prefix CLI Eric Coissac 2023-02-23 23:32:59 +01:00
• 0b8f35cbf6 Update Release-notes.md Eric Coissac 2023-02-18 19:57:21 +01:00
• a0ab14c205 Complete the documentation and add a Release note file Eric Coissac 2023-02-18 19:54:21 +01:00
• 56722895e4 Adds to every obitools the ability to save in gzip compressed files Eric Coissac 2023-02-18 12:06:52 +01:00
• 1a08ad4254 Flush the buffered io Eric Coissac 2023-02-18 07:23:14 +01:00
• 3e1f88b37b adds the subspc function to the gval language Eric Coissac 2023-02-17 23:10:43 +01:00
• d04eb915b3 adds a directory option to obidistribute Eric Coissac 2023-02-17 22:52:53 +01:00