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Commit Graph

  • ff51cc7393 Adds a --transpose option to obimatrix coissac 2023-11-22 07:05:22 +01:00
  • 9384876416 Push version 4.1.0 coissac 2023-11-16 07:51:43 +01:00
  • 8620ea1637 First version of obimatrix coissac 2023-11-12 20:40:56 +01:00
  • 677775bf04 Patch a bug in the fasq reader allowing to read only lower case sequence files coissac 2023-11-10 09:10:54 +01:00
  • 4017e213e9 release note coissac 2023-11-10 00:45:11 +01:00
  • 9ee45701b7 correction of two warnings coissac 2023-11-09 22:37:55 +02:00
  • 5ea2b8afcf a first version of obisummary coissac 2023-11-09 22:33:06 +02:00
  • a96ecb4837 Adds some unit test coissac 2023-11-08 11:13:56 +02:00
  • dedf125f6e Patch a bug in Subsequence and adds few unit tests. coissac 2023-11-08 10:16:34 +02:00
  • 8f96517f3c small changes coissac 2023-11-07 21:20:45 +02:00
  • aa0443e484 correction to release notes coissac 2023-11-07 12:20:40 +02:00
  • f991886155 Force json encoding to ascii coissac 2023-11-07 12:10:14 +02:00
  • 185b974d13 Adds a JSON output format coissac 2023-11-07 11:56:49 +02:00
  • 61c30f9b6a Patch rev complement and first implementation of --auto in obicsv coissac 2023-11-07 09:37:07 +02:00
  • 6a6a6f6f2c Correctly handle empty files coissac 2023-10-16 15:34:06 +02:00
  • e8c55a2b6b optimize sequence readers and patch a bug in the format guesser coissac 2023-10-13 21:52:57 +02:00
  • ddf0f2cede Add the -D (--delta) option to obipcr coissac 2023-10-13 17:04:10 +02:00
  • 157c26cdc7 Patch a bug in the fasta and fastq readers coissac 2023-10-13 14:21:27 +02:00
  • 6acce603a1 Patch a bug in the new version of setDefinition() coissac 2023-10-05 07:48:47 +02:00
  • 0a8f7afb2a Patch sequence writers to remove definition from header when json format is used. coissac 2023-10-05 07:31:31 +02:00
  • d23a911080 Change the way sequence definition are managed. They are now when present stored as an attribute coissac 2023-10-05 07:21:12 +02:00
  • 5c30ec354f Go implementation of fasta and fastq parser coissac 2023-09-03 19:16:37 +02:00
  • 6d1ac60c48 Convert first nucleotide of sequence to lower case in fasta reader coissac 2023-09-01 09:40:02 +02:00
  • 62b57f4ede A go implementation of the fasta reader 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 coissac 2023-08-30 19:59:46 +02:00
  • c2533667b2 Tag a Fatal bug release 4.0.5 coissac 2023-08-29 18:32:00 +02:00
  • 8ebf368a8f Patch an extra mutex unlock in biosequence constructor coissac 2023-08-29 18:24:02 +02:00
  • 45ea4dacf7 Every small changes to include into Release 4.0.4 coissac 2023-08-27 17:22:51 +02:00
  • d437fba535 Doc change coissac 2023-08-27 17:06:36 +02:00
  • 0303244e3c Adds doc and unit tests coissac 2023-08-27 16:48:15 +02:00
  • cd7414d471 Unit tests for obiutils.Set coissac 2023-08-27 16:40:41 +02:00
  • bfe6fa630a Adds unit tests coissac 2023-08-27 16:23:09 +02:00
  • 5b7d88ccc6 Patch a bug in the Dim function coissac 2023-08-27 16:18:10 +02:00
  • 18d3eec24a Change the annotation locker to a pointer to mutex to avoid coying mutex coissac 2023-08-27 16:00:35 +02:00
  • 7b7128196a small refactoring including doc coissac 2023-08-27 15:52:28 +02:00
  • f1025f97b8 Add a missing prototype coissac 2023-08-27 15:51:23 +02:00
  • 9bf006af93 A first prototype for the space of sequences coissac 2023-08-27 14:58:55 +02:00
  • cbd42d5b30 Implements a parallel version of Kmeans coissac 2023-08-26 01:26:40 +02:00
  • 077f3b5bb5 first trial of obilandmark coissac 2023-08-25 23:23:23 +02:00
  • 2a11adb346 Add some doc and switch to the parallel gzip library coissac 2023-08-25 14:36:38 +02:00
  • 8a98210103 A small bug in logging and API documentation coissac 2023-08-14 15:21:30 +02:00
  • 845c76abeb documentation updates coissac 2023-08-14 15:20:02 +02:00
  • 70a77c9ec6 Adds doc coissac 2023-08-14 10:04:16 +02:00
  • fd4c7c2572 Adds some docs coissac 2023-08-14 00:12:17 +02:00
  • be47ec909c add the --skip-empty option 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 coissac 2023-06-08 16:40:03 +02:00
  • 1cedc0765d update release note and the install script coissac 2023-06-07 17:54:02 +02:00
  • d46f6b06c5 several small changes coissac 2023-06-07 17:50:10 +02:00
  • 49fa1a76cb correction in obitag to save partially indexed reference db coissac 2023-06-07 17:48:38 +02:00
  • 63dc67f344 add debuging log coissac 2023-06-07 17:47:58 +02:00
  • e29dacc1ba change default of output options and add the actual printing of the column sequence coissac 2023-06-07 17:47:06 +02:00
  • 7f08f58336 several correction in obitag and adds the --save-db option coissac 2023-06-07 17:45:11 +02:00
  • 8895381c92 Correct a bug when sequence length is shorter than kmer size in debruijngraph coissac 2023-06-07 17:43:32 +02:00
  • 68a290d564 Update install_obitools.sh coissac 2023-06-06 10:13:13 +02:00
  • 3e27c1f432 Update install_obitools.sh coissac 2023-06-06 10:11:37 +02:00
  • 19e43e8916 Update install_obitools.sh coissac 2023-06-06 10:02:24 +02:00
  • c6b59c0c80 Update install_obitools.sh to print on stderr coissac 2023-06-06 09:21:16 +02:00
  • f6628a1ba2 Update install script coissac 2023-05-23 10:09:42 +02:00
  • 670876d3a4 adds info coissac 2023-05-05 14:15:05 +02:00
  • e9574bae07 Small change to increase efficiency (a little) 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 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. coissac 2023-05-04 09:32:47 +02:00
  • 870cb1aabb New refdb indexing algorithm coissac 2023-05-03 15:32:31 +02:00
  • e8bd130ffc Tagging of the 4.0.3 version. coissac 2023-05-02 11:02:58 +02:00
  • bffcab1096 Complete release notes and change obiannotate options accordingly coissac 2023-05-02 11:01:26 +02:00
  • 60c187404d Restore old obisort and add LCA functionnality to obiannotate. coissac 2023-05-02 10:43:22 +02:00
  • e9dcacbf24 Correction of one base deletion in the consensus coissac 2023-04-19 09:12:12 +02:00
  • 450e54f4aa Rename forward and reverse mitmatches tags coissac 2023-04-18 12:08:13 +02:00
  • 9bac7f387a Patch a bug in the help messages 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 coissac 2023-04-07 17:45:22 +02:00
  • dbf69b7da5 Patch a bug in obiseq.GetSlice coissac 2023-04-07 17:44:11 +02:00
  • 74babcec55 adds the contains function to the language coissac 2023-04-07 16:54:57 +02:00
  • d70bb45f3f Small change in parallelisation tuning coissac 2023-04-05 14:15:47 +02:00
  • 2e7fc9a589 Release 4.0.2 coissac 2023-03-31 15:56:37 +02:00
  • 3f69fa41d6 Patch a bug for multiple amplicon per sequence. coissac 2023-03-31 15:10:25 +02:00
  • 84b3e4d097 Reduce memomry inprint of obipcr coissac 2023-03-31 10:53:53 +02:00
  • 2c9bca5c8a realease-notes coissac 2023-03-29 11:16:25 +07:00
  • e7b9ba3f30 Limit allocation during genbank parsing coissac 2023-03-28 22:42:58 +07:00
  • 446ba06c63 edited .gitignore coissac 2023-03-28 21:31:31 +07:00
  • 0746c95f4f Update the package dependencies coissac 2023-03-28 21:30:25 +07:00
  • 4bf041be62 Add some option to the obiconsensus command coissac 2023-03-28 21:23:27 +07:00
  • e863dc456a Add an option --pprof coissac 2023-03-28 20:07:26 +07:00
  • 988ae79989 Optimize memory allocation of the apat algorithms coissac 2023-03-28 19:37:05 +07:00
  • 21819cd41e Add some geometry data to the GML edges 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 coissac 2023-03-28 11:43:04 +07:00
  • e8a8f746d3 few bug in the graph algorithm coissac 2023-03-27 22:43:45 +07:00
  • 245230ae12 A small correction coissac 2023-03-27 19:51:38 +07:00
  • a33e471b39 First attempt for obiconsensus... The graph traversing algorithm is too simple coissac 2023-03-27 19:51:10 +07:00
  • d5e84ec676 rename goutils to obiutils coissac 2023-03-24 10:25:12 +07:00
  • 42aae88520 complete the correction related to the tag detection coissac 2023-03-23 11:52:08 +07:00
  • 57474214e7 Patch excessive log in obimultiplex and an error in detecting the tag. coissac 2023-03-23 11:40:24 +07:00
  • 98eac2360c adds a rule to update packages and push the corresponding updates module files coissac 2023-03-21 22:02:18 +07:00
  • 7ed567fbad Make the --help or -h options working when mandatory options are declared coissac 2023-03-21 22:01:20 +07:00
  • d09011fac2 Finalyse the obimultiplex with indels coissac 2023-03-21 22:01:02 +07:00
  • 27d6c60e25 Add the possibility to look for patterns allowing indels. coissac 2023-03-20 15:28:24 +07:00
  • 5fbe52368c Patch the empty batch bug coissac 2023-03-07 20:16:06 +07:00
  • 1e7756ec91 Add comment on release notes coissac 2023-03-07 17:36:35 +07:00
  • 9a48614a9b Merge branch 'master' of git.metabarcoding.org:obitools/obitools4/obitools4 coissac 2023-03-07 17:34:34 +07:00
  • b3922c3896 Produce less weird crash on non existing files coissac 2023-03-07 17:34:25 +07:00
  • 42cf8cea73 Update README.md coissac 2023-03-07 05:50:19 +01:00