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Release_4.3.0

Release_4.4.0

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• d29f82a28d Update kmeans.go Eric Coissac 2023-12-01 16:45:47 +01:00
• 5682247ff8 Update main.go Eric Coissac 2023-12-01 16:42:12 +01:00
• 71bb5f3f89 Update options.go Eric Coissac 2023-12-01 16:38:02 +01:00
• a0d77d8a60 Update obilandmark.go Eric Coissac 2023-12-01 16:37:32 +01:00
• e7481f8f0f patch for impot bug Eric Coissac 2023-12-01 16:31:35 +01:00
• 82040dbe55 Patch a bug leading to loose taxonomical identification (set to root) when best_id = 1 Eric Coissac 2023-11-30 13:07:51 +01:00
• 8d77cc4133 Change path of the obitools pkg Eric Coissac 2023-11-29 12:14:37 +01:00
• 72ad84c2d4 remove a forgotten debug log Eric Coissac 2023-11-25 14:04:22 +01:00
• db6de58548 Patch bug in ngsfilter reader Eric Coissac 2023-11-25 13:55:43 +01:00
• 5d24522aa6 update the release notes Eric Coissac 2023-11-24 17:45:13 +01:00
• b556e045e5 Adds option to tune the pairing of the sequences in obipairing and some stats to the results Eric Coissac 2023-11-24 12:29:37 +01:00
• ec31ae86b9 Adds some stats in obiparing about fast align results Eric Coissac 2023-11-24 10:57:10 +01:00
• ce66b0af2f Patch a bug in the pair-end alignement in case of equality between scores. Eric Coissac 2023-11-24 09:59:29 +01:00
• 72e5855ee9 Adds changes Eric Coissac 2023-11-22 14:58:21 +01:00
• 6141d404cd patch a bug related to --count option of obicsv Eric Coissac 2023-11-22 14:51:56 +01:00
• 2e0c1bd801 Correct the number of workers Eric Coissac 2023-11-22 09:46:30 +01:00
• 8905a16bc0 Inverts the default on-disk / in-memory for obiuniq Eric Coissac 2023-11-22 07:10:03 +01:00
• ff51cc7393 Adds a --transpose option to obimatrix Eric Coissac 2023-11-22 07:05:22 +01:00
• 9384876416 Push version 4.1.0 Eric Coissac 2023-11-16 07:51:43 +01:00
• 8620ea1637 First version of obimatrix Eric 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 Eric Coissac 2023-11-10 09:10:54 +01:00
• 4017e213e9 release note Eric Coissac 2023-11-10 00:45:11 +01:00
• 9ee45701b7 correction of two warnings Eric Coissac 2023-11-09 22:37:55 +02:00
• 5ea2b8afcf a first version of obisummary Eric Coissac 2023-11-09 22:33:06 +02:00
• a96ecb4837 Adds some unit test Eric Coissac 2023-11-08 11:13:56 +02:00
• dedf125f6e Patch a bug in Subsequence and adds few unit tests. Eric Coissac 2023-11-08 10:16:34 +02:00
• 8f96517f3c small changes Eric Coissac 2023-11-07 21:20:45 +02:00
• aa0443e484 correction to release notes Eric Coissac 2023-11-07 12:20:40 +02:00
• f991886155 Force json encoding to ascii Eric Coissac 2023-11-07 12:10:14 +02:00
• 185b974d13 Adds a JSON output format Eric Coissac 2023-11-07 11:56:49 +02:00
• 61c30f9b6a Patch rev complement and first implementation of --auto in obicsv Eric Coissac 2023-11-07 09:37:07 +02:00
• 6a6a6f6f2c Correctly handle empty files Eric Coissac 2023-10-16 15:34:06 +02:00
• e8c55a2b6b optimize sequence readers and patch a bug in the format guesser Eric Coissac 2023-10-13 21:52:57 +02:00
• ddf0f2cede Add the -D (--delta) option to obipcr Eric Coissac 2023-10-13 17:04:10 +02:00
• 157c26cdc7 Patch a bug in the fasta and fastq readers Eric Coissac 2023-10-13 14:21:27 +02:00
• 6acce603a1 Patch a bug in the new version of setDefinition() Eric Coissac 2023-10-05 07:48:47 +02:00
• 0a8f7afb2a Patch sequence writers to remove definition from header when json format is used. Eric 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 Eric Coissac 2023-10-05 07:21:12 +02:00
• 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