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V4.3

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microasm

taxonomy

Release_4.3.0

Release_4.4.0

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• 98b3bc2a8c Patch a bug on the reading of each last sequence of a chunck in the fasta reader Eric Coissac 2024-05-27 10:17:17 +02:00
• d249902073 A lot of changes and debug... A complete first version of the recipy in the Cookbook about avaluating primers Eric Coissac 2024-05-26 12:56:29 +02:00
• 55ce36f329 Update of obipcr and homogenization of logging Eric Coissac 2024-05-16 15:18:30 +02:00
• 61be8a55b1 Merge obiminion and obiconsensus Eric Coissac 2024-05-14 17:53:32 +02:00
• 7fcb0538a3 Cleaning of obiminion Eric Coissac 2024-05-14 11:45:46 +02:00
• 017030bcce Add obiminion first version Eric Coissac 2024-05-14 08:16:12 +02:00
• 9e63013bc2 Correction on obiformat of bug leading to partial parsing and add godocs Eric Coissac 2024-05-07 10:54:12 +02:00
• 5b98393a68 Refactor sequence file reading Eric Coissac 2024-05-01 00:50:23 +02:00
• 33d4d63acd Adds a warning on max-cpu = 1 Eric Coissac 2024-04-30 13:27:19 +02:00
• d30d736e48 Simplify the workers code by removing dupplicates Eric Coissac 2024-04-30 12:22:22 +02:00
• f37477b26c Progress bar are automagically disabled if stderr is redirected Eric Coissac 2024-04-22 12:23:59 +02:00
• 8f08959ebb Make the --no-progressbar option effective on graph building progress too. Eric Coissac 2024-04-22 12:01:43 +02:00
• df74b2b2bd Add a basic managment of obisequenceslice to obiscript Eric Coissac 2024-04-16 12:58:25 +02:00
• cb35612a6c new --version option and qualities method in obiscript Eric Coissac 2024-04-13 12:40:43 +02:00
• 0a2ea962db obitag bug Eric Coissac 2024-04-03 16:28:06 +02:00
• 3d1d9f32df Make obiconsensus using the count of the sequences Eric Coissac 2024-04-03 12:58:32 +02:00
• d68210ef94 Tag version 4.2.0 Eric Coissac 2024-04-03 12:57:00 +02:00
• bf41d16e67 Patch a bug in obitag on the identification of the best match Eric Coissac 2024-04-03 12:30:40 +02:00
• e25c3b7365 Bug in the json parsing Eric Coissac 2024-03-19 13:50:13 +01:00
• 11a14b6dc8 Parse correctly json header when a curly brace is included in a string. Eric Coissac 2024-03-19 13:47:03 +01:00
• b428c48353 Obitag, allow for reference sequences with bad taxid, which are discarded with the emission of a warning Eric Coissac 2024-03-18 19:11:41 +01:00
• aa07ef2127 adds a obisplit_nfrg attribute Eric Coissac 2024-03-13 10:41:53 +01:00
• 6758ee6a8a Patch conversion from lua table to go slice or map Eric Coissac 2024-03-12 17:18:29 +01:00
• f4d71d4a66 Patch a bug in the subseq and revcomplement methods. That patchs the bug in the option -c of obipcr Eric Coissac 2024-03-11 10:54:37 +01:00
• 8a2bbd1c3b Patch a bug in the genbank reader when reading CONTIG entries Eric Coissac 2024-03-11 10:53:25 +01:00
• 65933ca031 A working version of obiscript Eric Coissac 2024-03-08 21:39:05 +01:00
• b40015deb7 first preliminary version of obiscript. Eric Coissac 2024-03-06 12:56:44 -03:00
• b4afd784dc few small correction Eric Coissac 2024-03-06 12:52:22 -03:00
• 7bd073ccd4 First version of obisplit and patch a bug in the new workers API Eric Coissac 2024-03-03 11:16:24 -04:00
• 0f3871d203 Change the API of workers Eric Coissac 2024-03-02 16:03:46 -04:00
• 4a0b20484f Add the --taxonomic-path option to obiannotate Eric Coissac 2024-02-27 20:10:26 +01:00
• 4127ddb26f .gitignore Eric Coissac 2024-02-27 07:29:14 +01:00
• c9fe6f6ebf Make some correction on genbank/embl parser Eric Coissac 2024-02-27 07:28:56 +01:00
• 38c49e9f38 Switch GOPATH to the local directory in Makefile Eric Coissac 2024-02-27 07:22:57 +01:00
• 1542ce4c63 Work on EMBL and Genbank parser efficienct Eric Coissac 2024-02-20 13:23:07 +01:00
• 95caebec8f update modules Eric Coissac 2024-02-16 18:12:59 +01:00
• c1d9bea6bb Release 4.1.2 Eric Coissac 2024-02-16 18:05:08 +01:00
• 54ec09037e Patch a genbank & embl parsing error. Eric Coissac 2024-02-16 15:20:37 +01:00
• 69b4d9ed20 Patch e bug in the ngsfilter library when match with indel are at the extremities Eric Coissac 2024-02-01 09:54:34 +01:00
• 6cc5c44a32 Correct the bug in embl reader Eric Coissac 2024-01-31 15:50:14 +01:00
• 23758b00f6 Patch a bug in the embl reader and adds some doc Eric Coissac 2024-01-31 15:43:02 +01:00
• f2f7b4574e update the geometric obitag Eric Coissac 2024-01-17 23:38:51 +01:00
• 13cfebd737 some more cleaning Eric Coissac 2024-01-16 21:11:38 +01:00
• 3c48bafab0 patch a low level bug in EnsureCapacity Eric Coissac 2024-01-16 20:51:45 +01:00
• 6fca03227a Archive cleaning Eric Coissac 2024-01-04 14:27:33 +01:00
• 5b57139450 Reduce doc size Eric Coissac 2024-01-04 14:17:44 +01:00
• 74854fa65c remove bade files Eric Coissac 2024-01-04 09:11:00 +01:00
• 344de1d494 remove bad files Eric Coissac 2024-01-04 09:09:26 +01:00
• ff54ef93d8 remove bad files Eric Coissac 2024-01-04 09:05:44 +01:00
• 43728146bb remove bad files Eric Coissac 2024-01-04 09:04:12 +01:00
• 0a62e39ee0 remove wrongly pushed files Eric Coissac 2024-01-04 09:00:21 +01:00
• e3938c7ba0 Update release date Eric Coissac 2023-12-20 10:06:17 +01:00
• 1a0ca8c847 Tags release 4.1.1 Eric Coissac 2023-12-20 10:02:40 +01:00
• a36e830de3 homogenize worker count Eric Coissac 2023-12-20 08:14:07 +01:00
• 7a31d5b07b Adds some more error controle on taxonomy reading Eric Coissac 2023-12-14 09:17:46 +01:00
• b9a7961c91 Add more error checks on taxonomy reading Eric Coissac 2023-12-14 08:09:06 +01:00
• 2caaa62485 Implements the kmeans++ algo to select the landmarks in the geometric method Eric Coissac 2023-12-11 16:07:03 +01:00
• 37c3e16d5d Adds the option --pairing-scale to obipairing Eric Coissac 2023-12-07 12:28:16 +01:00
• 008f33aee4 Adds a better detection of invalid format of ngsfilter files Eric Coissac 2023-12-07 10:47:34 +01:00
• 0f8066d367 many changes ;-) Eric Coissac 2023-12-05 15:28:29 +01:00
• 03bef6461d Complement to the documentation Eric Coissac 2023-12-04 13:16:34 +01:00
• eb351a7530 patch bug in worker Eric Coissac 2023-12-03 22:44:13 +01:00
• 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