obitools4

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Release_4.3.0

Release_4.4.0

Release_4.4.10

Release_4.4.11

Release_4.4.12

Release_4.4.13

Release_4.4.14

Release_4.4.15

Release_4.4.16

Release_4.4.17

Release_4.4.18

Release_4.4.19

Release_4.4.20

Release_4.4.21

Release_4.4.22

Release_4.4.23

Release_4.4.24

Release_4.4.25

Release_4.4.26

Release_4.4.27

Release_4.4.28

Release_4.4.29

Release_4.4.5

Release_4.4.6

Release_4.4.7

Release_4.4.8

Release_4.4.9

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
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

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