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taxonomy

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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

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Release_4.4.5

Release_4.4.6

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• 40fb4e9767 reduce the memory impact of obiuniq. Eric Coissac 2024-11-27 13:30:16 +01:00
• d29a56dcbf Changes to be committed: modified: Release-notes.md modified: pkg/obialign/pairedendalign.go modified: pkg/obilua/obiseq.go modified: pkg/obioptions/version.go modified: pkg/obiseq/biosequence.go modified: pkg/obitools/obipairing/pairing.go Eric Coissac 2024-11-27 09:56:22 +01:00
• 69ef1758a2 obicsv debug Eric Coissac 2024-11-24 23:38:49 +01:00
• 3d06978808 a functional new version of obifind Eric Coissac 2024-11-24 19:33:24 +01:00
• 7884a74f9c Patch a bug in obitagpcr Eric Coissac 2024-11-18 21:10:47 +01:00
• 36327c79c8 Changes to be committed: modified: .gitignore new file: pkg/obitax/default_taxonomy.go modified: pkg/obitax/taxon.go modified: pkg/obitax/taxonnode.go modified: pkg/obitax/taxonomy.go modified: pkg/obitax/taxonset.go modified: pkg/obitax/taxonslice.go modified: pkg/obitools/obifind/iterator.go modified: pkg/obitools/obifind/options.go Eric Coissac 2024-11-16 10:01:49 +01:00
• f3d8707c08 Add default taxonomy Eric Coissac 2024-11-16 10:01:07 +01:00
• 7633fc4d23 update documentation Eric Coissac 2024-11-16 06:00:27 +01:00
• f5d79d0bc4 update api documentation Eric Coissac 2024-11-16 05:59:41 +01:00
• 03f4e88a17 Fisrt functional version Eric Coissac 2024-11-14 19:10:23 +01:00
• 9471fedfa1 Fisrt step in the obitax rewriting Eric Coissac 2024-11-08 09:48:16 +01:00
• 4b65bfce84 Changes to be committed: modified: pkg/obioptions/version.go modified: pkg/obitools/obitagpcr/pcrtag.go Eric Coissac 2024-11-04 14:30:17 +01:00
• fc75974c68 Changes to be committed: modified: pkg/obioptions/version.go modified: pkg/obitools/obitagpcr/options.go Eric Coissac 2024-11-04 13:25:52 +01:00
• 422f11cceb Changes to be committed: modified: pkg/obitools/obitagpcr/pcrtag.go Eric Coissac 2024-10-29 16:53:10 +01:00
• fefc360f80 Changes to be committed: modified: pkg/obioptions/version.go modified: pkg/obitools/obitagpcr/pcrtag.go modified: pkg/obiutils/abs.go new file: pkg/obiutils/abs_test.go Eric Coissac 2024-10-28 21:51:21 +01:00
• 3e00d39d47 In obimultiplex, patch a bug when no tag are associated to a primer. Eric Coissac 2024-10-22 14:12:20 +02:00
• 9e8a7fd9be Patch a bug in fastq reader Eric Coissac 2024-10-20 16:07:43 +02:00
• 74280e4704 Merge branch 'no-pools' Eric Coissac 2024-09-24 16:38:23 +02:00
• 7255c71576 commit version Eric Coissac 2024-09-24 16:36:59 +02:00
• 241f2286f2 remove the slice pool management Eric Coissac 2024-09-24 16:31:30 +02:00
• b37fc39ead switch to go version 1.23.1 Eric Coissac 2024-09-24 15:55:01 +02:00
• 2b4a633c30 EndGapFree alignments Eric Coissac 2024-09-24 15:52:12 +02:00
• 05bf2bfd6c Add option related to agrep match on obigrep and obiannotate Eric Coissac 2024-09-09 16:52:13 +02:00
• 65ae82622e correction of several small bugs Eric Coissac 2024-09-03 06:08:07 -03:00
• 373464cb06 On development genome skim tools Eric Coissac 2024-08-30 11:17:33 +02:00
• cd330db672 Add option to obimicrosat to control microsat length and orientation Eric Coissac 2024-08-30 11:16:43 +02:00
• 31bfc88eb9 Patch a bug on writing to stdout, and add clearer error on openning data files Eric Coissac 2024-08-13 09:45:28 +02:00
• bdb96dda94 Adds the obimicrosat command Eric Coissac 2024-08-05 15:31:20 +02:00
• 3f57935328 Adjust the size of the genbank and embl buffer size Eric Coissac 2024-08-05 11:32:37 +02:00
• 886b5d9a96 Optimize memory for readers and writers Eric Coissac 2024-08-05 10:48:28 +02:00
• f83032e643 Tag version Eric Coissac 2024-08-02 14:30:53 +02:00
• c0c18030c8 Adds information on the new github address Release_4.3.0 Eric Coissac 2024-08-02 14:26:20 +02:00
• 242f4d8f56 Realease notes Eric Coissac 2024-08-02 13:50:33 +02:00
• 1b1cd41fd3 Add some code refactoring from the blackboard branch Eric Coissac 2024-08-02 12:35:46 +02:00
• 6a2f867ae1 Factorize code between fasta and fastq writers blackboard Eric Coissac 2024-08-01 17:22:46 +02:00
• 776b8f75b7 Muspelling chunck -> chunk Eric Coissac 2024-08-01 16:43:23 +02:00
• 882cc82f23 Write results as a csv file Eric Coissac 2024-08-01 16:41:50 +02:00
• f36b39bfa3 First functional version of a blackboard and a blackboard based obicount Eric Coissac 2024-07-31 23:16:45 +02:00
• bc1aaaf7d9 New install script updated for github Eric Coissac 2024-07-29 14:35:21 +02:00
• dfe2fc3d43 Last changes on blackboard Eric Coissac 2024-07-29 11:25:54 +02:00
• 2247c3bc0a obitag xprize version Eric Coissac 2024-07-25 18:11:11 -04:00
• cba355cdde first blackboard Eric Coissac 2024-07-25 18:10:28 -04:00
• 67665a6b40 Xprize update Eric Coissac 2024-07-25 18:09:03 -04:00
• 4e4fac491f Fisrt versin of the two levels indexing Eric Coissac 2024-07-12 15:17:48 +02:00
• 42c5881ddc some cleanning on the new tools Eric Coissac 2024-07-11 10:46:11 +02:00
• c7ed47e110 first version of obidemerge, obijoin and a new filter for obicleandb but to be finnished Eric Coissac 2024-07-10 15:21:42 +02:00
• bd855c4965 Adds CSV as an input format Eric Coissac 2024-07-03 21:04:27 +02:00
• 5d9ac261ff correct an attribute name Eric Coissac 2024-07-01 17:44:18 +02:00
• fd663357b5 First version of obicleandb... Eric Coissac 2024-07-01 17:12:42 +02:00
• 0187a82c5f Patch a bug in obimultiplex loosing sequence with primer dimer Eric Coissac 2024-06-30 17:42:28 +02:00
• 154753de90 Same bug but for fastq sequence writing only Eric Coissac 2024-06-26 18:46:47 +02:00
• e40d0bfbe7 Debug fasta and fastq writer when the first sequence is hudge Eric Coissac 2024-06-26 18:39:42 +02:00
• 1835cb2cf3 remove sonic which only works on AMD64 Eric Coissac 2024-06-24 14:53:18 +02:00
• c1f03cb1f6 Switch to faster json library go-json and sonic Eric Coissac 2024-06-23 00:36:08 +02:00
• 93f9dcb95f Reducing memory allocation events Eric Coissac 2024-06-22 22:32:31 +02:00
• e6b87ecd02 Reduce memory allocation events Eric Coissac 2024-06-22 21:01:53 +02:00
• 54a138196c Patch a bug in fasta and fastq reading Eric Coissac 2024-06-21 14:28:57 +02:00
• 818ce87bab Patch some bugs in writing files Eric Coissac 2024-06-19 13:15:30 +02:00
• 73996bb0b7 Small change in consensus weight Eric Coissac 2024-06-19 09:11:59 +02:00
• a812fe8b72 debug of obimultiplex Eric Coissac 2024-06-18 23:38:33 +02:00
• 44533fb61e Bugs in the non stric tag matching algorithm Eric Coissac 2024-06-10 21:19:26 +02:00
• 2d4813614b Update the release Notes Eric Coissac 2024-06-07 09:11:06 +02:00
• 3a7661f324 obimultiplex2 in now obimultiplex Eric Coissac 2024-06-07 09:04:37 +02:00
• bc12b1aaa2 Add a complete documented example of the new obitag format Eric Coissac 2024-06-06 23:44:23 +02:00
• e47b50de7f Patch a bug in seting of the tag delimiter with an upper case Eric Coissac 2024-06-06 23:25:16 +02:00
• 1b43fa4247 First complete version of obimultiplex2 Eric Coissac 2024-06-06 23:11:13 +02:00
• 985c91452a correction of bug and format in obisplit Eric Coissac 2024-06-05 17:18:44 +02:00
• 87a7219ab4 Adds the reading of the options through the csv formated ngsfilter configuration file Eric Coissac 2024-06-04 22:57:07 +02:00
• c8ad96f5e6 First fonctionnal version with fixed tag length and strict matching Eric Coissac 2024-06-04 21:46:09 +02:00
• a0a9fb461c trial on rewriting obimultiplex Eric Coissac 2024-06-04 16:50:07 +02:00
• 65f5109957 Plenty of small bugs Eric Coissac 2024-06-04 16:49:12 +02:00
• e843d2aa5c Patch a tricky bug in parsing of json header and save the last sequence from files Eric Coissac 2024-06-04 13:46:23 +02:00
• aa42df326a Correct a bug in the fastq reader affecting the quality of the last record of each chunk Eric Coissac 2024-06-04 11:57:16 +02:00
• 411124d1b3 Add automatic rules to manage version number Eric Coissac 2024-06-01 17:26:16 +02:00
• 38945d0a41 Adds the --template option to obimultiplex Eric Coissac 2024-05-31 11:34:06 +02:00
• 4487723d14 Adds possibility to provide the ngsfilter configuration as a CSV file Eric Coissac 2024-05-31 11:08:20 +02:00
• dbeb44bc79 Patch a bug in the quality string writing Eric Coissac 2024-05-31 11:07:25 +02:00
• 3e1d9a41ec Adds more format checking during fasta parsing Eric Coissac 2024-05-30 18:12:06 +02:00
• dd9307a4cd Swich to the system min and max functions and remove the version from obiutils Eric Coissac 2024-05-30 08:27:24 +02:00
• 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