obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2026-02-03 06:40:33 +00:00
Code Issues Packages Projects Releases Wiki Activity

Commit Graph

  • 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
  • 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