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Release_4.3.0

Release_4.4.0

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• 21819cd41e Add some geometry data to the GML edges Eric Coissac 2023-03-28 11:43:46 +07:00
• bc82422bc5 Reduce redundante call to bytes.ToLower and substitute the last call by an home made version doing the conversion in place Eric Coissac 2023-03-28 11:43:04 +07:00
• e8a8f746d3 few bug in the graph algorithm Eric Coissac 2023-03-27 22:43:45 +07:00
• 245230ae12 A small correction Eric Coissac 2023-03-27 19:51:38 +07:00
• a33e471b39 First attempt for obiconsensus... The graph traversing algorithm is too simple Eric Coissac 2023-03-27 19:51:10 +07:00
• d5e84ec676 rename goutils to obiutils Eric Coissac 2023-03-24 10:25:12 +07:00
• 42aae88520 complete the correction related to the tag detection Eric Coissac 2023-03-23 11:52:08 +07:00
• 57474214e7 Patch excessive log in obimultiplex and an error in detecting the tag. Eric Coissac 2023-03-23 11:40:24 +07:00
• 98eac2360c adds a rule to update packages and push the corresponding updates module files Eric Coissac 2023-03-21 22:02:18 +07:00
• 7ed567fbad Make the --help or -h options working when mandatory options are declared Eric Coissac 2023-03-21 22:01:20 +07:00
• d09011fac2 Finalyse the obimultiplex with indels Eric Coissac 2023-03-21 22:01:02 +07:00
• 27d6c60e25 Add the possibility to look for patterns allowing indels. Eric Coissac 2023-03-20 15:28:24 +07:00
• 5fbe52368c Patch the empty batch bug Eric Coissac 2023-03-07 20:16:06 +07:00
• 1e7756ec91 Add comment on release notes Eric Coissac 2023-03-07 17:36:35 +07:00
• 9a48614a9b Merge branch 'master' of git.metabarcoding.org:obitools/obitools4/obitools4 Eric Coissac 2023-03-07 17:34:34 +07:00
• b3922c3896 Produce less weird crash on non existing files Eric Coissac 2023-03-07 17:34:25 +07:00
• 42cf8cea73 Update README.md Eric Coissac 2023-03-07 05:50:19 +01:00
• 7b4249b775 Update README.md Eric Coissac 2023-03-07 05:48:50 +01:00
• fbfed52508 Tag realease 4.0.1 in release notes Eric Coissac 2023-03-07 11:15:06 +07:00
• bb0282b6a1 Progress on the development Eric Coissac 2023-03-07 11:13:25 +07:00
• d4b185b716 Adds some new dependencies Eric Coissac 2023-03-07 11:12:39 +07:00
• d88de15cdc Refactoring codes for removing buffer size options. An some other changes... Eric Coissac 2023-03-07 11:12:13 +07:00
• 9811e440b8 Takes into account the option parsing errors Eric Coissac 2023-03-07 11:06:08 +07:00
• 6b52dc0700 Correct the Makefile for a default rule Eric Coissac 2023-03-02 20:48:55 +07:00
• b9bf88d4df Adds some new columns to the ratio file. Eric Coissac 2023-02-25 15:56:23 +01:00
• 6f28d2ab68 Patch a bug introduced by the new model for paired sequences Eric Coissac 2023-02-24 10:23:26 +01:00
• 6ce3053409 Merge branch 'master' of git.metabarcoding.org:obitools/obitools4/obitools4 Eric Coissac 2023-02-23 23:50:57 +01:00
• 6c5fc8f65b Save change in various files Eric Coissac 2023-02-23 23:45:41 +01:00
• 05323f960c Start writing of the man pages Eric Coissac 2023-02-23 23:43:54 +01:00
• c94b2974fb Reorganization of the documentation book directory Eric Coissac 2023-02-23 23:41:24 +01:00
• 072b85e155 change the model for representing paired reads and extend its usage to other commands Eric Coissac 2023-02-23 23:35:58 +01:00
• ebb05fcdf7 code refactoring. Prefix function name having behaviour depending on command line option by the prefix CLI Eric Coissac 2023-02-23 23:32:59 +01:00
• 0b8f35cbf6 Update Release-notes.md Eric Coissac 2023-02-18 19:57:21 +01:00
• a0ab14c205 Complete the documentation and add a Release note file Eric Coissac 2023-02-18 19:54:21 +01:00
• 56722895e4 Adds to every obitools the ability to save in gzip compressed files Eric Coissac 2023-02-18 12:06:52 +01:00
• 1a08ad4254 Flush the buffered io Eric Coissac 2023-02-18 07:23:14 +01:00
• 3e1f88b37b adds the subspc function to the gval language Eric Coissac 2023-02-17 23:10:43 +01:00
• d04eb915b3 adds a directory option to obidistribute Eric Coissac 2023-02-17 22:52:53 +01:00
• 9554a32490 Add capacity to obidistribute to save gzipped files Eric Coissac 2023-02-17 12:52:19 +01:00
• 6fd426d8be Update obiapat.c Eric Coissac 2023-02-17 11:29:27 +01:00
• 9cf9d4d504 Update obiapat.c by removing dependancy to asprintf by using snprintf Eric Coissac 2023-02-17 11:28:14 +01:00
• 8458c0cd8b Patch a bug in the genbank reader for the sequence longer than 10kb. Eric Coissac 2023-02-17 10:54:03 +01:00
• ed87f821eb adds the _taxid suffix to the rank taxid attributes. Eric Coissac 2023-02-16 16:13:55 +01:00
• 2975042982 Adds the possiblility to append to files to obidistribute Eric Coissac 2023-02-16 16:13:13 +01:00
• 85349668d0 Add some options to obiannotate Eric Coissac 2023-02-16 13:32:27 +01:00
• 6e36b22040 Normalise the managment of speed measure Eric Coissac 2023-02-16 13:31:49 +01:00
• f56363a100 Patch an embl/genbank parser error Eric Coissac 2023-02-16 13:30:42 +01:00
• 08521c74e2 Adds Aho-Corasick matching to obiannotate Eric Coissac 2023-02-09 15:59:11 +01:00
• 8b70b1a5d8 Last bug on sequence writing Eric Coissac 2023-02-08 13:56:50 +01:00
• 526bf79c7f Patch for some lost of data during sequence writing Eric Coissac 2023-02-08 13:14:26 +01:00
• 4117cbdd08 Stabilize the obipairing output. whant run twice on the same dataset results are identical Eric Coissac 2023-02-05 11:06:31 +01:00
• a6af0abdd8 Documentation writting Eric Coissac 2023-02-03 23:00:23 +01:00
• 14a4522a07 site wed Eric Coissac 2023-02-02 23:47:22 +01:00
• 99be9dd5fd Update .gitlab-ci.yml Eric Coissac 2023-02-02 23:36:13 +01:00
• 61ba3bd648 Add new directory Eric Coissac 2023-02-02 23:30:04 +01:00
• 36e6a3edef Add new file Eric Coissac 2023-02-02 23:29:04 +01:00
• 7756aebab1 more doc Eric Coissac 2023-02-02 23:11:08 +01:00
• 2002299b7f reorder some edits Eric Coissac 2023-02-02 23:09:16 +01:00
• 060f7db082 Adds code for the --length option of obiannotate Eric Coissac 2023-02-02 17:15:06 +01:00
• 5639a09fb9 Add the --with-taxon-at-rank option code to obiannotate Eric Coissac 2023-02-02 16:36:32 +01:00
• 886c5118e3 install script with options of install directory and command prefix Eric Coissac 2023-02-02 13:37:27 +01:00
• a1fbaed6e9 install script with options of install directory and command prefix Eric Coissac 2023-02-02 13:36:55 +01:00
• f0a2744435 install script with options of install directory and command prefix Eric Coissac 2023-02-02 13:23:16 +01:00
• 49e4cefd5b install script with options of install directory and command prefix Eric Coissac 2023-02-02 13:15:59 +01:00
• 5dbf8d6203 remove the g prefix by default Eric Coissac 2023-02-02 13:11:04 +01:00
• 2cb3542d30 adds installation instructions Eric Coissac 2023-02-02 12:42:44 +01:00
• 994da5d710 adds installation instructions Eric Coissac 2023-02-02 12:41:30 +01:00
• 822e584f9a install script with options of install directory and command prefix Eric Coissac 2023-02-02 12:21:49 +01:00
• ab0c93d303 install script with options of install directory and command prefix Eric Coissac 2023-02-02 12:18:04 +01:00
• c0df4357dd install script with options of install directory and command prefix Eric Coissac 2023-02-02 12:16:56 +01:00
• 03b124f400 Patch a bug in MamberSub for primers longer than 32 Eric Coissac 2023-02-01 16:23:14 +01:00
• 7c44243032 Change the URL of the obitools repository Eric Coissac 2023-02-01 08:34:25 +01:00
• e3d4da2859 small things... Eric Coissac 2023-02-01 08:14:29 +01:00
• 3a151fc0a0 updated gitignire Eric Coissac 2023-01-31 23:14:33 +01:00
• 871f22b83d Latest version of the doc in HTML Eric Coissac 2023-01-31 23:04:28 +01:00
• fa6853fca1 Comment profiling code Eric Coissac 2023-01-31 22:39:34 +01:00
• e5835310cc Simplify code of the JSON header formater Eric Coissac 2023-01-31 17:16:55 +01:00
• 57c7187e6d Patch the JSON header formater Eric Coissac 2023-01-31 17:15:10 +01:00
• 9f98075510 Patched version of install script Eric Coissac 2023-01-27 14:50:45 +01:00
• f74c0bd517 First prelease of obiannotate Eric Coissac 2023-01-27 11:35:39 +01:00
• 39b47a32bf Complement on the doc Eric Coissac 2023-01-27 10:49:28 +01:00
• cfddc78161 Patch an aligment bug on obipairing Eric Coissac 2023-01-25 13:22:56 +01:00
• 9b7edf0908 Add an install script to help in installing obitools 4 on Linux or MacOS computers Eric Coissac 2023-01-23 15:44:23 +01:00
• 2d375df94f move the worker class to the obiseq package Eric Coissac 2023-01-22 22:39:13 +01:00
• f97f92df72 rename the iterator class Eric Coissac 2023-01-22 22:04:17 +01:00
• 4592855095 Adds the new version of the doc as a quarto book Eric Coissac 2023-01-17 19:06:14 +01:00
• f873645e8e Remove old bookdown version of the documentation Eric Coissac 2023-01-17 19:02:27 +01:00
• 20b16c0ba1 Force sequence reading to produce lowercase sequences. Adds two columns to the obiclean ratio csv file Eric Coissac 2022-11-22 15:06:09 +01:00
• f4daa7f97f Modify the gitignore Eric Coissac 2022-11-17 12:05:11 +01:00
• 95b28a6612 Beginning of the documentation Eric Coissac 2022-11-17 11:16:12 +01:00
• 29563aa94e Rename the Length methods Len to follow GO standart Eric Coissac 2022-11-17 11:09:58 +01:00
• eb32089305 Refactoring related to iterators Eric Coissac 2022-11-16 17:13:40 +01:00
• 09fc426b67 Refactoring related to iterators Eric Coissac 2022-11-16 17:13:03 +01:00
• 6f853da9df Remove single sequence ierators. Only batch iterators persist Eric Coissac 2022-11-16 10:58:59 +01:00
• f674200a6e FastLCS with maxError=-1 is equivalent to FullLCS. Eric Coissac 2022-11-16 09:57:36 +01:00
• 4375dbd9bb Switxh alignment to the new LCS method and make a copy of the sequences before annotating them to prevent concurrent map access bug Eric Coissac 2022-11-16 09:27:04 +01:00
• 18447e66a7 Patch a critical bug into the CopySlice function. Eric Coissac 2022-11-16 09:24:17 +01:00
• 7f863fb383 Prevens errors on FASTA formating an empty sequence Eric Coissac 2022-11-16 09:22:55 +01:00
• 493c7fddef Adds API documentation Eric Coissac 2022-11-16 09:21:54 +01:00
• abe210d811 Correct option alias name to remove dupplicate Eric Coissac 2022-11-15 08:58:41 +01:00