 coissac
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c94b2974fb
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Reorganization of the documentation book directory
Former-commit-id: 095acaf9c8649b0e527c6253dc79330feedac865
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2023-02-23 23:41:24 +01:00 |
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coissac
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072b85e155
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change the model for representing paired reads and extend its usage to other commands
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2023-02-23 23:35:58 +01:00 |
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coissac
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ebb05fcdf7
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code refactoring. Prefix function name having behaviour depending on command line option by the prefix CLI
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2023-02-23 23:32:59 +01:00 |
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coissac
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a0ab14c205
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Complete the documentation and add a Release note file
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2023-02-18 19:54:21 +01:00 |
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coissac
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56722895e4
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Adds to every obitools the ability to save in gzip compressed files
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2023-02-18 12:06:52 +01:00 |
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coissac
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1a08ad4254
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Flush the buffered io
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2023-02-18 07:23:14 +01:00 |
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coissac
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3e1f88b37b
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adds the subspc function to the gval language
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2023-02-17 23:10:43 +01:00 |
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coissac
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d04eb915b3
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adds a directory option to obidistribute
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2023-02-17 22:52:53 +01:00 |
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coissac
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9554a32490
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Add capacity to obidistribute to save gzipped files
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2023-02-17 12:52:19 +01:00 |
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coissac
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6fd426d8be
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Update obiapat.c
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2023-02-17 11:29:27 +01:00 |
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coissac
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9cf9d4d504
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Update obiapat.c by removing dependancy to asprintf by using snprintf
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2023-02-17 11:28:14 +01:00 |
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coissac
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8458c0cd8b
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Patch a bug in the genbank reader for the sequence longer than 10kb.
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2023-02-17 10:54:03 +01:00 |
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coissac
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ed87f821eb
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adds the _taxid suffix to the rank taxid attributes.
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2023-02-16 16:13:55 +01:00 |
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coissac
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2975042982
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Adds the possiblility to append to files to obidistribute
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2023-02-16 16:13:13 +01:00 |
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coissac
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85349668d0
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Add some options to obiannotate
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2023-02-16 13:32:27 +01:00 |
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coissac
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6e36b22040
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Normalise the managment of speed measure
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2023-02-16 13:31:49 +01:00 |
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coissac
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f56363a100
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Patch an embl/genbank parser error
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2023-02-16 13:30:42 +01:00 |
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coissac
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08521c74e2
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Adds Aho-Corasick matching to obiannotate
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2023-02-09 15:59:11 +01:00 |
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coissac
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8b70b1a5d8
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Last bug on sequence writing
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2023-02-08 13:56:50 +01:00 |
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coissac
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526bf79c7f
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Patch for some lost of data during sequence writing
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2023-02-08 13:14:26 +01:00 |
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coissac
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4117cbdd08
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Stabilize the obipairing output. whant run twice on the same dataset results are identical
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2023-02-05 11:06:31 +01:00 |
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coissac
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a6af0abdd8
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Documentation writting
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2023-02-03 23:00:23 +01:00 |
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coissac
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14a4522a07
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site wed
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2023-02-02 23:47:22 +01:00 |
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coissac
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99be9dd5fd
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Update .gitlab-ci.yml
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2023-02-02 23:36:13 +01:00 |
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coissac
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61ba3bd648
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Add new directory
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2023-02-02 23:30:04 +01:00 |
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coissac
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36e6a3edef
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Add new file
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2023-02-02 23:29:04 +01:00 |
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coissac
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7756aebab1
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more doc
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2023-02-02 23:11:08 +01:00 |
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coissac
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2002299b7f
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reorder some edits
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2023-02-02 23:09:16 +01:00 |
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coissac
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060f7db082
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Adds code for the --length option of obiannotate
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2023-02-02 17:15:06 +01:00 |
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coissac
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5639a09fb9
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Add the --with-taxon-at-rank option code to obiannotate
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2023-02-02 16:36:32 +01:00 |
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coissac
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886c5118e3
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install script with options of install directory and command prefix
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2023-02-02 13:37:27 +01:00 |
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coissac
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a1fbaed6e9
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install script with options of install directory and command prefix
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2023-02-02 13:36:55 +01:00 |
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coissac
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f0a2744435
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install script with options of install directory and command prefix
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2023-02-02 13:23:16 +01:00 |
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coissac
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49e4cefd5b
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install script with options of install directory and command prefix
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2023-02-02 13:15:59 +01:00 |
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coissac
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5dbf8d6203
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remove the g prefix by default
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2023-02-02 13:11:04 +01:00 |
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coissac
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2cb3542d30
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adds installation instructions
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2023-02-02 12:42:44 +01:00 |
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coissac
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994da5d710
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adds installation instructions
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2023-02-02 12:41:30 +01:00 |
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coissac
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822e584f9a
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install script with options of install directory and command prefix
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2023-02-02 12:21:49 +01:00 |
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coissac
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ab0c93d303
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install script with options of install directory and command prefix
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2023-02-02 12:18:04 +01:00 |
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coissac
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c0df4357dd
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install script with options of install directory and command prefix
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2023-02-02 12:16:56 +01:00 |
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coissac
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03b124f400
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Patch a bug in MamberSub for primers longer than 32
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2023-02-01 16:23:14 +01:00 |
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coissac
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7c44243032
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Change the URL of the obitools repository
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2023-02-01 08:34:25 +01:00 |
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coissac
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e3d4da2859
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small things...
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2023-02-01 08:14:29 +01:00 |
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coissac
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3a151fc0a0
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updated gitignire
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2023-01-31 23:14:33 +01:00 |
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coissac
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871f22b83d
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Latest version of the doc in HTML
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2023-01-31 23:04:28 +01:00 |
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coissac
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fa6853fca1
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Comment profiling code
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2023-01-31 22:39:34 +01:00 |
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coissac
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e5835310cc
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Simplify code of the JSON header formater
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2023-01-31 17:16:55 +01:00 |
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coissac
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57c7187e6d
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Patch the JSON header formater
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2023-01-31 17:15:10 +01:00 |
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coissac
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9f98075510
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Patched version of install script
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2023-01-27 14:50:45 +01:00 |
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coissac
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f74c0bd517
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First prelease of obiannotate
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2023-01-27 11:35:39 +01:00 |
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coissac
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39b47a32bf
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Complement on the doc
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2023-01-27 10:49:28 +01:00 |
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coissac
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cfddc78161
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Patch an aligment bug on obipairing
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2023-01-25 13:22:56 +01:00 |
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coissac
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9b7edf0908
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Add an install script to help in installing obitools 4 on Linux or MacOS computers
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2023-01-23 15:44:23 +01:00 |
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coissac
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2d375df94f
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move the worker class to the obiseq package
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2023-01-22 22:39:13 +01:00 |
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coissac
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f97f92df72
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rename the iterator class
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2023-01-22 22:04:17 +01:00 |
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coissac
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4592855095
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Adds the new version of the doc as a quarto book
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2023-01-17 19:06:14 +01:00 |
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coissac
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f873645e8e
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Remove old bookdown version of the documentation
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2023-01-17 19:02:27 +01:00 |
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coissac
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20b16c0ba1
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Force sequence reading to produce lowercase sequences.
Adds two columns to the obiclean ratio csv file
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2022-11-22 15:06:09 +01:00 |
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coissac
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f4daa7f97f
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Modify the gitignore
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2022-11-17 12:05:11 +01:00 |
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coissac
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95b28a6612
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Beginning of the documentation
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2022-11-17 11:16:12 +01:00 |
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coissac
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29563aa94e
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Rename the Length methods Len to follow GO standart
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2022-11-17 11:09:58 +01:00 |
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coissac
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eb32089305
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Refactoring related to iterators
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2022-11-16 17:13:40 +01:00 |
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coissac
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09fc426b67
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Refactoring related to iterators
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2022-11-16 17:13:03 +01:00 |
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coissac
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6f853da9df
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Remove single sequence ierators. Only batch iterators persist
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2022-11-16 10:58:59 +01:00 |
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coissac
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f674200a6e
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FastLCS with maxError=-1 is equivalent to FullLCS.
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2022-11-16 09:57:36 +01:00 |
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coissac
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4375dbd9bb
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Switxh alignment to the new LCS method and make a copy of the sequences before annotating them to prevent concurrent map access bug
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2022-11-16 09:27:04 +01:00 |
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coissac
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18447e66a7
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Patch a critical bug into the CopySlice function.
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2022-11-16 09:24:17 +01:00 |
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coissac
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7f863fb383
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Prevens errors on FASTA formating an empty sequence
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2022-11-16 09:22:55 +01:00 |
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coissac
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493c7fddef
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Adds API documentation
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2022-11-16 09:21:54 +01:00 |
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coissac
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abe210d811
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Correct option alias name to remove dupplicate
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2022-11-15 08:58:41 +01:00 |
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coissac
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340579f6d7
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New version of LCS computation, with abug on alignment length patched patched
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2022-11-15 08:21:46 +01:00 |
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coissac
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18be4becec
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Add some new packages
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2022-11-14 14:36:04 +01:00 |
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coissac
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0f99f9a6ba
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First trial of a fastest LCS implementation
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2022-11-14 07:42:15 +01:00 |
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coissac
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6429f24c57
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Accellerate a bit LCS computation
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2022-10-27 17:30:55 +02:00 |
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coissac
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f3ddac0f50
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Small adjustment
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2022-10-27 11:18:44 +02:00 |
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coissac
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8aa323dad5
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Add a first version of obitag the successor of ecotag
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2022-10-26 13:16:56 +02:00 |
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coissac
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e17d1fbca6
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Patch the error message stored in sequences by obimultiplex
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2022-10-17 21:32:24 +02:00 |
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coissac
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f8df48338d
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Several bug in annotation management
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2022-10-12 23:01:47 +02:00 |
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coissac
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aae3398701
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Replace the CopyMap function by the MustFillMap and adds a InterfaceToIntMap function
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2022-10-12 22:56:38 +02:00 |
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coissac
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58dbdd8698
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requires that father.count > son.count
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2022-10-05 09:53:56 +02:00 |
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coissac
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d9c18ab0b5
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Add a reverse complement worker
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2022-10-05 09:41:59 +02:00 |
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coissac
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935fc31982
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Adds the new obicomplement command
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2022-10-05 09:40:09 +02:00 |
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coissac
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7873b90902
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Patch a bug in obigrep...
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2022-10-02 20:52:26 +02:00 |
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coissac
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65210755cc
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Patch reading of annotation from stdin
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2022-09-29 14:48:05 +02:00 |
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coissac
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d0f63fda56
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add functionalities to the expression
predicate evaluations
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2022-09-28 16:13:20 +02:00 |
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coissac
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fe5d8e3340
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Patch a bug in ngsfilter reading and sample matching
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2022-09-28 14:29:19 +02:00 |
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coissac
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ebefa28cc0
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Patch memory error related to []byte pool
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2022-09-28 14:28:37 +02:00 |
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coissac
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57ba460929
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add the obi_mutation attribute to the sequences
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2022-09-20 22:03:44 +02:00 |
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coissac
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da8e3fd7b7
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Correct the orientation of the mutation pattern
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2022-09-20 22:03:01 +02:00 |
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coissac
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49b4d97803
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Remove HTML escaping to json marshaling
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2022-09-20 22:01:52 +02:00 |
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coissac
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3cd8aabd83
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Correct some misspelling in option helps
Changes to be committed:
modified: pkg/obitools/obiclean/options.go
modified: pkg/obitools/obiconvert/options.go
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2022-09-20 21:59:38 +02:00 |
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coissac
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f6735a634e
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Correctly patch the memory leak related to the apatsequence
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2022-09-12 15:19:46 +02:00 |
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coissac
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448f5f83fa
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Patch a bug in comparison of attibutes during sequence annotation merging
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2022-09-08 07:50:17 +02:00 |
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coissac
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6b8f4490cf
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Change obiclean algorithm for a better evaluation of ratio
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2022-08-31 20:38:03 +02:00 |
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coissac
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90ba980de6
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correct the gml writer
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2022-08-30 10:28:05 +02:00 |
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coissac
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cd202ba72e
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Adds of new modules
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2022-08-23 15:09:51 +02:00 |
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coissac
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91c2ce551d
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Add new modules
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2022-08-23 15:09:03 +02:00 |
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coissac
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d04161a0fb
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small code refactoring
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2022-08-23 15:08:35 +02:00 |
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coissac
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d2f4919bc8
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comment out to option that need to be rethought
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2022-08-23 15:07:48 +02:00 |
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coissac
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989e678f6b
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refactor code and change algorithm used to read from many files
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2022-08-23 15:07:06 +02:00 |
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