 coissac
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d5e84ec676
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rename goutils to obiutils
Former-commit-id: 2147f53db972bba571dfdae30c51b62d3e69cec5
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2023-03-24 10:25:12 +07:00 |
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coissac
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42aae88520
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complete the correction related to the tag detection
Former-commit-id: 98326fb0f27788de672cdbd686b32b4dc2615038
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2023-03-23 11:52:08 +07:00 |
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coissac
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57474214e7
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Patch excessive log in obimultiplex and an error in detecting the tag.
Former-commit-id: e6f427ac743cae373247a15bf49b0a27273b2569
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2023-03-23 11:40:24 +07:00 |
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coissac
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98eac2360c
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adds a rule to update packages and push the corresponding updates module files
Former-commit-id: 1ffa805e74571f9d970dcb185f187dd586c1a190
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2023-03-21 22:02:18 +07:00 |
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coissac
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7ed567fbad
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Make the --help or -h options working when mandatory options are declared
Former-commit-id: db502ff81dcf20449d126978fcebf890edb814ae
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2023-03-21 22:01:20 +07:00 |
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coissac
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d09011fac2
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Finalyse the obimultiplex with indels
Former-commit-id: cef0ac39dac0e02d16d4bd321966a0f8a67f2c85
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2023-03-21 22:01:02 +07:00 |
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coissac
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27d6c60e25
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Add the possibility to look for patterns allowing indels.
Former-commit-id: 0599c2b0ad16df086dbdb08e491503870d8904be
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2023-03-20 15:28:24 +07:00 |
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coissac
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5fbe52368c
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Patch the empty batch bug
Former-commit-id: fcee04b58f2c4a0bf2c27792f991391c0b6ce78e
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2023-03-07 20:16:06 +07:00 |
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coissac
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1e7756ec91
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Add comment on release notes
Former-commit-id: 79bc0a68e46c92cfac60d1cf25604a1bcba0ba34
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2023-03-07 17:36:35 +07:00 |
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coissac
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9a48614a9b
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Merge branch 'master' of git.metabarcoding.org:obitools/obitools4/obitools4
Former-commit-id: 45c52be778d3d5c61db438c18c38a85171be86cd
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2023-03-07 17:34:34 +07:00 |
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coissac
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b3922c3896
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Produce less weird crash on non existing files
Former-commit-id: 74bb27bd53c685be530632994bd2ba24c1f362e1
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2023-03-07 17:34:25 +07:00 |
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coissac
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42cf8cea73
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Update README.md
Former-commit-id: c2d9f79cceb8f059f65a417bea5041fc2abc362b
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2023-03-07 05:50:19 +01:00 |
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coissac
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7b4249b775
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Update README.md
Former-commit-id: 544600322dd3c4465bf02d99ea76c802529b9aed
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2023-03-07 05:48:50 +01:00 |
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coissac
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fbfed52508
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Tag realease 4.0.1 in release notes
Former-commit-id: 55d009baf1b975c2da397a93406d132c8a52cdd6
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2023-03-07 11:15:06 +07:00 |
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coissac
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bb0282b6a1
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Progress on the development
Former-commit-id: a8aa6fd60480d4453838d6846a08c84dd5a2f1d9
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2023-03-07 11:13:25 +07:00 |
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coissac
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d4b185b716
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Adds some new dependencies
Former-commit-id: 2f31ea6f852651e1ffca1d9ce78b17bddd26f2bb
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2023-03-07 11:12:39 +07:00 |
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coissac
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d88de15cdc
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Refactoring codes for removing buffer size options. An some other changes...
Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce
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2023-03-07 11:12:13 +07:00 |
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coissac
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9811e440b8
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Takes into account the option parsing errors
Former-commit-id: d0b3ed0b96a72f79f887df8fbc325427e63d7a73
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2023-03-07 11:06:08 +07:00 |
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coissac
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6b52dc0700
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Correct the Makefile for a default rule
Former-commit-id: 7ac32f3f9778842fecd65cdd796b81f61b7fa41f
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2023-03-02 20:48:55 +07:00 |
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coissac
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b9bf88d4df
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Adds some new columns to the ratio file.
Former-commit-id: 1b2d6116622b754670e86b683077aceac2db4ce7
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2023-02-25 15:56:23 +01:00 |
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coissac
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6f28d2ab68
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Patch a bug introduced by the new model for paired sequences
Former-commit-id: 7947e28ac8252b7ed46bdb9175077d412bad0aca
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2023-02-24 10:23:26 +01:00 |
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coissac
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6ce3053409
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Merge branch 'master' of git.metabarcoding.org:obitools/obitools4/obitools4
Former-commit-id: 042e2300185f1b399cc19ea4d710a7cb15cb015f
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2023-02-23 23:50:57 +01:00 |
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coissac
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6c5fc8f65b
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Save change in various files
Former-commit-id: 428f8ee77c584b79cc2ef45eef2902c3e0754c77
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2023-02-23 23:45:41 +01:00 |
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coissac
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05323f960c
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Start writing of the man pages
Former-commit-id: 533a8a6380a5a0b66314081a5ec2aeb973ebadec
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2023-02-23 23:43:54 +01:00 |
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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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0b8f35cbf6
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Update Release-notes.md
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2023-02-18 19:57:21 +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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