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e9574bae07
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Small change to increase efficiency (a little)
Former-commit-id: fa54c9bf82b8ba60653255ab2a5f671619dcfdcb
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2023-05-05 13:33:15 +02:00 |
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3778ae9266
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Correction a a bug and transfert of the new matching rules from obirefidx to obitag
Former-commit-id: a28540f72a504ad4e7e8a8b6f7609116913445b4
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2023-05-05 07:37:19 +02:00 |
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88a9e38952
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Took better advantage of taxonomy structure and LCA upperbound base on common word. Accelleration by a factor two of obirefidx compared to previous version.
Former-commit-id: 35f40498d642058e9dbff20128d11303a314018d
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2023-05-04 09:32:47 +02:00 |
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870cb1aabb
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New refdb indexing algorithm
Former-commit-id: 7ae480cec5d277a08620a2e666b5c9b69bb6cd73
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2023-05-03 15:32:31 +02:00 |
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bffcab1096
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Complete release notes and change obiannotate options accordingly
Former-commit-id: 947db1f4606d57893cf758df57a4c954e3949e6b
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2023-05-02 11:01:26 +02:00 |
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60c187404d
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Restore old obisort and add LCA functionnality to obiannotate.
Former-commit-id: aecaacc9dae49f74bd888a8eb8140822d31a42a6
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2023-05-02 10:43:22 +02:00 |
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e9dcacbf24
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Correction of one base deletion in the consensus
Former-commit-id: 6aabd8bfdb5263a2285718cb2eca27628c0e717c
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2023-04-19 09:12:12 +02:00 |
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9bac7f387a
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Patch a bug in the help messages
Former-commit-id: 61ffea65db66215c072139540ec19c11c52efbbc
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2023-04-17 11:32:10 +02:00 |
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71023423e6
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Add a new command obitagpcr able to tag reads according to their corresponding pcr samples
Former-commit-id: 1f34bf0a27d55afc3556efd64f6ccee6d2329aff
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2023-04-07 17:45:22 +02:00 |
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d70bb45f3f
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Small change in parallelisation tuning
Former-commit-id: 3fe2495b7fd86a0ba47dd87907323a457bae481a
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2023-04-05 14:15:47 +02:00 |
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84b3e4d097
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Reduce memomry inprint of obipcr
Former-commit-id: bd25be2d454f083c729346a828e27f07ad1a216e
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2023-03-31 10:53:53 +02:00 |
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4bf041be62
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Add some option to the obiconsensus command
Former-commit-id: cf30a404a4943e4527106c977b01712ef454e028
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2023-03-28 21:23:27 +07:00 |
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e8a8f746d3
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few bug in the graph algorithm
Former-commit-id: b61bdd9f671e2f5e90d32c1beac1ed84efa5e05c
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2023-03-27 22:43:45 +07:00 |
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a33e471b39
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First attempt for obiconsensus... The graph traversing algorithm is too simple
Former-commit-id: 0456e6c7fd55d6d0fcf9856c40386b976b912cba
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2023-03-27 19:51:10 +07:00 |
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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7756aebab1
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more doc
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2023-02-02 23:11:08 +01:00 |
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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f3ddac0f50
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Small adjustment
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2022-10-27 11:18:44 +02:00 |
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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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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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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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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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