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3a1cf4fe97
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Accelerate the speed of very long fasta sequences, and more generaly of every format
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2025-03-12 13:29:41 +01:00 |
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3137c1f841
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Adds the ability to read gzip-tar file for the taxonomy dump
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2025-01-24 11:47:59 +01:00 |
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00b0edc15a
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refactoring of the file chunck writing
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2024-11-29 18:15:03 +01:00 |
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3f57935328
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Adjust the size of the genbank and embl buffer size
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2024-08-05 11:32:37 +02:00 |
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886b5d9a96
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Optimize memory for readers and writers
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2024-08-05 10:48:28 +02:00 |
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1b1cd41fd3
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Add some code refactoring from the blackboard branch
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2024-08-02 12:35:46 +02:00 |
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e6b87ecd02
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Reduce memory allocation events
Former-commit-id: fbdb2afc857b02adc2593e2278d3bd838e99b0b2
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2024-06-22 21:01:53 +02:00 |
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55ce36f329
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Update of obipcr and homogenization of logging
Former-commit-id: 46abf47c19ace5248042c02cf1f81d9f6c12eb10
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2024-05-16 15:18:30 +02:00 |
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5b98393a68
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Refactor sequence file reading
Former-commit-id: 3dcb96e68da648d72bb585da047e3496427d7851
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2024-05-01 00:50:23 +02:00 |
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c9fe6f6ebf
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Make some correction on genbank/embl parser
Former-commit-id: fb2ebb351f61d78432bb9648d0a509b6557651a2
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2024-02-27 07:28:56 +01:00 |
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1542ce4c63
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Work on EMBL and Genbank parser efficienct
Former-commit-id: 309cc9ce4eea4c8085d7d4451a66a81710532f07
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2024-02-20 13:23:07 +01:00 |
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54ec09037e
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Patch a genbank & embl parsing error.
Former-commit-id: 060e80f42d176e6982e63d1128993fbcb4ad395f
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2024-02-16 15:20:37 +01:00 |
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6cc5c44a32
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Correct the bug in embl reader
Former-commit-id: 579d397ca16e8c4cf2f8ba01e503e62b2fffa06f
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2024-01-31 15:50:14 +01:00 |
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23758b00f6
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Patch a bug in the embl reader and adds some doc
Former-commit-id: 9b5f75fb14bcc3043da1647055279987a295d271
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2024-01-31 15:43:02 +01:00 |
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8d77cc4133
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Change path of the obitools pkg
Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
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2023-11-29 12:14:37 +01:00 |
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8f96517f3c
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small changes
Former-commit-id: 1fee30445f03ff627dab1c335e75c3f278621f6e
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2023-11-07 21:20:45 +02:00 |
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6a6a6f6f2c
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Correctly handle empty files
Former-commit-id: d166aa352ce4bf32739ddc2f7d1c9967918822fd
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2023-10-16 15:34:06 +02:00 |
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e8c55a2b6b
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optimize sequence readers and patch a bug in the format guesser
Former-commit-id: 9dce1e96c57ae9a88c26fac5c8e1bdcdc2c0c7a5
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2023-10-13 21:52:57 +02:00 |
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62b57f4ede
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A go implementation of the fasta reader
Former-commit-id: 603592c4761fb0722e9e0501d78de1bd3ba238fa
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2023-09-01 09:30:12 +02:00 |
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3f69fa41d6
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Patch a bug for multiple amplicon per sequence.
Former-commit-id: b252d2de8e1a85d65c2951aa1958ee038e35741d
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2023-03-31 15:10:25 +02:00 |
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bc82422bc5
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Reduce redundante call to bytes.ToLower and substitute the last call by an home made version doing the conversion in place
Former-commit-id: d9ea22f649d97be352f8dbb37acc1495df830118
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2023-03-28 11:43:04 +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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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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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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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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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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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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9677f531c4
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Improved performance and ability to read very long sequences.
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2022-08-21 13:38:13 +02:00 |
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abcf02e488
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Start to use leveled log
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2022-02-24 12:14:52 +01:00 |
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eaf65fbcce
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Some code refactoring, a new version of obiuniq more efficient in memory and a first make file allowing to build obitools
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2022-02-24 07:08:40 +01:00 |
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2e7c1834b0
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Big change iin the data model, and a first version of obiuniq
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2022-02-21 19:00:23 +01:00 |
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4551df08b1
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Adds a reader for NGS filter files and change some API for the apat library
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2022-01-18 13:09:32 +01:00 |
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576a9f4d2d
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A global version of a Slice pool
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2022-01-16 00:21:42 +01:00 |
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ef66ca4972
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Code refactoring
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2022-01-14 17:32:12 +01:00 |
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ff40222902
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Code reefactoring
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2022-01-14 16:10:19 +01:00 |
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b9b9c0f179
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Patch module name from oa2 to obitools
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2022-01-13 23:43:01 +01:00 |
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f53bf1b804
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First commit
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2022-01-13 23:27:39 +01:00 |
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