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5a3705b6bb
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Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.
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2025-03-25 16:44:46 +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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31bfc88eb9
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Patch a bug on writing to stdout, and add clearer error on openning data files
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2024-08-13 09:45:28 +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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e40d0bfbe7
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Debug fasta and fastq writer when the first sequence is hudge
Former-commit-id: d208ff838abb7e19e117067f6243298492d60f14
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2024-06-26 18:39:42 +02:00 |
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93f9dcb95f
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Reducing memory allocation events
Former-commit-id: c94e79ba116464504580fc397270ead154063971
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2024-06-22 22:32:31 +02:00 |
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818ce87bab
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Patch some bugs in writing files
Former-commit-id: 612868a281dc0ecf4e6c5776973735e5c71bd517
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2024-06-19 13:15:30 +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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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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0a8f7afb2a
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Patch sequence writers to remove definition from header when json format is used.
Former-commit-id: a8a74cccb52d577d4ea1c0ad88b121a8e511149d
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2023-10-05 07:31:31 +02:00 |
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70a77c9ec6
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Adds doc
Former-commit-id: e720718686da480e1abd4302ebff145aeee5eb4a
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2023-08-14 10:04:16 +02:00 |
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fd4c7c2572
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Adds some docs
Former-commit-id: 7e96983ed707b2a574425799c32c32243f4876cf
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2023-08-14 00:12:17 +02:00 |
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be47ec909c
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add the --skip-empty option
Former-commit-id: ec9cb0ecaf90a61bf9289cf4c089b5cc2fcb65a5
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2023-07-17 14:24:02 +02:00 |
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988ae79989
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Optimize memory allocation of the apat algorithms
Former-commit-id: 5010c5a666b322715b3b81c1078d325e1f647ede
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2023-03-28 19:37:05 +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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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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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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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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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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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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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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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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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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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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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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3586ecc483
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second version of obidistribute and a first buggy version of obiuniq
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2022-02-15 00:47:02 +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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e8fff6477b
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Work on iterators and recycling of biosequences
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2022-01-14 23:11:36 +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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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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