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38dcd98d4a
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Patch the genbank parser automata
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2025-06-17 08:52:45 +02:00 |
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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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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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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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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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8a2bbd1c3b
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Patch a bug in the genbank reader when reading CONTIG entries
Former-commit-id: dfe1433fbb68a79d59a3ee45e7e5b58c1599dad6
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2024-03-11 10:53:25 +01:00 |
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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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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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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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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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e7b9ba3f30
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Limit allocation during genbank parsing
Former-commit-id: eee3c1fa7ffb79943109ee32dbf21e78bf11b14f
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2023-03-28 22:42:58 +07:00 |
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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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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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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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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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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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5a81525e46
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Adds a genbank parser
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2022-08-23 11:04:57 +02:00 |
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