a186bd1c92
fix: validate non-empty sequence IDs in FASTA and FASTQ writers
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Adds a pre-processing guard that checks for empty sequence identifiers before formatting. This prevents malformed FASTA output and stops downstream processing of invalid FASTQ data by terminating early. The check is placed before existing sequence-length validations to enforce non-empty IDs during batch processing.
2026-05-05 18:07:58 +02:00
b246025907
Optimize Fasta batch formatting
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Optimize FormatFastaBatch to pre-allocate buffer and write sequences directly without intermediate strings, improving performance and memory usage.
2026-03-10 15:43:59 +01:00
5a3705b6bb
Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.
2025-03-25 16:44:46 +01:00
00b0edc15a
refactoring of the file chunck writing
2024-11-29 18:15:03 +01:00
31bfc88eb9
Patch a bug on writing to stdout, and add clearer error on openning data files
2024-08-13 09:45:28 +02:00
886b5d9a96
Optimize memory for readers and writers
2024-08-05 10:48:28 +02:00
1b1cd41fd3
Add some code refactoring from the blackboard branch
2024-08-02 12:35:46 +02:00
e40d0bfbe7
Debug fasta and fastq writer when the first sequence is hudge
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Former-commit-id: d208ff838abb7e19e117067f6243298492d60f14
2024-06-26 18:39:42 +02:00
93f9dcb95f
Reducing memory allocation events
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Former-commit-id: c94e79ba116464504580fc397270ead154063971
2024-06-22 22:32:31 +02:00
818ce87bab
Patch some bugs in writing files
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Former-commit-id: 612868a281dc0ecf4e6c5776973735e5c71bd517
2024-06-19 13:15:30 +02:00
55ce36f329
Update of obipcr and homogenization of logging
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Former-commit-id: 46abf47c19ace5248042c02cf1f81d9f6c12eb10
2024-05-16 15:18:30 +02:00
coissac
8d77cc4133
Change path of the obitools pkg
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Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
2023-11-29 12:14:37 +01:00
coissac
0a8f7afb2a
Patch sequence writers to remove definition from header when json format is used.
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Former-commit-id: a8a74cccb52d577d4ea1c0ad88b121a8e511149d
2023-10-05 07:31:31 +02:00
coissac
70a77c9ec6
Adds doc
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Former-commit-id: e720718686da480e1abd4302ebff145aeee5eb4a
2023-08-14 10:04:16 +02:00
coissac
fd4c7c2572
Adds some docs
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Former-commit-id: 7e96983ed707b2a574425799c32c32243f4876cf
2023-08-14 00:12:17 +02:00
coissac
be47ec909c
add the --skip-empty option
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Former-commit-id: ec9cb0ecaf90a61bf9289cf4c089b5cc2fcb65a5
2023-07-17 14:24:02 +02:00
coissac
988ae79989
Optimize memory allocation of the apat algorithms
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Former-commit-id: 5010c5a666b322715b3b81c1078d325e1f647ede
2023-03-28 19:37:05 +07:00
coissac
d5e84ec676
rename goutils to obiutils
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Former-commit-id: 2147f53db972bba571dfdae30c51b62d3e69cec5
2023-03-24 10:25:12 +07:00
coissac
5fbe52368c
Patch the empty batch bug
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Former-commit-id: fcee04b58f2c4a0bf2c27792f991391c0b6ce78e
2023-03-07 20:16:06 +07:00
coissac
d88de15cdc
Refactoring codes for removing buffer size options. An some other changes...
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Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce
2023-03-07 11:12:13 +07:00
coissac
072b85e155
change the model for representing paired reads and extend its usage to other commands
2023-02-23 23:35:58 +01:00
coissac
56722895e4
Adds to every obitools the ability to save in gzip compressed files
2023-02-18 12:06:52 +01:00
coissac
d04eb915b3
adds a directory option to obidistribute
2023-02-17 22:52:53 +01:00
coissac
9554a32490
Add capacity to obidistribute to save gzipped files
2023-02-17 12:52:19 +01:00
coissac
2975042982
Adds the possiblility to append to files to obidistribute
2023-02-16 16:13:13 +01:00
coissac
8b70b1a5d8
Last bug on sequence writing
2023-02-08 13:56:50 +01:00
coissac
526bf79c7f
Patch for some lost of data during sequence writing
2023-02-08 13:14:26 +01:00
coissac
f97f92df72
rename the iterator class
2023-01-22 22:04:17 +01:00
coissac
09fc426b67
Refactoring related to iterators
2022-11-16 17:13:03 +01:00
coissac
6f853da9df
Remove single sequence ierators. Only batch iterators persist
2022-11-16 10:58:59 +01:00
coissac
7f863fb383
Prevens errors on FASTA formating an empty sequence
2022-11-16 09:22:55 +01:00
coissac
989e678f6b
refactor code and change algorithm used to read from many files
2022-08-23 15:07:06 +02:00
coissac
abcf02e488
Start to use leveled log
2022-02-24 12:14:52 +01:00
coissac
eaf65fbcce
Some code refactoring, a new version of obiuniq more efficient in memory and a first make file allowing to build obitools
2022-02-24 07:08:40 +01:00
coissac
2e7c1834b0
Big change iin the data model, and a first version of obiuniq
2022-02-21 19:00:23 +01:00
coissac
3586ecc483
second version of obidistribute and a first buggy version of obiuniq
2022-02-15 00:47:02 +01:00
coissac
4551df08b1
Adds a reader for NGS filter files and change some API for the apat library
2022-01-18 13:09:32 +01:00
coissac
e8fff6477b
Work on iterators and recycling of biosequences
2022-01-14 23:11:36 +01:00
coissac
ef66ca4972
Code refactoring
2022-01-14 17:32:12 +01:00
coissac
b9b9c0f179
Patch module name from oa2 to obitools
2022-01-13 23:43:01 +01:00
coissac
f53bf1b804
First commit
2022-01-13 23:27:39 +01:00
Eric Coissac
coissac