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809 Commits 13 Branches 41 Tags
438893d910f6e0bec57f906cecd5f53261eb270c
Commit Graph
49 Commits
Author SHA1 Message Date
Eric Coissac 438893d910 refactor: improve FASTQ error messages with explicit filenames 
The options system now tracks explicit file paths via a new accessor and functional option. This filename is threaded through the FASTQ parser chain to replace generic source references in fatal error messages, providing clearer, file-specific diagnostics without altering core parsing logic or test suites.
 2026-08-19 16:47:36 +02:00
Eric Coissac 07cdd6f758 debug obimultiplex 
bug option obimultiplex
 2025-11-06 15:43:13 +01:00
Eric Coissac 13ff892ac9 Patch type mismatch in apat C library 2025-04-23 16:14:10 +02:00
Eric Coissac 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
Eric Coissac 7c4042df6b introduce obidefault 2025-01-27 17:12:45 +01:00
Eric Coissac 241f2286f2 remove the slice pool management 2024-09-24 16:31:30 +02:00
Eric Coissac 05bf2bfd6c Add option related to agrep match on obigrep and obiannotate 2024-09-09 16:52:13 +02:00
Eric Coissac 65ae82622e correction of several small bugs 2024-09-03 06:08:07 -03:00
Eric Coissac a812fe8b72 debug of obimultiplex 
Former-commit-id: 1cf276840feb9d6135d96bd1bf63627d3085ae6e
 2024-06-18 23:38:33 +02:00
Eric Coissac dd9307a4cd Swich to the system min and max functions and remove the version from obiutils 
Former-commit-id: 8c4558921b0d0c266b070f16e83813de6e6d4a0f
 2024-05-30 08:27:24 +02:00
Eric Coissac 017030bcce Add obiminion first version 
Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d
 2024-05-14 08:16:12 +02:00
coissac f4d71d4a66 Patch a bug in the subseq and revcomplement methods. That patchs the bug in the option -c of obipcr 
Former-commit-id: 7999b917d07545271036af6e66f53aea27fc6e7b
 2024-03-11 10:54:37 +01:00
coissac 7bd073ccd4 First version of obisplit and patch a bug in the new workers API 
Former-commit-id: f28af9f104c08d68e29fd866739d8dd58241da63
 2024-03-03 11:16:24 -04:00
coissac 0f3871d203 Change the API of workers 
Former-commit-id: 9b07306edd8cf28266f86f95823948fa99d39ea9
 2024-03-02 16:03:46 -04:00
coissac a36e830de3 homogenize worker count 
Former-commit-id: 4352ac6694c08023cdf0e090723fac8af655cea4
 2023-12-20 08:14:07 +01:00
coissac 8d77cc4133 Change path of the obitools pkg 
Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
 2023-11-29 12:14:37 +01:00
coissac e8c55a2b6b optimize sequence readers and patch a bug in the format guesser 
Former-commit-id: 9dce1e96c57ae9a88c26fac5c8e1bdcdc2c0c7a5
 2023-10-13 21:52:57 +02:00
coissac ddf0f2cede Add the -D (--delta) option to obipcr 
Former-commit-id: 753079807faaddb23e03fd6350125bfa67f98c7f
 2023-10-13 17:04:10 +02:00
coissac d23a911080 Change the way sequence definition are managed. They are now when present stored as an attribute 
Former-commit-id: 6e618377c05b42937d2eace3c9668390980ab68c
 2023-10-05 07:21:12 +02:00
coissac d437fba535 Doc change 
Former-commit-id: 5cd4547147804f887ad699d4886702545584ba32
 2023-08-27 17:06:36 +02:00
coissac f1025f97b8 Add a missing prototype 
Former-commit-id: 6c5b476f30adba6e0eb41e11e152124090c3f04e
 2023-08-27 15:51:23 +02:00
coissac 3f69fa41d6 Patch a bug for multiple amplicon per sequence. 
Former-commit-id: b252d2de8e1a85d65c2951aa1958ee038e35741d
 2023-03-31 15:10:25 +02:00
coissac 988ae79989 Optimize memory allocation of the apat algorithms 
Former-commit-id: 5010c5a666b322715b3b81c1078d325e1f647ede
 2023-03-28 19:37:05 +07:00
coissac d5e84ec676 rename goutils to obiutils 
Former-commit-id: 2147f53db972bba571dfdae30c51b62d3e69cec5
 2023-03-24 10:25:12 +07:00
coissac 57474214e7 Patch excessive log in obimultiplex and an error in detecting the tag. 
Former-commit-id: e6f427ac743cae373247a15bf49b0a27273b2569
 2023-03-23 11:40:24 +07:00
coissac d09011fac2 Finalyse the obimultiplex with indels 
Former-commit-id: cef0ac39dac0e02d16d4bd321966a0f8a67f2c85
 2023-03-21 22:01:02 +07:00
coissac 27d6c60e25 Add the possibility to look for patterns allowing indels. 
Former-commit-id: 0599c2b0ad16df086dbdb08e491503870d8904be
 2023-03-20 15:28:24 +07:00
coissac d88de15cdc Refactoring codes for removing buffer size options. An some other changes... 
Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce
 2023-03-07 11:12:13 +07:00
coissac 6fd426d8be Update obiapat.c 2023-02-17 11:29:27 +01:00
coissac 9cf9d4d504 Update obiapat.c by removing dependancy to asprintf by using snprintf 2023-02-17 11:28:14 +01:00
coissac 03b124f400 Patch a bug in MamberSub for primers longer than 32 2023-02-01 16:23:14 +01:00
coissac 2d375df94f move the worker class to the obiseq package 2023-01-22 22:39:13 +01:00
coissac 29563aa94e Rename the Length methods Len to follow GO standart 2022-11-17 11:09:58 +01:00
coissac f8df48338d Several bug in annotation management 2022-10-12 23:01:47 +02:00
coissac f6735a634e Correctly patch the memory leak related to the apatsequence 2022-09-12 15:19:46 +02:00
coissac 3e40ae9d52 Patch a memory leak in apat sequence 2022-08-21 13:40:20 +02:00
coissac 5dd835d3e7 A first functional version of obiclean 2022-08-20 18:01:07 +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 76d9309508 Remame PCR struct to PCRSim 2022-01-27 12:13:27 +01:00
coissac b9da72d379 Adds finalizer to ApatSequence 2022-01-24 22:54:41 +01:00
coissac 251d3be923 Add automatic garbage collection on ApatPattern 2022-01-24 17:26:30 +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 5753723618 Code refactoring 2022-01-14 17:17:54 +01:00
coissac ff40222902 Code reefactoring 2022-01-14 16:10:19 +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