obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2026-08-24 13:51:18 +00:00
Code Issues Packages Projects Releases Wiki Activity
810 Commits 13 Branches 41 Tags
620646d412719fa374d265f6a225cc97b96d9d08
Commit Graph
50 Commits
Author SHA1 Message Date
Eric Coissac 620646d412 fix: validate inputs and fix coordinate offsets in pattern matching 
Introduce explicit input validation and a `(-1, -1, -1)` sentinel return value to signal invalid or unreliable matches. Add pre-call length checks and early returns to prevent panics during indel relocation. Fix an index offset bug in coordinate calculation by preserving the original fragment position before applying alignment deltas. Update match filtering to enforce reliability checks only on successfully relocated alignments. Comprehensive tests validate edge cases, boundary constraints, and error thresholds.
 2026-08-19 17:25:44 +02:00
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