Eric Coissac
eae41ac81c
fix: respect config defaults when --allowed-mismatches is unset
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The change replaces numeric threshold checks with an explicit flag state tracker for the `--allowed-mismatches` option. This ensures per-primer mismatch settings from configuration files are preserved when the CLI parameter is omitted or zero, making the command-line flag act strictly as an explicit override rather than a default fallback.
2026-08-19 16:40:48 +02:00
Eric Coissac
1c6ab1c559
Changes to be committed:
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modified: pkg/obingslibrary/multimatch.go
modified: pkg/obioptions/version.go
2025-06-17 09:06:42 +02:00
Eric Coissac
f9324dd8f4
add min and max to the obitools expression language
2025-05-13 16:03:03 +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
3e00d39d47
In obimultiplex, patch a bug when no tag are associated to a primer.
2024-10-22 14:12:20 +02:00
Eric Coissac
65ae82622e
correction of several small bugs
2024-09-03 06:08:07 -03:00
Eric Coissac
0187a82c5f
Patch a bug in obimultiplex loosing sequence with primer dimer
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Former-commit-id: ea14e1aa2e4670c19fe8ee7ec61565bd21cc25b0
2024-06-30 17:42:28 +02:00
Eric Coissac
818ce87bab
Patch some bugs in writing files
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Former-commit-id: 612868a281dc0ecf4e6c5776973735e5c71bd517
2024-06-19 13:15:30 +02:00
Eric Coissac
a812fe8b72
debug of obimultiplex
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Former-commit-id: 1cf276840feb9d6135d96bd1bf63627d3085ae6e
2024-06-18 23:38:33 +02:00
Eric Coissac
44533fb61e
Bugs in the non stric tag matching algorithm
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Former-commit-id: efad98d6521322209ce22bc58fab54c7bddd19ec
2024-06-10 21:19:26 +02:00
Eric Coissac
e47b50de7f
Patch a bug in seting of the tag delimiter with an upper case
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Former-commit-id: a3962400b7ab91b25102c4c7c35cd824bf7ceaf0
2024-06-06 23:25:16 +02:00
Eric Coissac
1b43fa4247
First complete version of obimultiplex2
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Former-commit-id: 170593bd597c7914d3f1fd3d2b865186d7f11966
2024-06-06 23:11:13 +02:00
Eric Coissac
87a7219ab4
Adds the reading of the options through the csv formated ngsfilter configuration file
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Former-commit-id: 0e9a13689da2ba45293c7de1f728d3d0d34d3238
2024-06-04 22:57:07 +02:00
Eric Coissac
c8ad96f5e6
First fonctionnal version with fixed tag length and strict matching
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Former-commit-id: 5affee2c7c66dd1da5b17c2d1ea64f44db76df50
2024-06-04 21:46:09 +02:00
Eric Coissac
65f5109957
Plenty of small bugs
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Former-commit-id: 42c7fab7d65906c80ab4cd32da6867ff21842ea8
2024-06-04 16:49:12 +02:00
Eric Coissac
dd9307a4cd
Swich to the system min and max functions and remove the version from obiutils
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Former-commit-id: 8c4558921b0d0c266b070f16e83813de6e6d4a0f
2024-05-30 08:27:24 +02:00
Eric Coissac
017030bcce
Add obiminion first version
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Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d
2024-05-14 08:16:12 +02:00
coissac
b4afd784dc
few small correction
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Former-commit-id: 9319387ef5379b66e008233dbd7b6ea60b5d3b1e
2024-03-06 12:52:22 -03:00
coissac
0f3871d203
Change the API of workers
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Former-commit-id: 9b07306edd8cf28266f86f95823948fa99d39ea9
2024-03-02 16:03:46 -04:00
coissac
69b4d9ed20
Patch e bug in the ngsfilter library when match with indel are at the extremities
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Former-commit-id: 5a8a3100ac4b3eca104644597abe599eb7f2a5f4
2024-02-01 09:54:34 +01:00
coissac
a36e830de3
homogenize worker count
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Former-commit-id: 4352ac6694c08023cdf0e090723fac8af655cea4
2023-12-20 08:14:07 +01:00
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
d23a911080
Change the way sequence definition are managed. They are now when present stored as an attribute
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Former-commit-id: 6e618377c05b42937d2eace3c9668390980ab68c
2023-10-05 07:21:12 +02:00
coissac
450e54f4aa
Rename forward and reverse mitmatches tags
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Former-commit-id: faa0f41bf725da3c416326572cc90701704092da
2023-04-18 12:08:13 +02:00
coissac
d5e84ec676
rename goutils to obiutils
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Former-commit-id: 2147f53db972bba571dfdae30c51b62d3e69cec5
2023-03-24 10:25:12 +07:00
coissac
42aae88520
complete the correction related to the tag detection
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Former-commit-id: 98326fb0f27788de672cdbd686b32b4dc2615038
2023-03-23 11:52:08 +07:00
coissac
57474214e7
Patch excessive log in obimultiplex and an error in detecting the tag.
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Former-commit-id: e6f427ac743cae373247a15bf49b0a27273b2569
2023-03-23 11:40:24 +07:00
coissac
d09011fac2
Finalyse the obimultiplex with indels
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Former-commit-id: cef0ac39dac0e02d16d4bd321966a0f8a67f2c85
2023-03-21 22:01:02 +07:00
coissac
27d6c60e25
Add the possibility to look for patterns allowing indels.
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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...
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Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce
2023-03-07 11:12:13 +07:00
coissac
2d375df94f
move the worker class to the obiseq package
2023-01-22 22:39:13 +01:00
coissac
e17d1fbca6
Patch the error message stored in sequences by obimultiplex
2022-10-17 21:32:24 +02:00
coissac
f8df48338d
Several bug in annotation management
2022-10-12 23:01:47 +02:00
coissac
fe5d8e3340
Patch a bug in ngsfilter reading and sample matching
2022-09-28 14:29:19 +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
cb125bb2a4
Adds an error message when no sample can be associated
2022-02-18 09:58:56 +01:00
coissac
38e4655f38
Correct for a strange bug...
2022-02-07 11:51:35 +01:00
coissac
8dbda68746
Adds the command obimultiplex
2022-02-01 17:31:28 +01:00
Eric Coissac
coissac