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Eric Coissac eae41ac81c fix: respect config defaults when --allowed-mismatches is unset 
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
..
obiannotate
obiannotate --cut bug
2025-12-18 14:11:11 +01:00
obiclean
Fix CompressStream call to use compressed variable
2026-03-12 18:48:22 +01:00
obicleandb
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
obiclust
some renaming of functions
2025-08-06 15:54:50 -04:00
obiconsensus
Manage a lock on StatsOnValues
2025-06-17 16:46:11 +02:00
obiconvert
feat: add JSON input support for biological sequences
2026-07-03 10:16:55 +02:00
obicount
Add automatic garbage collection on ApatPattern
2022-01-24 17:26:30 +01:00
obicsv
Refactor: Extract utility function for string reversal
2026-04-16 13:42:51 +02:00
obidemerge
Manage a lock on StatsOnValues
2025-06-17 16:46:11 +02:00
obidistribute
refactor: replace fixed batch size with dynamic flushing based on count and memory
2026-03-16 22:06:44 +01:00
obigrep
Several bugs dicoverd during the doc writing
2025-04-04 16:59:27 +02:00
obijoin
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
obik
Refactor k-mer matching pipeline with improved concurrency and memory management
2026-02-10 22:10:36 +01:00
obikmersim
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
obilandmark
Add progress bar configuration and conditional display
2026-02-08 16:14:02 +01:00
obimatrix
obimatrix bugs
2025-11-21 13:24:06 +01:00
obimicrosat
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
obimultiplex
fix: respect config defaults when --allowed-mismatches is unset
2026-08-19 16:40:48 +02:00
obipairing
[obitools] Add validation for paired files and config template support
2026-04-29 15:01:37 +02:00
obipcr
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
obirefidx
Replace Rebatch with RebatchBySize using default batch parameters
2026-03-13 15:16:33 +01:00
obiscript
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
obisplit
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
obisummary
+feat: add support for map_summaries aggregation in obisummary
2026-04-16 14:58:18 +02:00
obitag
Patch a bug in obitag
2025-06-04 14:47:28 +02:00
obitagpcr
fix: respect config defaults when --allowed-mismatches is unset
2026-08-19 16:40:48 +02:00
obitaxonomy
Changes to be committed:
2025-06-04 09:48:10 +02:00
obiuniq
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