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Eric Coissac 49225030ca Implement core clustering logic and scoring features 
This update introduces the core clustering algorithm, including parallel execution, dynamic block sizing, and SIMD-accelerated scoring methods. It also adds robust sequence preparation, k-mer analysis, and comprehensive test data fixtures for validation.
2026-11-03 09:32:40 +11:00
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obialign
Implement core clustering logic and scoring features
2026-11-03 09:32:40 +11:00
obiapat
fix: validate inputs and fix coordinate offsets in pattern matching
2026-08-19 17:25:44 +02:00
obichunk
Fix classifier cloning and reset in chunk processing
2026-02-08 15:52:25 +01:00
obicorazick
Add progress bar configuration and conditional display
2026-02-08 16:14:02 +01:00
obidefault
Implement progress tracking for clique finding
2026-11-03 09:26:29 +11:00
obidist
Add Jaccard distance and similarity computations for KmerSet and KmerSetGroup
2026-02-05 17:39:23 +01:00
obiformats
refactor: improve FASTQ error messages with explicit filenames
2026-08-19 16:47:36 +02:00
obifp
fix: update uint128 test expectations and improve log formatting
2026-08-19 17:33:57 +02:00
obigraph
Implement robust clique search configuration and testing
2026-11-03 09:27:21 +11:00
obiiter
Refactor batch iterator filtering and update project configuration
2026-11-03 09:22:46 +11:00
obiitercsv
break the import cyccle
2025-01-27 17:23:07 +01:00
obikmer
Implement robust clique search configuration and testing
2026-11-03 09:27:21 +11:00
obilog
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
obilua
chore: bump version to 4.4.39
2026-04-14 14:48:29 +02:00
obingslibrary
fix: respect config defaults when --allowed-mismatches is unset
2026-08-19 16:40:48 +02:00
obioptions
Release 4.5.0
2026-08-19 17:35:06 +02:00
obiphylo
Changes to be committed:
2025-06-04 09:48:10 +02:00
obiseq
Feature: Implement constrained k-mer generation and clique search
2026-11-03 09:25:34 +11:00
obistats
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
obisuffix
Swich to the system min and max functions and remove the version from obiutils
2024-05-30 08:27:24 +02:00
obitable
many changes ;-)
2023-12-05 15:28:29 +01:00
obitax
feat(obiconvert): add --raw-taxid option and refactor taxID formatting
2026-04-30 16:57:38 +02:00
obitools
Implement core clustering logic and scoring features
2026-11-03 09:32:40 +11:00
obiutils
feat: add JSON input support for biological sequences
2026-07-03 10:16:55 +02:00