Eric Coissac ad065f6853 Introduce new sequence matching logic and corpus handling ...

This commit introduces the core matching functionality, including parallel corpus loading, the `Corpus` data structure, and implementations for `matchNaive` and `matchApat`. It also defines new matching rules, variant handling, and comprehensive unit and integration tests to validate the new logic and parameter handling.

2026-11-03 22:35:51 +11:00

..

obialign

Refactor similarity engine and implement parallel clustering

2026-11-03 14:04:32 +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 similarity engine and implement parallel clustering

2026-11-03 14:04:32 +11:00

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 k-mer counting and sequence handling

2026-11-03 22:33:44 +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

obiprimer

Introduce new sequence matching logic and corpus handling

2026-11-03 22:35:51 +11:00

obiseq

Feature: Implement constrained k-mer generation and clique search

2026-11-03 09:25:34 +11:00

obisimilarity

Refactor similarity engine and implement parallel clustering

2026-11-03 14:04:32 +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

obithermo

Refactor similarity engine and implement parallel clustering

2026-11-03 14:04:32 +11:00

obitools

Refactor similarity engine and implement parallel clustering

2026-11-03 14:04:32 +11:00

obiutils

Fix: Prevent race condition during pipe registration

2026-11-03 22:34:22 +11:00