Eric Coissac 56f5fe33d7 Implement strict word finding and sequence filtering ...

This introduces new structures for defining sequence roles and constraints, core logic for strict word identification, and comprehensive unit tests to ensure accuracy and correct behavior.

2026-11-03 22:34:10 +11:00

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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

Implement strict word finding and sequence filtering

2026-11-03 22:34:10 +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

feat: add JSON input support for biological sequences

2026-07-03 10:16:55 +02:00