Eric Coissac 8cc02aa9c1 Refactor sequence processing for parallel loading and memory management ...

This commit introduces significant changes to the sequence processing pipeline, implementing parallel loading, k-mer budget control, explicit memory management, and refined logic for pair evaluation and resolution.

2026-11-03 22:53:54 +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 taxonomy handling and improve performance

2026-11-03 22:44:44 +11:00

obiitercsv

break the import cyccle

2025-01-27 17:23:07 +01:00

obikmer

Refactor sequence processing for parallel loading and memory management

2026-11-03 22:53:54 +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

Refactor sequence processing for parallel loading and memory management

2026-11-03 22:53:54 +11:00

obiseq

Refactor primer logic and enhance taxonomy features

2026-11-03 22:46:34 +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 sequence processing for parallel loading and memory management

2026-11-03 22:53:54 +11:00

obiutils

Refactor primer logic and enhance taxonomy features

2026-11-03 22:46:34 +11:00