Eric Coissac 574221df42 Refactor taxonomy handling and improve performance ...

This update introduces logic for handling embedded taxonomy, allowing users to specify taxonomy or extract it from sequences, while optimizing performance through reduced memory usage. It also adds batch reordering capabilities and implements comprehensive testing to ensure correct precedence rules and robust error handling for missing taxonomic paths.

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

..

batch.go

remove the slice pool management

2024-09-24 16:31:30 +02:00

batchiterator.go

Refactor taxonomy handling and improve performance

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

distribute.go

refactor: replace fixed batch size with dynamic flushing based on count and memory

2026-03-16 22:06:44 +01:00

extract_taxonomy.go

Debug on taxonomy extraction and CSV conversion

2025-07-07 15:29:40 +02:00

fragment.go

Replace Rebatch with RebatchBySize using default batch parameters

2026-03-13 15:16:33 +01:00

limitmemory.go

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

merge.go

Patch a bug in fasta and fastq reading

2024-06-21 14:28:57 +02:00

numbering.go

Add the --number option to obiannotate

2025-04-22 18:35:51 +02:00

paired.go

introduce obidefault

2025-01-27 17:12:45 +01:00

pipe.go

change the model for representing paired reads and extend its usage to other commands

2023-02-23 23:35:58 +01:00

sequence_workers.go

rename goutils to obiutils

2023-03-24 10:25:12 +07:00

speed.go

Add progress bar configuration and conditional display

2026-02-08 16:14:02 +01:00

workers.go

patch a bug in obiannotate

2025-03-11 16:35:38 +01:00