Eric Coissac 40769bf827 Add memory-based batching support ...

Implement memory-aware batch sizing with --batch-mem CLI option, enabling adaptive batching based on estimated sequence memory footprint. Key changes:
- Added _BatchMem and related getters/setters in pkg/obidefault
- Implemented RebatchBySize() in pkg/obiter for memory-constrained batching
- Added BioSequence.MemorySize() for conservative memory estimation
- Integrated batch-mem option in pkg/obioptions with human-readable size parsing (e.g., 128K, 64M, 1G)
- Added obiutils.ParseMemSize/FormatMemSize for unit conversion
- Enhanced pool GC in pkg/obiseq/pool.go to trigger explicit GC for large slice discards
- Updated sequence_reader.go to apply memory-based rebatching when enabled

2026-03-13 14:54:21 +01:00

..

batch.go

remove the slice pool management

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

batchiterator.go

Add memory-based batching support

2026-03-13 14:54:21 +01:00

distribute.go

introduce obidefault

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

extract_taxonomy.go

Debug on taxonomy extraction and CSV conversion

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

fragment.go

some cleaning

2025-02-24 11:31:49 +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