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

..

attributes.go

obicsv bug with stat on value map fields

2025-11-21 14:03:31 +01:00

biosequence_test.go

correction of several small bugs

2024-09-03 06:08:07 -03:00

biosequence.go

Add memory-based batching support

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

biosequenceslice.go

Replace SplitInTwo with LeftSplitInTwo/RightSplitInTwo for precise splitting

2026-03-12 18:41:28 +01:00

class.go

Update obiuniq for very large dataset

2025-12-18 14:11:11 +01:00

compare.go

Add the possibility to look for patterns allowing indels.

2023-03-20 15:28:24 +07:00

eval.go

Change the API of workers

2024-03-02 16:03:46 -04:00

iupac_nog.go

work on obiclean chimera detection

2025-10-20 17:29:47 +02:00

join.go

Adds some documentation

2022-08-23 11:11:36 +02:00

kmers.go

implementation de obilowmask

2025-11-18 15:30:20 +01:00

language.go

add min and max to the obitools expression language

2025-05-13 16:03:03 +02:00

merge.go

obicsv bug with stat on value map fields

2025-11-21 14:03:31 +01:00

paired_reads.go

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

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

pool.go

Add memory-based batching support

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

predicate.go

Manage a lock on StatsOnValues

2025-06-17 16:46:11 +02:00

revcomp_test.go

Patch a bug in Subsequence and adds few unit tests.

2023-11-08 10:16:34 +02:00

revcomp.go

Patch a bug in obitagpcr

2024-11-18 21:10:47 +01:00

subseq_test.go

Patch a bug in the pair-end alignement in case of equality between scores.

2023-11-24 09:59:29 +01:00

subseq.go

Patch a bug in the subseq and revcomplement methods. That patchs the bug in the option -c of obipcr

2024-03-11 10:54:37 +01:00

taxonomy_classifier.go

some cleaning

2025-02-24 11:31:49 +01:00

taxonomy_lca.go

Manage a lock on StatsOnValues

2025-06-17 16:46:11 +02:00

taxonomy_methods.go

Changes to be committed:

2025-06-04 09:48:10 +02:00

taxonomy_predicate.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

taxonomy_workers.go

Fisrt functional version

2024-11-14 19:10:23 +01:00

worker.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