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

..

abs_test.go

Refactoring of the default values

2025-01-24 18:09:59 +01:00

abs.go

Changes to be committed:

2024-10-28 21:51:21 +01:00

array_test.go

Adds unit tests

2023-08-27 16:23:09 +02:00

array.go

Adds unit tests

2023-08-27 16:23:09 +02:00

bytes_test.go

Adds unit tests

2023-08-27 16:23:09 +02:00

bytes.go

A first prototype for the space of sequences

2023-08-27 14:58:55 +02:00

cast_interface.go

Update obisummary to account new obiseq.StatsOnValues type

2025-06-19 17:21:30 +02:00

counter.go

Xprize update

2024-07-25 18:09:03 -04:00

download.go

add the --download-ncbi option to obitaxonomy

2025-01-29 12:38:39 +01:00

goutils.go

Adds possibility to extract a taxonomy from taxonomic path included in sequence files

2025-01-30 11:18:21 +01:00

gzipfile.go

Add some doc and switch to the parallel gzip library

2023-08-25 14:36:38 +02:00

memsize.go

Add memory-based batching support

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

mimetypes.go

Patch the fastq detector

2025-08-08 10:23:03 -04:00

minmax.go

Patch the Min and Max values of the expression language

2025-06-19 16:43:26 +02:00

minmultiset.go

implementation de obilowmask

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

path_test.go

Adds doc and unit tests

2023-08-27 16:48:15 +02:00

path.go

Refactoring of the default values

2025-01-24 18:09:59 +01:00

pipe.go

Refactoring of the default values

2025-01-24 18:09:59 +01:00

ranks.go

Implements the kmeans++ algo to select the landmarks in the geometric method

2023-12-11 16:07:03 +01:00

set_test.go

Patch the production of the ratio file

2025-02-27 10:19:39 +01:00

set.go

Patch the production of the ratio file

2025-02-27 10:19:39 +01:00

slices.go

A first prototype for the space of sequences

2023-08-27 14:58:55 +02:00

strings.go

Replace SplitInTwo with LeftSplitInTwo/RightSplitInTwo for precise splitting

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

tar.go

Adds the ability to read gzip-tar file for the taxonomy dump

2025-01-24 11:47:59 +01:00

unsafe.go

Patch a small bug on json write

2024-12-20 19:42:03 +01:00

xopen_test.go

Adds the ability to read gzip-tar file for the taxonomy dump

2025-01-24 11:47:59 +01:00

xopen.go

Adds the ability to read gzip-tar file for the taxonomy dump

2025-01-24 11:47:59 +01:00