Eric Coissac 761e0dbed3 Implémentation d'un parseur GenBank utilisant rope pour réduire l'usage de mémoire ...

Ajout d'un parseur GenBank basé sur rope pour réduire l'usage de mémoire (RSS) et les allocations heap.

- Ajout de `gbRopeScanner` pour lire les lignes sans allocation heap
- Implémentation de `GenbankChunkParserRope` qui utilise rope au lieu de `Pack()`
- Modification de `_ParseGenbankFile` et `ReadGenbank` pour utiliser le nouveau parseur
- Réduction du RSS attendue de 57 GB à ~128 MB × workers
- Conservation de l'ancien parseur pour compatibilité et tests

Réduction significative des allocations (~50M) et temps sys, avec un temps user comparable ou meilleur.

2026-03-10 15:35:36 +01:00

..

kseq

some more cleaning

2024-01-16 21:11:38 +01:00

batch_of_files_reader.go

Update of obipcr and homogenization of logging

2024-05-16 15:18:30 +02:00

batch_reader_type.go

Change path of the obitools pkg

2023-11-29 12:14:37 +01:00

csv_read.go

Refactoring of the default values

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

csv_writer.go

Refactoring of the default values

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

csviterator.go

Make sequence files recognized as a taxonomy

2025-03-14 14:22:22 +01:00

csvtaxdump_read.go

Changes to be committed:

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

dispatcher.go

reduce the memory impact of obiuniq.

2024-11-27 13:30:16 +01:00

ecopcr_read.go

Changes to be committed:

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

embl_read.go

Optimisation du parsing des grandes séquences

2026-03-10 14:20:21 +01:00

empty_file.go

Change path of the obitools pkg

2023-11-29 12:14:37 +01:00

fastaseq_read.go

Optimisation du parsing des grandes séquences

2026-03-10 14:20:21 +01:00

fastqseq_read.go

Optimisation du parsing des grandes séquences

2026-03-10 14:20:21 +01:00

fastqseq_write_generic.go

patch for impot bug

2023-12-01 16:31:35 +01:00

fastseq_header.go

Change the API of workers

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

fastseq_interface.go

Change path of the obitools pkg

2023-11-29 12:14:37 +01:00

fastseq_json_header.go

Manage a lock on StatsOnValues

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

fastseq_obi_header.go

Manage a lock on StatsOnValues

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

fastseq_read.c

Patch reading of annotation from stdin

2022-09-29 14:48:05 +02:00

fastseq_read.go

Refactoring of the default values

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

fastseq_read.h

First commit

2022-01-13 23:27:39 +01:00

fastseq_write_fasta.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

fastseq_write_fastq.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

fastseq_write_with_index.go

many changes ;-)

2023-12-05 15:28:29 +01:00

file_chunk_read.go

Optimisation du parsing des grandes séquences

2026-03-10 14:20:21 +01:00

file_chunk_write.go

Refactoring of the default values

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

genbank_read.go

Implémentation d'un parseur GenBank utilisant rope pour réduire l'usage de mémoire

2026-03-10 15:35:36 +01:00

json_writer.go

Patch a small bug on json write

2024-11-29 18:39:18 +01:00

ncbitaxdump_read.go

Changes to be committed:

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

ncbitaxdump_readtar.go

Changes to be committed:

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

newick_write.go

Changes to be committed:

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

ngsfilter_read.go

Patch the fastq detector

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

options.go

Debug on taxonomy extraction and CSV conversion

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

taxonomy_read.go

Changes to be committed:

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

universal_read.go

debug url reading

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

universal_write.go

Patch a bug on writing to stdout, and add clearer error on openning data files

2024-08-13 09:45:28 +02:00