Replace SplitInTwo calls with LeftSplitInTwo or RightSplitInTwo depending on the intended split direction. In fastseq_json_header.go, extract rank from suffix without splitting; in biosequenceslice.go and taxid.go, use LeftSplitInTwo to split from the left; add RightSplitInTwo utility function for splitting from the right.
Replace the fixed [256]byte carry buffer with a dynamic []byte slice to support arbitrarily long lines without heap allocation during accumulation. Update all carry buffer handling logic to use len(s.carry) and append instead of fixed-size copy operations.
Introduce EmblChunkParserRope function to parse EMBL chunks directly from a rope without using Pack(). Add extractEmblSeq helper to scan sequence sections and handle U to T conversion. Update parser logic to use rope-based parsing when available, and fix feature table handling for WGS entries.
This commit refactors the rope scanner implementation by renaming gbRopeScanner to ropeScanner and extracting the common functionality into a new file. It also introduces a new FastqChunkParserRope function that parses FASTQ chunks directly from a rope without Pack(), enabling more efficient memory usage. The existing parsers are updated to use the new rope-based parser when available. The BioSequence type is enhanced with a TakeQualities method for more efficient quality data handling.
Introduce FastaChunkParserRope for direct rope-based FASTA parsing, enhance sequence extraction with whitespace skipping and U->T conversion, and update parser logic to support both rope and raw data sources.
- Added extractFastaSeq function to scan sequence bytes directly from rope
- Implemented FastaChunkParserRope for rope-based parsing
- Modified _ParseFastaFile to use rope when available
- Updated sequence handling to support U->T conversion
- Fixed line ending detection for FASTA parsing
Replace NewBioSequence with NewBioSequenceOwning in genbank_read.go to take ownership of sequence slices without copying, improving performance. Update biosequence.go to add the new TakeSequence method and NewBioSequenceOwning constructor.
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.
Implémente une optimisation du parsing des grandes séquences en évitant l'allocation de mémoire inutile lors de la fusion des chunks. Ajoute un support pour le parsing direct de la structure rope, ce qui permet de réduire les allocations et d'améliorer les performances lors du traitement de fichiers GenBank/EMBL et FASTA/FASTQ de plusieurs Gbp. Les parseurs sont mis à jour pour utiliser la rope non-packée et le nouveau mécanisme d'écriture in-place pour les séquences GenBank.
This commit fixes an issue in the GenBank parser where empty parts were being included in the parsed data. It also introduces a new script `release_notes.sh` to automate the generation of GitHub-compatible release notes for OBITools4 versions, including support for LLM summarization and various output modes.
Eric Coissac