4.4.21: Parallel builds, robust installation, and rope-based parsing enhancements

This release introduces significant improvements to build reliability and performance, alongside key parsing enhancements for sequence data.

### Build & Installation Improvements
- Added support for parallel compilation via `-j/--jobs` option in both the Makefile and install script, enabling faster builds on multi-core systems. The default remains single-threaded for safety.
- Enhanced Makefile with `.DEFAULT_GOAL := all` for consistent behavior and a documented `help` target.
- Replaced fragile file operations with robust error handling, clear diagnostics, and automatic preservation of the build directory on copy failures to aid recovery.

### Rope-Based Parsing Enhancements (from 4.4.20)
- Introduced direct rope-based parsers for FASTA, EMBL, and FASTQ formats, improving memory efficiency for large files.
- Added U→T conversion support during sequence extraction and more reliable line ending detection.
- Unified rope scanning logic under a new `ropeScanner` for better maintainability.
- Added `TakeQualities()` method to BioSequence for more efficient handling of quality data.

### Bug Fixes (from 4.4.20)
- Fixed `CompressStream` to correctly respect the `compressed` variable.
- Replaced ambiguous string splitting utilities with precise left/right split variants (`LeftSplitInTwo`, `RightSplitInTwo`).

### Release Tooling (from 4.4.20)
- Streamlined release process with modular targets (`jjpush-notes`, `jjpush-push`, `jjpush-tag`) and AI-assisted note generation via `aichat`.
- Improved versioning support via the `VERSION` environment variable in `bump-version`.
- Switched PR submission from raw `jj git push` to `stakk` for consistency and reliability.

Note: This release incorporates key enhancements from 4.4.20 that impact end users, while focusing on build robustness and performance gains.

.gitignore

@@ -16,6 +16,7 @@
 **/*.tgz
 **/*.yaml
 **/*.csv
+**/*.pb.gz
 xx
 
 .rhistory

Makefile

@@ -2,6 +2,13 @@
 #export GOBIN=$(GOPATH)/bin
 #export PATH=$(GOBIN):$(shell echo $${PATH})
 
+.DEFAULT_GOAL := all
+
+GREEN  := \033[0;32m
+YELLOW := \033[0;33m
+BLUE   := \033[0;34m
+NC     := \033[0m
+
 GOFLAGS=
 GOCMD=go
 GOBUILD=$(GOCMD) build $(GOFLAGS)
@@ -60,6 +67,28 @@ endif
 
 OUTPUT:=$(shell mktemp)
 
+help:
+	@printf "$(GREEN)OBITools4 Makefile$(NC)\n\n"
+	@printf "$(BLUE)Main targets:$(NC)\n"
+	@printf "  %-20s %s\n" "all"          "Build all obitools (default)"
+	@printf "  %-20s %s\n" "obitools"     "Build all obitools binaries to build/"
+	@printf "  %-20s %s\n" "test"         "Run Go unit tests"
+	@printf "  %-20s %s\n" "obitests"     "Run integration tests (obitests/)"
+	@printf "  %-20s %s\n" "bump-version" "Increment patch version (or set with VERSION=x.y.z)"
+	@printf "  %-20s %s\n" "update-deps"  "Update all Go dependencies"
+	@printf "\n$(BLUE)Jujutsu workflow:$(NC)\n"
+	@printf "  %-20s %s\n" "jjnew"        "Document current commit and start a new one"
+	@printf "  %-20s %s\n" "jjpush"       "Release: describe, bump, generate notes, push PR, tag (VERSION=x.y.z optional)"
+	@printf "  %-20s %s\n" "jjfetch"      "Fetch latest commits from origin"
+	@printf "\n$(BLUE)Required tools:$(NC)\n"
+	@printf "  %-20s " "go";      command -v go      >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(go version)" || printf "$(YELLOW)✗ not found$(NC)\n"
+	@printf "  %-20s " "git";     command -v git     >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(git --version)" || printf "$(YELLOW)✗ not found$(NC)\n"
+	@printf "  %-20s " "jj";      command -v jj      >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(jj --version)" || printf "$(YELLOW)✗ not found$(NC)\n"
+	@printf "  %-20s " "gh";      command -v gh      >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(gh --version | head -1)" || printf "$(YELLOW)✗ not found$(NC)  (brew install gh)\n"
+	@printf "\n$(BLUE)Optional tools (release notes generation):$(NC)\n"
+	@printf "  %-20s " "aichat";  command -v aichat  >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(aichat --version)" || printf "$(YELLOW)✗ not found$(NC)  (https://github.com/sigoden/aichat)\n"
+	@printf "  %-20s " "jq";      command -v jq      >/dev/null 2>&1 && printf "$(GREEN)✓$(NC) %s\n" "$$(jq --version)" || printf "$(YELLOW)✗ not found$(NC)  (brew install jq)\n"
+
 all: install-githook obitools
 
 obitools: $(patsubst %,$(OBITOOLS_PREFIX)%,$(OBITOOLS))
@@ -106,15 +135,20 @@ pkg/obioptions/version.go: version.txt .FORCE
 	@rm -f $(OUTPUT)
 
 bump-version:
-	@echo "Incrementing version..."
 	@current=$$(cat version.txt); \
-	echo "  Current version: $$current"; \
+	if [ -n "$(VERSION)" ]; then \
-	major=$$(echo $$current | cut -d. -f1); \
+		new_version="$(VERSION)"; \
-	minor=$$(echo $$current | cut -d. -f2); \
+		echo "Setting version to $$new_version (was $$current)"; \
-	patch=$$(echo $$current | cut -d. -f3); \
+	else \
-	new_patch=$$((patch + 1)); \
+		echo "Incrementing version..."; \
-	new_version="$$major.$$minor.$$new_patch"; \
+		echo "  Current version: $$current"; \
-	echo "  New version: $$new_version"; \
+		major=$$(echo $$current | cut -d. -f1); \
+		minor=$$(echo $$current | cut -d. -f2); \
+		patch=$$(echo $$current | cut -d. -f3); \
+		new_patch=$$((patch + 1)); \
+		new_version="$$major.$$minor.$$new_patch"; \
+		echo "  New version: $$new_version"; \
+	fi; \
 	echo "$$new_version" > version.txt
 	@echo "✓ Version updated in version.txt"
 	@$(MAKE) pkg/obioptions/version.go
@@ -128,40 +162,76 @@ jjnew:
 	@echo "$(GREEN)✓ New commit created$(NC)"
 
 jjpush:
-	@echo "$(YELLOW)→ Pushing commit to repository...$(NC)"
+	@$(MAKE) jjpush-describe
+	@$(MAKE) jjpush-bump
+	@$(MAKE) jjpush-notes
+	@$(MAKE) jjpush-push
+	@$(MAKE) jjpush-tag
+	@echo "$(GREEN)✓ Release complete$(NC)"
+
+jjpush-describe:
 	@echo "$(BLUE)→ Documenting current commit...$(NC)"
 	@jj auto-describe
+
+jjpush-bump:
 	@echo "$(BLUE)→ Creating new commit for version bump...$(NC)"
 	@jj new
-	@previous_version=$$(cat version.txt); \
+	@$(MAKE) bump-version
-	$(MAKE) bump-version; \
+
-	version=$$(cat version.txt); \
+jjpush-notes:
-	tag_name="Release_$$version"; \
+	@version=$$(cat version.txt); \
-	previous_tag="Release_$$previous_version"; \
+	echo "$(BLUE)→ Generating release notes for version $$version...$(NC)"; \
-	echo "$(BLUE)→ Documenting version bump commit...$(NC)"; \
+	release_title="Release $$version"; \
-	jj auto-describe; \
+	release_body=""; \
-	echo "$(BLUE)→ Generating release notes from $$previous_tag to current commit...$(NC)"; \
+	if command -v aichat >/dev/null 2>&1; then \
-	if command -v orla >/dev/null 2>&1 && command -v jq >/dev/null 2>&1; then \
+		previous_tag=$$(git describe --tags --abbrev=0 --match 'Release_*' 2>/dev/null); \
-		release_json=$$(ORLA_MAX_TOOL_CALLS=50 jj log -r "$$previous_tag::@" -T 'commit_id.short() ++ " " ++ description' | \
+		if [ -z "$$previous_tag" ]; then \
-			orla agent -m ollama:qwen3-coder-next:latest \
+			echo "$(YELLOW)⚠ No previous Release tag found, skipping release notes$(NC)"; \
-			"Summarize the following commits into a GitHub release note for version $$version. Ignore commits related to version bumps, .gitignore changes, or any internal housekeeping that is irrelevant to end users. Describe each user-facing change precisely without exposing code. Eliminate redundancy. Output strictly valid JSON with no surrounding text, using this exact schema: {\"title\": \"<short release title>\", \"body\": \"<detailed markdown release notes>\"}"); \
-		release_json=$$(echo "$$release_json" | sed -n '/^{/,/^}/p'); \
-		release_title=$$(echo "$$release_json" | jq -r '.title // empty') ; \
-		release_body=$$(echo "$$release_json" | jq -r '.body // empty') ; \
-		if [ -n "$$release_title" ] && [ -n "$$release_body" ]; then \
-			release_message="$$release_title"$$'\n\n'"$$release_body"; \
 		else \
-			echo "$(YELLOW)⚠ JSON parsing failed, falling back to raw output$(NC)"; \
+			raw_output=$$(git log --format="%h %B" "$$previous_tag..HEAD" | \
-			release_message="Release $$version"$$'\n\n'"$$release_json"; \
+				aichat \
+				"Summarize the following commits into a GitHub release note for version $$version. Ignore commits related to version bumps, .gitignore changes, or any internal housekeeping that is irrelevant to end users. Describe each user-facing change precisely without exposing code. Eliminate redundancy. Output strictly valid JSON with no surrounding text, using this exact schema: {\"title\": \"<short release title>\", \"body\": \"<detailed markdown release notes>\"}" 2>/dev/null) || true; \
+			if [ -n "$$raw_output" ]; then \
+				notes=$$(printf '%s\n' "$$raw_output" | python3 tools/json2md.py 2>/dev/null); \
+				if [ -n "$$notes" ]; then \
+					release_title=$$(echo "$$notes" | head -1); \
+					release_body=$$(echo "$$notes" | tail -n +3); \
+				else \
+					echo "$(YELLOW)⚠ JSON parsing failed, using default release message$(NC)"; \
+				fi; \
+			fi; \
 		fi; \
-	else \
-		release_message="Release $$version"; \
 	fi; \
-	echo "$(BLUE)→ Pushing commits and creating tag $$tag_name...$(NC)"; \
+	printf '%s' "$$release_title" > /tmp/obitools4-release-title.txt; \
-	jj git push --change @; \
+	printf '%s' "$$release_body" > /tmp/obitools4-release-body.txt; \
-	git tag -a "$$tag_name" -m "$$release_message" 2>/dev/null || echo "Tag $$tag_name already exists"; \
+	echo "$(BLUE)→ Setting release notes as commit description...$(NC)"; \
-	git push origin "$$tag_name" 2>/dev/null || echo "Tag already pushed"
+	jj desc -m "$$release_title"$$'\n\n'"$$release_body"
-	@echo "$(GREEN)✓ Commits and tag pushed to repository$(NC)"
+
+jjpush-push:
+	@echo "$(BLUE)→ Pushing commits...$(NC)"
+	@jj git push --change @
+	@echo "$(BLUE)→ Creating/updating PR...$(NC)"
+	@release_title=$$(cat /tmp/obitools4-release-title.txt 2>/dev/null || echo "Release $$(cat version.txt)"); \
+	release_body=$$(cat /tmp/obitools4-release-body.txt 2>/dev/null || echo ""); \
+	branch=$$(jj log -r @ --no-graph -T 'bookmarks.map(|b| b.name()).join("\n")' 2>/dev/null | head -1); \
+	if [ -n "$$branch" ] && command -v gh >/dev/null 2>&1; then \
+		gh pr create --title "$$release_title" --body "$$release_body" --base master --head "$$branch" 2>/dev/null \
+		|| gh pr edit "$$branch" --title "$$release_title" --body "$$release_body" 2>/dev/null \
+		|| echo "$(YELLOW)⚠ Could not create/update PR$(NC)"; \
+	fi
+
+jjpush-tag:
+	@version=$$(cat version.txt); \
+	tag_name="Release_$$version"; \
+	release_title=$$(cat /tmp/obitools4-release-title.txt 2>/dev/null || echo "Release $$version"); \
+	release_body=$$(cat /tmp/obitools4-release-body.txt 2>/dev/null || echo ""); \
+	install_section=$$'\n## Installation\n\n### Pre-built binaries\n\nDownload the appropriate archive for your system from the\n[release assets](https://github.com/metabarcoding/obitools4/releases/tag/Release_'"$$version"')\nand extract it:\n\n#### Linux (AMD64)\n```bash\ntar -xzf obitools4_'"$$version"'_linux_amd64.tar.gz\n```\n\n#### Linux (ARM64)\n```bash\ntar -xzf obitools4_'"$$version"'_linux_arm64.tar.gz\n```\n\n#### macOS (Intel)\n```bash\ntar -xzf obitools4_'"$$version"'_darwin_amd64.tar.gz\n```\n\n#### macOS (Apple Silicon)\n```bash\ntar -xzf obitools4_'"$$version"'_darwin_arm64.tar.gz\n```\n\nAll OBITools4 binaries are included in each archive.\n\n### From source\n\nYou can also compile and install OBITools4 directly from source using the\ninstallation script:\n\n```bash\ncurl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --version '"$$version"'\n```\n\nBy default binaries are installed in `/usr/local/bin`. Use `--install-dir` to\nchange the destination and `--obitools-prefix` to add a prefix to command names:\n\n```bash\ncurl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | \\\n  bash -s -- --version '"$$version"' --install-dir ~/local --obitools-prefix k\n```\n'; \
+	release_message="$$release_title"$$'\n\n'"$$release_body$$install_section"; \
+	echo "$(BLUE)→ Creating tag $$tag_name...$(NC)"; \
+	git tag -a "$$tag_name" -m "$$release_message" 2>/dev/null || echo "$(YELLOW)⚠ Tag $$tag_name already exists$(NC)"; \
+	echo "$(BLUE)→ Pushing tag $$tag_name...$(NC)"; \
+	git push origin "$$tag_name" 2>/dev/null || echo "$(YELLOW)⚠ Tag push failed or already pushed$(NC)"; \
+	rm -f /tmp/obitools4-release-title.txt /tmp/obitools4-release-body.txt
 
 jjfetch:
 	@echo "$(YELLOW)→ Pulling latest commits...$(NC)"
@@ -169,5 +239,5 @@ jjfetch:
 	@jj new master@origin
 	@echo "$(GREEN)✓ Latest commits pulled$(NC)"
 
-.PHONY: all obitools update-deps obitests githubtests jjnew jjpush jjfetch bump-version .FORCE
+.PHONY: all obitools update-deps obitests githubtests help jjnew jjpush jjpush-describe jjpush-bump jjpush-notes jjpush-push jjpush-tag jjfetch bump-version .FORCE
 .FORCE:

README.md

@@ -32,8 +32,12 @@ The installation script offers several options:
 > 
 >  -p, --obitools-prefix   Prefix added to the obitools command names if you
 >                          want to have several versions of obitools at the
->                          same time on your system (as example `-p g` will produce 
+>                          same time on your system (as example `-p g` will produce
 >                          `gobigrep` command instead of `obigrep`).
+>
+>  -j, --jobs              Number of parallel jobs used for compilation
+>                          (default: 1). Increase this value to speed up
+>                          compilation on multi-core systems (e.g., `-j 4`).
 
 ### Examples
 

blackboard/Prospective/large_sequence_parsing.md

@@ -0,0 +1,264 @@
+# Optimisation du parsing des grandes séquences
+
+## Contexte
+
+OBITools4 doit pouvoir traiter des séquences de taille chromosomique (plusieurs Gbp), notamment
+issues de fichiers GenBank/EMBL (assemblages de génomes) ou de fichiers FASTA convertis depuis
+ces formats.
+
+## Architecture actuelle
+
+### Pipeline de lecture (`pkg/obiformats/`)
+
+```
+ReadFileChunk (goroutine)
+    → ChannelFileChunk
+    → N × _ParseGenbankFile / _ParseFastaFile (goroutines)
+    → IBioSequence
+```
+
+`ReadFileChunk` (`file_chunk_read.go`) lit le fichier par morceaux via une chaîne de
+`PieceOfChunk` (rope). Chaque nœud fait `fileChunkSize` bytes :
+
+- GenBank/EMBL : 128 MB (`1024*1024*128`)
+- FASTA/FASTQ  : 1 MB (`1024*1024`)
+
+La chaîne est accumulée jusqu'à trouver la fin du dernier enregistrement complet (splitter),
+puis `Pack()` est appelé pour fusionner tous les nœuds en un seul buffer contigu. Ce buffer
+est transmis au parseur via `FileChunk.Raw *bytes.Buffer`.
+
+### Parseur GenBank (`genbank_read.go`)
+
+`GenbankChunkParser` reçoit un `io.Reader` sur le buffer packé, lit ligne par ligne via
+`bufio.NewReader` (buffer 4096 bytes), et pour chaque ligne de la section `ORIGIN` :
+
+```go
+line = string(bline)                        // allocation par ligne
+cleanline := strings.TrimSpace(line)        // allocation
+parts := strings.SplitN(cleanline, " ", 7) // allocation []string + substrings
+for i := 1; i < lparts; i++ {
+    seqBytes.WriteString(parts[i])
+}
+```
+
+Point positif : `seqBytes` est pré-alloué grâce à `lseq` extrait de la ligne `LOCUS`.
+
+### Parseur FASTA (`fastaseq_read.go`)
+
+`FastaChunkParser` lit **octet par octet** via `scanner.ReadByte()`. Pour 3 Gbp :
+3 milliards d'appels. `seqBytes` est un `bytes.Buffer{}` sans pré-allocation.
+
+## Problème principal
+
+Pour une séquence de plusieurs Gbp, `Pack()` fusionne une chaîne de ~N nœuds de 128 MB en
+un seul buffer contigu. C'est une allocation de N × 128 MB suivie d'une copie de toutes les
+données. Bien que l'implémentation de `Pack()` soit efficace (libère les nœuds au fur et à
+mesure via `slices.Grow`), la copie est inévitable avec l'architecture actuelle.
+
+De plus, le parseur GenBank produit des dizaines de millions d'allocations temporaires pour
+parser la section `ORIGIN` (une par ligne).
+
+## Invariant clé découvert
+
+**Si la rope a plus d'un nœud, le premier nœud seul ne se termine pas sur une frontière
+d'enregistrement** (pas de `//\n` en fin de `piece1`).
+
+Preuve par construction dans `ReadFileChunk` :
+- `splitter` est appelé dès le premier nœud (ligne 157)
+- Si `end >= 0` → frontière trouvée dans 128 MB → boucle interne sautée → rope à 1 nœud
+- Si `end < 0` → boucle interne ajoute des nœuds → rope à ≥ 2 nœuds
+
+Corollaire : si rope à 1 nœud, `Pack()` ne fait rien (aucun nœud suivant).
+
+**Attention** : rope à ≥ 2 nœuds ne signifie pas qu'il n'y a qu'une seule séquence dans
+la rope. La rope packée peut contenir plusieurs enregistrements complets. Exemple : records
+de 80 MB → `nextpieces` (48 MB de reste) + nouveau nœud (128 MB) = rope à 2 nœuds
+contenant 2 records complets + début d'un troisième.
+
+L'invariant dit seulement que `piece1` seul est incomplet — pas que la rope entière
+ne contient qu'un seul record.
+
+**Invariant : le dernier FileChunk envoyé finit sur une frontière d'enregistrement.**
+
+Deux chemins dans `ReadFileChunk` :
+
+1. **Chemin normal** (`end >= 0` via `splitter`) : le buffer est explicitement tronqué à
+   `end` (ligne 200 : `pieces.data = pieces.data[:end]`). Frontière garantie par construction
+   pour tous les formats. ✓
+
+2. **Chemin EOF** (`end < 0`, `end = pieces.Len()`) : tout le reste du fichier est envoyé.
+   - **GenBank/EMBL** : présuppose fichier bien formé (se termine par `//\n`). Le parseur
+     lève un `log.Fatalf` sur tout état inattendu — filet de sécurité suffisant. ✓
+   - **FASTQ** : présupposé, vérifié par le parseur. ✓
+   - **FASTA** : garanti par le format lui-même (fin d'enregistrement = EOF ou `>`). ✓
+
+**Hypothèse de travail adoptée** : les fichiers d'entrée sont bien formés. Dans le pire cas,
+le parseur lèvera une erreur explicite. Il n'y a pas de risque de corruption silencieuse.
+
+## Piste d'optimisation : se dispenser de Pack()
+
+### Idée centrale
+
+Au lieu de fusionner la rope avant de la passer au parseur, **parser directement la rope
+nœud par nœud**, et **écrire la séquence compactée in-place dans le premier nœud**.
+
+Pourquoi c'est sûr :
+- Le header (LOCUS, DEFINITION, SOURCE, FEATURES) est **petit** et traité en premier
+- La séquence (ORIGIN) est **à la fin** du record
+- Au moment d'écrire la séquence depuis l'offset 0 de `piece1`, le pointeur de lecture
+  est profond dans la rope (offset >> 0) → jamais de collision
+- La séquence compactée est toujours plus courte que les données brutes
+
+### Pré-allocation
+
+Pour GenBank/EMBL : `lseq` est connu dès la ligne `LOCUS`/`ID` (première ligne, dans
+`piece1`). On peut faire `slices.Grow(piece1.data, lseq)` dès ce moment.
+
+Pour FASTA : pas de taille garantie dans le header, mais `rope.Len()` donne un majorant.
+On peut utiliser `rope.Len() / 2` comme estimation initiale.
+
+### Gestion des jonctions entre nœuds
+
+Une ligne peut chevaucher deux nœuds (rare avec 128 MB, mais possible). Solution : carry
+buffer de ~128 bytes pour les quelques bytes en fin de nœud.
+
+### Cas FASTA/FASTQ multi-séquences
+
+Un FileChunk peut contenir N séquences (notamment FASTA/FASTQ courts). Dans ce cas
+l'écriture in-place dans `piece1` n'est pas applicable directement — on écrase des données
+nécessaires aux séquences suivantes.
+
+Stratégie par cas :
+- **Rope à 1 nœud** (record ≤ 128 MB) : `Pack()` est trivial (no-op), parseur actuel OK
+- **Rope à ≥ 2 nœuds** : par l'invariant, `piece1` ne contient pas de record complet →
+  une seule grande séquence → in-place applicable
+
+### Format d'une ligne séquence GenBank (Après ORIGIN)
+
+```
+/^ *[0-9]+( [nuc]{10}){0,5} [nuc]{1,10}/
+```
+
+### Format d'une ligne séquence GenBank (Après SQ)
+
+La ligne SQ contient aussi la taille de la séquence
+
+```
+/^ *( [nuc]{10}){0,5} [nuc]{1,10} *[0-9]+/
+```
+
+Compactage in-place sur `bline` ([]byte brut, sans conversion `string`) :
+
+```go
+w := 0
+i := 0
+for i < len(bline) && bline[i] == ' '  { i++ }   // skip indentation
+for i < len(bline) && bline[i] <= '9'  { i++ }   // skip position number
+for ; i < len(bline); i++ {
+    if bline[i] != ' ' {
+        bline[w] = bline[i]
+        w++
+    }
+}
+// écrire bline[:w] directement dans piece1.data[seqOffset:]
+```
+
+## Changements nécessaires
+
+1. **`FileChunk`** : exposer la rope `*PieceOfChunk` non-packée en plus (ou à la place)
+   de `Raw *bytes.Buffer`
+2. **`GenbankChunkParser` / `EmblChunkParser`** : accepter `*PieceOfChunk`, parser la
+   rope séquentiellement avec carry buffer pour les jonctions
+3. **`FastaChunkParser`** : idem, avec in-place conditionnel selon taille de la rope
+4. **`ReadFileChunk`** : ne pas appeler `Pack()` avant envoi sur le channel (ou version
+   alternative `ReadFileChunkRope`)
+
+## Fichiers concernés
+
+- `pkg/obiformats/file_chunk_read.go` — structure rope, `ReadFileChunk`
+- `pkg/obiformats/genbank_read.go` — `GenbankChunkParser`, `_ParseGenbankFile`
+- `pkg/obiformats/embl_read.go` — `EmblChunkParser`, `ReadEMBL`
+- `pkg/obiformats/fastaseq_read.go` — `FastaChunkParser`, `_ParseFastaFile`
+- `pkg/obiformats/fastqseq_read.go` — parseur FASTQ (même structure)
+
+## Plan d'implémentation : parseur GenBank sur rope
+
+### Contexte
+
+Baseline mesurée : `obiconvert gbpln640.seq.gz` → 49s real, 42s user, 29s sys, **57 GB RSS**.
+Le sys élevé indique des allocations massives. Deux causes :
+1. `Pack()` : fusionne toute la rope (N × 128 MB) en un buffer contigu avant de parser
+2. Parser ORIGIN : `string(bline)` + `TrimSpace` + `SplitN` × millions de lignes
+
+### 1. `gbRopeScanner`
+
+Struct de lecture ligne par ligne sur la rope, sans allocation heap :
+
+```go
+type gbRopeScanner struct {
+    current *PieceOfChunk
+    pos     int
+    carry   [256]byte  // stack-allocated, max GenBank line = 80 chars
+    carryN  int
+}
+```
+
+`ReadLine()` :
+- Cherche `\n` dans `current.data[pos:]` via `bytes.IndexByte`
+- Si trouvé sans carry : retourne slice direct du node (zéro alloc)
+- Si trouvé avec carry : copie dans carry buffer, retourne `carry[:n]`
+- Si non trouvé : copie le reste dans carry, avance au node suivant, recommence
+- EOF : retourne `carry[:carryN]` puis nil
+
+`extractSequence(dest []byte, UtoT bool) int` :
+- Scan direct des bytes pour section ORIGIN, sans passer par ReadLine
+- Machine d'états : lineStart → skip espaces/digits → copier nucléotides dans dest
+- Stop sur `//` en début de ligne
+- Zéro allocation, UtoT inline
+
+### 2. `GenbankChunkParserRope`
+
+```go
+func GenbankChunkParserRope(source string, rope *PieceOfChunk,
+    withFeatureTable, UtoT bool) (obiseq.BioSequenceSlice, error)
+```
+
+- Même machine d'états que `GenbankChunkParser`, sur `[]byte` (`bytes.HasPrefix`)
+- LOCUS : extrait `id` et `lseq` par scan direct (remplace `_seqlenght_rx`)
+- FEATURES / default inFeature : taxid extrait par scan de `/db_xref="taxon:`
+  dans la source feature ; `featBytes` rempli seulement si `withFeatureTable=true`
+- DEFINITION : toujours conservée
+- ORIGIN : `dest = make([]byte, 0, lseq+20)` puis `s.extractSequence(dest, UtoT)`
+
+### 3. Modifications `_ParseGenbankFile` et `ReadGenbank`
+
+`_ParseGenbankFile` utilise `chunk.Rope` :
+```go
+sequences, err := GenbankChunkParserRope(chunk.Source, chunk.Rope, ...)
+```
+
+`ReadGenbank` passe `pack=false` :
+```go
+entry_channel := ReadFileChunk(..., false)
+```
+
+### 4. Ce qui NE change pas
+
+- `GenbankChunkParser` reste (référence, tests)
+- `ReadFileChunk`, `Pack()`, autres parseurs (EMBL, FASTA, FASTQ) : inchangés
+
+### 5. Gains attendus
+
+- **RSS** : pic ≈ 128 MB × workers (au lieu de N × 128 MB)
+- **Temps sys** : élimination des mmap/munmap pour les gros buffers
+- **Temps user** : ~50M allocations éliminées
+
+### 6. Vérification
+
+```bash
+/usr/local/go/bin/go build ./...
+diff <(obiconvert gbpln640.seq.gz) gbpln640.reference.fasta
+cd bugs/genbank && ./benchmark.sh gbpln640.seq.gz
+```
+
+Cible : RSS < 1 GB, temps comparable ou meilleur.

install_obitools.sh

@@ -7,6 +7,7 @@ INSTALL_DIR="/usr/local"
 OBITOOLS_PREFIX=""
 VERSION=""
 LIST_VERSIONS=false
+JOBS=1
 
 # Help message
 function display_help {
@@ -21,6 +22,7 @@ function display_help {
   echo "                          gobigrep command instead of obigrep)."
   echo "  -v, --version           Install a specific version (e.g., 4.4.8)."
   echo "                          If not specified, installs the latest version."
+  echo "  -j, --jobs              Number of parallel jobs for compilation (default: 1)."
   echo "  -l, --list              List all available versions and exit."
   echo "  -h, --help              Display this help message."
   echo ""
@@ -65,6 +67,10 @@ while [ "$#" -gt 0 ]; do
       VERSION="$2"
       shift 2
       ;;
+    -j|--jobs)
+      JOBS="$2"
+      shift 2
+      ;;
     -l|--list)
       LIST_VERSIONS=true
       shift
@@ -122,9 +128,15 @@ mkdir -p "${WORK_DIR}/cache" \
       exit 1)
 
 # Create installation directory
-mkdir -p "${INSTALL_DIR}/bin" 2> /dev/null \
+if ! mkdir -p "${INSTALL_DIR}/bin" 2>/dev/null; then
-  || (echo "Please enter your password for installing obitools in ${INSTALL_DIR}" 1>&2
+  if [ ! -w "$(dirname "${INSTALL_DIR}")" ] && [ ! -w "${INSTALL_DIR}" ]; then
-      sudo mkdir -p "${INSTALL_DIR}/bin")
+    echo "Please enter your password for installing obitools in ${INSTALL_DIR}" 1>&2
+    sudo mkdir -p "${INSTALL_DIR}/bin"
+  else
+    echo "Error: Could not create ${INSTALL_DIR}/bin (check path or disk space)" 1>&2
+    exit 1
+  fi
+fi
 
 if [[ ! -d "${INSTALL_DIR}/bin" ]]; then
   echo "Could not create ${INSTALL_DIR}/bin directory for installing obitools" 1>&2
@@ -208,16 +220,29 @@ mkdir -p vendor
 
 # Build with or without prefix
 if [[ -z "$OBITOOLS_PREFIX" ]] ; then
-  make GOFLAGS="-buildvcs=false"
+  make -j"${JOBS}" obitools GOFLAGS="-buildvcs=false"
 else
-  make GOFLAGS="-buildvcs=false" OBITOOLS_PREFIX="${OBITOOLS_PREFIX}"
+  make -j"${JOBS}" obitools GOFLAGS="-buildvcs=false" OBITOOLS_PREFIX="${OBITOOLS_PREFIX}"
 fi
 
 # Install binaries
 echo "Installing binaries to ${INSTALL_DIR}/bin..." 1>&2
-(cp build/* "${INSTALL_DIR}/bin" 2> /dev/null) \
+if ! cp build/* "${INSTALL_DIR}/bin" 2>/dev/null; then
-   || (echo "Please enter your password for installing obitools in ${INSTALL_DIR}" 1>&2
+  if [ ! -w "${INSTALL_DIR}/bin" ]; then
-       sudo cp build/* "${INSTALL_DIR}/bin")
+    echo "Please enter your password for installing obitools in ${INSTALL_DIR}" 1>&2
+    sudo cp build/* "${INSTALL_DIR}/bin"
+  else
+    echo "Error: Could not copy binaries to ${INSTALL_DIR}/bin" 1>&2
+    echo "  Source files: $(ls build/ 2>/dev/null || echo 'none found')" 1>&2
+    echo "" 1>&2
+    echo "The build directory has been preserved for manual recovery:" 1>&2
+    echo "  $(pwd)/build/" 1>&2
+    echo "You can install manually with:" 1>&2
+    echo "  cp $(pwd)/build/* ${INSTALL_DIR}/bin/" 1>&2
+    popd > /dev/null || true
+    exit 1
+  fi
+fi
 
 popd > /dev/null || exit
 

pkg/obiformats/embl_read.go

@@ -161,6 +161,149 @@ func EmblChunkParser(withFeatureTable, UtoT bool) func(string, io.Reader) (obise
 	return parser
 }
 
+// extractEmblSeq scans the sequence section of an EMBL record directly on the
+// rope. EMBL sequence lines start with 5 spaces followed by bases in groups of
+// 10, separated by spaces, with a position number at the end. The section ends
+// with "//".
+func (s *ropeScanner) extractEmblSeq(dest []byte, UtoT bool) []byte {
+	// We use ReadLine and scan each line for bases (skip digits, spaces, newlines).
+	for {
+		line := s.ReadLine()
+		if line == nil {
+			break
+		}
+		if len(line) >= 2 && line[0] == '/' && line[1] == '/' {
+			break
+		}
+		// Lines start with 5 spaces; bases follow separated by single spaces.
+		// Digits at the end are the position counter — skip them.
+		// Simplest: take every byte that is a letter.
+		for _, b := range line {
+			if b >= 'A' && b <= 'Z' {
+				b += 'a' - 'A'
+			}
+			if UtoT && b == 'u' {
+				b = 't'
+			}
+			if b >= 'a' && b <= 'z' {
+				dest = append(dest, b)
+			}
+		}
+	}
+	return dest
+}
+
+// EmblChunkParserRope parses an EMBL chunk directly from a rope without Pack().
+func EmblChunkParserRope(source string, rope *PieceOfChunk, withFeatureTable, UtoT bool) (obiseq.BioSequenceSlice, error) {
+	scanner := newRopeScanner(rope)
+	sequences := obiseq.MakeBioSequenceSlice(100)[:0]
+
+	var id string
+	var scientificName string
+	defBytes := make([]byte, 0, 256)
+	featBytes := make([]byte, 0, 1024)
+	var taxid int
+	inSeq := false
+
+	for {
+		line := scanner.ReadLine()
+		if line == nil {
+			break
+		}
+
+		if inSeq {
+			// Should not happen — extractEmblSeq consumed up to "//"
+			inSeq = false
+			continue
+		}
+
+		switch {
+		case bytes.HasPrefix(line, []byte("ID   ")):
+			id = string(bytes.SplitN(line[5:], []byte(";"), 2)[0])
+		case bytes.HasPrefix(line, []byte("OS   ")):
+			scientificName = string(bytes.TrimSpace(line[5:]))
+		case bytes.HasPrefix(line, []byte("DE   ")):
+			if len(defBytes) > 0 {
+				defBytes = append(defBytes, ' ')
+			}
+			defBytes = append(defBytes, bytes.TrimSpace(line[5:])...)
+		case withFeatureTable && bytes.HasPrefix(line, []byte("FH   ")):
+			featBytes = append(featBytes, line...)
+		case withFeatureTable && bytes.Equal(line, []byte("FH")):
+			featBytes = append(featBytes, '\n')
+			featBytes = append(featBytes, line...)
+		case bytes.HasPrefix(line, []byte("FT   ")):
+			if withFeatureTable {
+				featBytes = append(featBytes, '\n')
+				featBytes = append(featBytes, line...)
+			}
+			if bytes.HasPrefix(line, []byte(`FT                   /db_xref="taxon:`)) {
+				rest := line[37:]
+				end := bytes.IndexByte(rest, '"')
+				if end > 0 {
+					taxid, _ = strconv.Atoi(string(rest[:end]))
+				}
+			}
+		case bytes.HasPrefix(line, []byte("     ")):
+			// First sequence line: extract all bases via extractEmblSeq,
+			// which also consumes this line's remaining content.
+			// But ReadLine already consumed this line — we need to process it
+			// plus subsequent lines. Process this line inline then call helper.
+			seqDest := make([]byte, 0, 4096)
+			for _, b := range line {
+				if b >= 'A' && b <= 'Z' {
+					b += 'a' - 'A'
+				}
+				if UtoT && b == 'u' {
+					b = 't'
+				}
+				if b >= 'a' && b <= 'z' {
+					seqDest = append(seqDest, b)
+				}
+			}
+			seqDest = scanner.extractEmblSeq(seqDest, UtoT)
+
+			seq := obiseq.NewBioSequenceOwning(id, seqDest, string(defBytes))
+			seq.SetSource(source)
+			if withFeatureTable {
+				seq.SetFeatures(featBytes)
+			}
+			annot := seq.Annotations()
+			annot["scientific_name"] = scientificName
+			annot["taxid"] = taxid
+			sequences = append(sequences, seq)
+
+			// Reset state
+			id = ""
+			scientificName = ""
+			defBytes = defBytes[:0]
+			featBytes = featBytes[:0]
+			taxid = 1
+
+		case bytes.Equal(line, []byte("//")):
+			// record ended without SQ/sequence section (e.g. WGS entries)
+			if id != "" {
+				seq := obiseq.NewBioSequenceOwning(id, []byte{}, string(defBytes))
+				seq.SetSource(source)
+				if withFeatureTable {
+					seq.SetFeatures(featBytes)
+				}
+				annot := seq.Annotations()
+				annot["scientific_name"] = scientificName
+				annot["taxid"] = taxid
+				sequences = append(sequences, seq)
+			}
+			id = ""
+			scientificName = ""
+			defBytes = defBytes[:0]
+			featBytes = featBytes[:0]
+			taxid = 1
+		}
+	}
+
+	return sequences, nil
+}
+
 func _ParseEmblFile(
 	input ChannelFileChunk,
 	out obiiter.IBioSequence,
@@ -171,7 +314,14 @@ func _ParseEmblFile(
 
 	for chunks := range input {
 		order := chunks.Order
-		sequences, err := parser(chunks.Source, chunks.Raw)
+		var sequences obiseq.BioSequenceSlice
+		var err error
+
+		if chunks.Rope != nil {
+			sequences, err = EmblChunkParserRope(chunks.Source, chunks.Rope, withFeatureTable, UtoT)
+		} else {
+			sequences, err = parser(chunks.Source, chunks.Raw)
+		}
 
 		if err != nil {
 			log.Fatalf("%s : Cannot parse the embl file : %v", chunks.Source, err)
@@ -196,6 +346,7 @@ func ReadEMBL(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, er
 		1024*1024*128,
 		EndOfLastFlatFileEntry,
 		"\nID   ",
+		false,
 	)
 
 	newIter := obiiter.MakeIBioSequence()

pkg/obiformats/fastaseq_read.go

@@ -209,28 +209,121 @@ func FastaChunkParser(UtoT bool) func(string, io.Reader) (obiseq.BioSequenceSlic
 	return parser
 }
 
+// extractFastaSeq scans sequence bytes from the rope directly into dest,
+// appending valid nucleotide characters and skipping whitespace.
+// Stops when '>' is found at the start of a line (next record) or at EOF.
+// Returns (dest with appended bases, hasMore).
+// hasMore=true means scanner is now positioned at '>' of the next record.
+func (s *ropeScanner) extractFastaSeq(dest []byte, UtoT bool) ([]byte, bool) {
+	lineStart := true
+
+	for s.current != nil {
+		data := s.current.data[s.pos:]
+		for i, b := range data {
+			if lineStart && b == '>' {
+				s.pos += i
+				if s.pos >= len(s.current.data) {
+					s.current = s.current.Next()
+					s.pos = 0
+				}
+				return dest, true
+			}
+			if b == '\n' || b == '\r' {
+				lineStart = true
+				continue
+			}
+			lineStart = false
+			if b == ' ' || b == '\t' {
+				continue
+			}
+			if b >= 'A' && b <= 'Z' {
+				b += 'a' - 'A'
+			}
+			if UtoT && b == 'u' {
+				b = 't'
+			}
+			dest = append(dest, b)
+		}
+		s.current = s.current.Next()
+		s.pos = 0
+	}
+	return dest, false
+}
+
+// FastaChunkParserRope parses a FASTA chunk directly from the rope without Pack().
+func FastaChunkParserRope(source string, rope *PieceOfChunk, UtoT bool) (obiseq.BioSequenceSlice, error) {
+	scanner := newRopeScanner(rope)
+	sequences := obiseq.MakeBioSequenceSlice(100)[:0]
+
+	for {
+		bline := scanner.ReadLine()
+		if bline == nil {
+			break
+		}
+		if len(bline) == 0 || bline[0] != '>' {
+			continue
+		}
+
+		// Parse header: ">id definition"
+		header := bline[1:]
+		var id string
+		var definition string
+		sp := bytes.IndexByte(header, ' ')
+		if sp < 0 {
+			sp = bytes.IndexByte(header, '\t')
+		}
+		if sp < 0 {
+			id = string(header)
+		} else {
+			id = string(header[:sp])
+			definition = string(bytes.TrimSpace(header[sp+1:]))
+		}
+
+		seqDest := make([]byte, 0, 4096)
+		var hasMore bool
+		seqDest, hasMore = scanner.extractFastaSeq(seqDest, UtoT)
+
+		if len(seqDest) == 0 {
+			log.Fatalf("%s [%s]: sequence is empty", source, id)
+		}
+
+		seq := obiseq.NewBioSequenceOwning(id, seqDest, definition)
+		seq.SetSource(source)
+		sequences = append(sequences, seq)
+
+		if !hasMore {
+			break
+		}
+	}
+
+	return sequences, nil
+}
+
 func _ParseFastaFile(
 	input ChannelFileChunk,
 	out obiiter.IBioSequence,
 	UtoT bool,
 ) {
-
 	parser := FastaChunkParser(UtoT)
 
 	for chunks := range input {
-		sequences, err := parser(chunks.Source, chunks.Raw)
+		var sequences obiseq.BioSequenceSlice
-		// obilog.Warnf("Chunck(%d:%d) -%d- ", chunks.Order, l, sequences.Len())
+		var err error
+
+		if chunks.Rope != nil {
+			sequences, err = FastaChunkParserRope(chunks.Source, chunks.Rope, UtoT)
+		} else {
+			sequences, err = parser(chunks.Source, chunks.Raw)
+		}
 
 		if err != nil {
 			log.Fatalf("File %s : Cannot parse the fasta file : %v", chunks.Source, err)
 		}
 
 		out.Push(obiiter.MakeBioSequenceBatch(chunks.Source, chunks.Order, sequences))
-
 	}
 
 	out.Done()
-
 }
 
 func ReadFasta(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, error) {
@@ -245,6 +338,7 @@ func ReadFasta(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, e
 		1024*1024,
 		EndOfLastFastaEntry,
 		"\n>",
+		false,
 	)
 
 	for i := 0; i < nworker; i++ {

pkg/obiformats/fastqseq_read.go

@@ -303,6 +303,80 @@ func FastqChunkParser(quality_shift byte, with_quality bool, UtoT bool) func(str
 	return parser
 }
 
+// FastqChunkParserRope parses a FASTQ chunk directly from a rope without Pack().
+func FastqChunkParserRope(source string, rope *PieceOfChunk, quality_shift byte, with_quality, UtoT bool) (obiseq.BioSequenceSlice, error) {
+	scanner := newRopeScanner(rope)
+	sequences := obiseq.MakeBioSequenceSlice(100)[:0]
+
+	for {
+		// Line 1: @id [definition]
+		hline := scanner.ReadLine()
+		if hline == nil {
+			break
+		}
+		if len(hline) == 0 || hline[0] != '@' {
+			continue
+		}
+		header := hline[1:]
+		var id string
+		var definition string
+		sp := bytes.IndexByte(header, ' ')
+		if sp < 0 {
+			sp = bytes.IndexByte(header, '\t')
+		}
+		if sp < 0 {
+			id = string(header)
+		} else {
+			id = string(header[:sp])
+			definition = string(bytes.TrimSpace(header[sp+1:]))
+		}
+
+		// Line 2: sequence
+		sline := scanner.ReadLine()
+		if sline == nil {
+			log.Fatalf("@%s[%s]: unexpected EOF after header", id, source)
+		}
+		seqDest := make([]byte, len(sline))
+		w := 0
+		for _, b := range sline {
+			if b >= 'A' && b <= 'Z' {
+				b += 'a' - 'A'
+			}
+			if UtoT && b == 'u' {
+				b = 't'
+			}
+			seqDest[w] = b
+			w++
+		}
+		seqDest = seqDest[:w]
+		if len(seqDest) == 0 {
+			log.Fatalf("@%s[%s]: sequence is empty", id, source)
+		}
+
+		// Line 3: + (skip)
+		scanner.ReadLine()
+
+		// Line 4: quality
+		qline := scanner.ReadLine()
+
+		seq := obiseq.NewBioSequenceOwning(id, seqDest, definition)
+		seq.SetSource(source)
+
+		if with_quality && qline != nil {
+			qDest := make([]byte, len(qline))
+			copy(qDest, qline)
+			for i := range qDest {
+				qDest[i] -= quality_shift
+			}
+			seq.TakeQualities(qDest)
+		}
+
+		sequences = append(sequences, seq)
+	}
+
+	return sequences, nil
+}
+
 func _ParseFastqFile(
 	input ChannelFileChunk,
 	out obiiter.IBioSequence,
@@ -313,7 +387,14 @@ func _ParseFastqFile(
 	parser := FastqChunkParser(quality_shift, with_quality, UtoT)
 
 	for chunks := range input {
-		sequences, err := parser(chunks.Source, chunks.Raw)
+		var sequences obiseq.BioSequenceSlice
+		var err error
+
+		if chunks.Rope != nil {
+			sequences, err = FastqChunkParserRope(chunks.Source, chunks.Rope, quality_shift, with_quality, UtoT)
+		} else {
+			sequences, err = parser(chunks.Source, chunks.Raw)
+		}
 
 		if err != nil {
 			log.Fatalf("File %s : Cannot parse the fastq file : %v", chunks.Source, err)
@@ -339,6 +420,7 @@ func ReadFastq(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, e
 		1024*1024,
 		EndOfLastFastqEntry,
 		"\n@",
+		false,
 	)
 
 	for i := 0; i < nworker; i++ {

pkg/obiformats/fastseq_json_header.go

@@ -296,7 +296,7 @@ func _parse_json_header_(header string, sequence *obiseq.BioSequence) string {
 
 			case strings.HasSuffix(skey, "_taxid"):
 				if dataType == jsonparser.Number || dataType == jsonparser.String {
-					rank, _ := obiutils.SplitInTwo(skey, '_')
+					rank := skey[:len(skey)-len("_taxid")]
 
 					taxid := string(value)
 					sequence.SetTaxid(taxid, rank)

pkg/obiformats/fastseq_write_fasta.go

@@ -77,45 +77,47 @@ func FormatFasta(seq *obiseq.BioSequence, formater FormatHeader) string {
 //
 // It returns a byte array containing the formatted sequences.
 func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader, skipEmpty bool) *bytes.Buffer {
-	// Create a buffer to store the formatted sequences
 	var bs bytes.Buffer
 
 	lt := 0
-
 	for _, seq := range batch.Slice() {
 		lt += seq.Len()
 	}
 
-	// Iterate over each sequence in the batch
+	// Pre-allocate: sequence data + newlines every 60 chars + ~100 bytes header per sequence
+	bs.Grow(lt + lt/60 + 100*batch.Len() + 1)
+
 	log.Debugf("FormatFastaBatch: #%d : %d seqs", batch.Order(), batch.Len())
-	first := true
+
 	for _, seq := range batch.Slice() {
-		// Check if the sequence is empty
 		if seq.Len() > 0 {
-			// Format the sequence using the provided formater function
+			// Write header directly into bs — no intermediate string
-			formattedSeq := FormatFasta(seq, formater)
+			bs.WriteByte('>')
-
+			bs.WriteString(seq.Id())
-			if first {
+			bs.WriteByte(' ')
-				bs.Grow(lt + (len(formattedSeq)-seq.Len())*batch.Len()*5/4)
+			bs.WriteString(formater(seq))
-				first = false
-			}
-
-			// Append the formatted sequence to the buffer
-			bs.WriteString(formattedSeq)
 			bs.WriteByte('\n')
+
+			// Write folded sequence directly into bs — no copies
+			s := seq.Sequence()
+			l := len(s)
+			for i := 0; i < l; i += 60 {
+				to := i + 60
+				if to > l {
+					to = l
+				}
+				bs.Write(s[i:to])
+				bs.WriteByte('\n')
+			}
 		} else {
-			// Handle empty sequences
 			if skipEmpty {
-				// Skip empty sequences if skipEmpty is true
 				obilog.Warnf("Sequence %s is empty and skipped in output", seq.Id())
 			} else {
-				// Terminate the program if skipEmpty is false
 				log.Fatalf("Sequence %s is empty", seq.Id())
 			}
 		}
 	}
 
-	// Return the byte array representation of the buffer
 	return &bs
 }
 

pkg/obiformats/file_chunk_read.go

@@ -16,6 +16,7 @@ type SeqFileChunkParser func(string, io.Reader) (obiseq.BioSequenceSlice, error)
 type FileChunk struct {
 	Source string
 	Raw    *bytes.Buffer
+	Rope   *PieceOfChunk
 	Order  int
 }
 
@@ -97,11 +98,17 @@ func (piece *PieceOfChunk) IsLast() bool {
 	return piece.next == nil
 }
 
-func (piece *PieceOfChunk) FileChunk(source string, order int) FileChunk {
+func (piece *PieceOfChunk) FileChunk(source string, order int, pack bool) FileChunk {
-	piece.Pack()
+	piece = piece.Head()
+	var raw *bytes.Buffer
+	if pack {
+		piece.Pack()
+		raw = bytes.NewBuffer(piece.data)
+	}
 	return FileChunk{
 		Source: source,
-		Raw:    bytes.NewBuffer(piece.data),
+		Raw:    raw,
+		Rope:   piece,
 		Order:  order,
 	}
 }
@@ -133,7 +140,8 @@ func ReadFileChunk(
 	reader io.Reader,
 	fileChunkSize int,
 	splitter LastSeqRecord,
-	probe string) ChannelFileChunk {
+	probe string,
+	pack bool) ChannelFileChunk {
 
 	chunk_channel := make(ChannelFileChunk)
 
@@ -205,7 +213,7 @@ func ReadFileChunk(
 
 				if len(pieces.data) > 0 {
 					// obilog.Warnf("chuck %d :Read %d bytes from file %s", i, io.Len(), source)
-					chunk_channel <- pieces.FileChunk(source, i)
+					chunk_channel <- pieces.FileChunk(source, i, pack)
 					i++
 				}
 
@@ -222,7 +230,7 @@ func ReadFileChunk(
 
 		// Send the last chunk to the channel
 		if pieces.Len() > 0 {
-			chunk_channel <- pieces.FileChunk(source, i)
+			chunk_channel <- pieces.FileChunk(source, i, pack)
 		}
 
 		// Close the readers channel when the end of the file is reached

pkg/obiformats/genbank_read.go

@@ -29,6 +29,265 @@ const (
 
 var _seqlenght_rx = regexp.MustCompile(" +([0-9]+) bp")
 
+// extractSequence scans the ORIGIN section byte-by-byte directly on the rope,
+// appending compacted bases to dest. Returns the extended slice.
+// Stops and returns when "//" is found at the start of a line.
+// The scanner is left positioned after the "//" line.
+func (s *ropeScanner) extractSequence(dest []byte, UtoT bool) []byte {
+	lineStart := true
+	skipDigits := true
+
+	for s.current != nil {
+		data := s.current.data[s.pos:]
+		for i, b := range data {
+			if lineStart {
+				if b == '/' {
+					// End-of-record marker "//"
+					s.pos += i + 1
+					if s.pos >= len(s.current.data) {
+						s.current = s.current.Next()
+						s.pos = 0
+					}
+					s.skipToNewline()
+					return dest
+				}
+				lineStart = false
+				skipDigits = true
+			}
+			switch {
+			case b == '\n':
+				lineStart = true
+			case b == '\r':
+				// skip
+			case skipDigits:
+				if b != ' ' && (b < '0' || b > '9') {
+					skipDigits = false
+					if UtoT && b == 'u' {
+						b = 't'
+					}
+					dest = append(dest, b)
+				}
+			case b != ' ':
+				if UtoT && b == 'u' {
+					b = 't'
+				}
+				dest = append(dest, b)
+			}
+		}
+		s.current = s.current.Next()
+		s.pos = 0
+	}
+	return dest
+}
+
+// parseLseqFromLocus extracts the declared sequence length from a LOCUS line.
+// Format: "LOCUS       <id> <length> bp ..."
+// Returns -1 if not found or parse error.
+func parseLseqFromLocus(line []byte) int {
+	if len(line) < 13 {
+		return -1
+	}
+	i := 12
+	for i < len(line) && line[i] != ' ' {
+		i++
+	}
+	for i < len(line) && line[i] == ' ' {
+		i++
+	}
+	start := i
+	for i < len(line) && line[i] >= '0' && line[i] <= '9' {
+		i++
+	}
+	if i == start {
+		return -1
+	}
+	n, err := strconv.Atoi(string(line[start:i]))
+	if err != nil {
+		return -1
+	}
+	return n
+}
+
+// Prefix constants for GenBank section headers (byte slices for zero-alloc comparison).
+var (
+	gbPfxLocus      = []byte("LOCUS       ")
+	gbPfxDefinition = []byte("DEFINITION  ")
+	gbPfxContinue   = []byte("            ")
+	gbPfxSource     = []byte("SOURCE      ")
+	gbPfxFeatures   = []byte("FEATURES    ")
+	gbPfxOrigin     = []byte("ORIGIN")
+	gbPfxContig     = []byte("CONTIG")
+	gbPfxEnd        = []byte("//")
+	gbPfxDbXref     = []byte(`                     /db_xref="taxon:`)
+)
+
+// GenbankChunkParserRope parses a GenBank FileChunk directly from the rope
+// (PieceOfChunk linked list) without calling Pack(). This eliminates the large
+// contiguous allocation required for chromosomal-scale sequences.
+func GenbankChunkParserRope(source string, rope *PieceOfChunk,
+	withFeatureTable, UtoT bool) (obiseq.BioSequenceSlice, error) {
+
+	state := inHeader
+	scanner := newRopeScanner(rope)
+	sequences := obiseq.MakeBioSequenceSlice(100)[:0]
+
+	id := ""
+	lseq := -1
+	scientificName := ""
+	defBytes := new(bytes.Buffer)
+	featBytes := new(bytes.Buffer)
+	var seqDest []byte
+	taxid := 1
+	nl := 0
+
+	for bline := scanner.ReadLine(); bline != nil; bline = scanner.ReadLine() {
+		nl++
+		processed := false
+		for !processed {
+			switch {
+
+			case bytes.HasPrefix(bline, gbPfxLocus):
+				if state != inHeader {
+					log.Fatalf("Line %d - Unexpected state %d while reading LOCUS: %s", nl, state, bline)
+				}
+				rest := bline[12:]
+				sp := bytes.IndexByte(rest, ' ')
+				if sp < 0 {
+					id = string(rest)
+				} else {
+					id = string(rest[:sp])
+				}
+				lseq = parseLseqFromLocus(bline)
+				cap0 := lseq + 20
+				if cap0 < 1024 {
+					cap0 = 1024
+				}
+				seqDest = make([]byte, 0, cap0)
+				state = inEntry
+				processed = true
+
+			case bytes.HasPrefix(bline, gbPfxDefinition):
+				if state != inEntry {
+					log.Fatalf("Line %d - Unexpected state %d while reading DEFINITION: %s", nl, state, bline)
+				}
+				defBytes.Write(bytes.TrimSpace(bline[12:]))
+				state = inDefinition
+				processed = true
+
+			case state == inDefinition:
+				if bytes.HasPrefix(bline, gbPfxContinue) {
+					defBytes.WriteByte(' ')
+					defBytes.Write(bytes.TrimSpace(bline[12:]))
+					processed = true
+				} else {
+					state = inEntry
+				}
+
+			case bytes.HasPrefix(bline, gbPfxSource):
+				if state != inEntry {
+					log.Fatalf("Line %d - Unexpected state %d while reading SOURCE: %s", nl, state, bline)
+				}
+				scientificName = string(bytes.TrimSpace(bline[12:]))
+				processed = true
+
+			case bytes.HasPrefix(bline, gbPfxFeatures):
+				if state != inEntry {
+					log.Fatalf("Line %d - Unexpected state %d while reading FEATURES: %s", nl, state, bline)
+				}
+				if withFeatureTable {
+					featBytes.Write(bline)
+				}
+				state = inFeature
+				processed = true
+
+			case bytes.HasPrefix(bline, gbPfxOrigin):
+				if state != inFeature && state != inContig {
+					log.Fatalf("Line %d - Unexpected state %d while reading ORIGIN: %s", nl, state, bline)
+				}
+				// Use fast byte-scan to extract sequence and consume through "//"
+				seqDest = scanner.extractSequence(seqDest, UtoT)
+				// Emit record
+				if id == "" {
+					log.Warn("Empty id when parsing genbank file")
+				}
+				sequence := obiseq.NewBioSequenceOwning(id, seqDest, defBytes.String())
+				sequence.SetSource(source)
+				if withFeatureTable {
+					sequence.SetFeatures(featBytes.Bytes())
+				}
+				annot := sequence.Annotations()
+				annot["scientific_name"] = scientificName
+				annot["taxid"] = taxid
+				sequences = append(sequences, sequence)
+
+				defBytes = bytes.NewBuffer(obiseq.GetSlice(200))
+				featBytes = new(bytes.Buffer)
+				nl = 0
+				taxid = 1
+				seqDest = nil
+				state = inHeader
+				processed = true
+
+			case bytes.HasPrefix(bline, gbPfxContig):
+				if state != inFeature && state != inContig {
+					log.Fatalf("Line %d - Unexpected state %d while reading CONTIG: %s", nl, state, bline)
+				}
+				state = inContig
+				processed = true
+
+			case bytes.Equal(bline, gbPfxEnd):
+				// Reached for CONTIG records (no ORIGIN section)
+				if state != inContig {
+					log.Fatalf("Line %d - Unexpected state %d while reading end of record %s", nl, state, id)
+				}
+				if id == "" {
+					log.Warn("Empty id when parsing genbank file")
+				}
+				sequence := obiseq.NewBioSequenceOwning(id, seqDest, defBytes.String())
+				sequence.SetSource(source)
+				if withFeatureTable {
+					sequence.SetFeatures(featBytes.Bytes())
+				}
+				annot := sequence.Annotations()
+				annot["scientific_name"] = scientificName
+				annot["taxid"] = taxid
+				sequences = append(sequences, sequence)
+
+				defBytes = bytes.NewBuffer(obiseq.GetSlice(200))
+				featBytes = new(bytes.Buffer)
+				nl = 0
+				taxid = 1
+				seqDest = nil
+				state = inHeader
+				processed = true
+
+			default:
+				switch state {
+				case inFeature:
+					if withFeatureTable {
+						featBytes.WriteByte('\n')
+						featBytes.Write(bline)
+					}
+					if bytes.HasPrefix(bline, gbPfxDbXref) {
+						rest := bline[len(gbPfxDbXref):]
+						q := bytes.IndexByte(rest, '"')
+						if q >= 0 {
+							taxid, _ = strconv.Atoi(string(rest[:q]))
+						}
+					}
+					processed = true
+				case inHeader, inEntry, inContig:
+					processed = true
+				default:
+					log.Fatalf("Unexpected state %d while reading: %s", state, bline)
+				}
+			}
+		}
+	}
+
+	return sequences, nil
+}
+
 func GenbankChunkParser(withFeatureTable, UtoT bool) func(string, io.Reader) (obiseq.BioSequenceSlice, error) {
 	return func(source string, input io.Reader) (obiseq.BioSequenceSlice, error) {
 		state := inHeader
@@ -125,13 +384,10 @@ func GenbankChunkParser(withFeatureTable, UtoT bool) func(string, io.Reader) (ob
 					if state != inSequence && state != inContig {
 						log.Fatalf("Line %d - Unexpected state %d while reading end of record %s", nl, state, id)
 					}
-					// log.Debugln("Total lines := ", nl)
 					if id == "" {
 						log.Warn("Empty id when parsing genbank file")
 					}
 
-					// log.Debugf("End of sequence %s: %dbp ", id, seqBytes.Len())
-
 					sequence := obiseq.NewBioSequence(id,
 						seqBytes.Bytes(),
 						defBytes.String())
@@ -144,9 +400,6 @@ func GenbankChunkParser(withFeatureTable, UtoT bool) func(string, io.Reader) (ob
 					annot := sequence.Annotations()
 					annot["scientific_name"] = scientificName
 					annot["taxid"] = taxid
-					// log.Println(FormatFasta(sequence, FormatFastSeqJsonHeader))
-					// log.Debugf("Read sequences %s: %dbp (%d)", sequence.Id(),
-					//	sequence.Len(), seqBytes.Len())
 
 					sequences = append(sequences, sequence)
 
@@ -159,12 +412,11 @@ func GenbankChunkParser(withFeatureTable, UtoT bool) func(string, io.Reader) (ob
 					processed = true
 
 				case state == inSequence:
-					// log.Debugf("Chunk %d : Genbank: line %d, state = %d : %s", chunks.order, nl, state, line)
-
 					sl++
-					parts := strings.SplitN(line[10:], " ", 6)
+					cleanline := strings.TrimSpace(line)
+					parts := strings.SplitN(cleanline, " ", 7)
 					lparts := len(parts)
-					for i := 0; i < lparts; i++ {
+					for i := 1; i < lparts; i++ {
 						if UtoT {
 							parts[i] = strings.ReplaceAll(parts[i], "u", "t")
 						}
@@ -197,6 +449,7 @@ func GenbankChunkParser(withFeatureTable, UtoT bool) func(string, io.Reader) (ob
 
 		}
 
+		_ = sl
 		return sequences, nil
 	}
 }
@@ -205,10 +458,16 @@ func _ParseGenbankFile(input ChannelFileChunk,
 	out obiiter.IBioSequence,
 	withFeatureTable, UtoT bool) {
 
-	parser := GenbankChunkParser(withFeatureTable, UtoT)
-
 	for chunks := range input {
-		sequences, err := parser(chunks.Source, chunks.Raw)
+		var sequences obiseq.BioSequenceSlice
+		var err error
+
+		if chunks.Rope != nil {
+			sequences, err = GenbankChunkParserRope(chunks.Source, chunks.Rope, withFeatureTable, UtoT)
+		} else {
+			parser := GenbankChunkParser(withFeatureTable, UtoT)
+			sequences, err = parser(chunks.Source, chunks.Raw)
+		}
 
 		if err != nil {
 			log.Fatalf("File %s : Cannot parse the genbank file : %v", chunks.Source, err)
@@ -224,7 +483,6 @@ func _ParseGenbankFile(input ChannelFileChunk,
 
 func ReadGenbank(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, error) {
 	opt := MakeOptions(options)
-	// entry_channel := make(chan _FileChunk)
 
 	entry_channel := ReadFileChunk(
 		opt.Source(),
@@ -232,13 +490,13 @@ func ReadGenbank(reader io.Reader, options ...WithOption) (obiiter.IBioSequence,
 		1024*1024*128,
 		EndOfLastFlatFileEntry,
 		"\nLOCUS       ",
+		false, // do not pack: rope-based parser avoids contiguous allocation
 	)
 
 	newIter := obiiter.MakeIBioSequence()
 
 	nworkers := opt.ParallelWorkers()
 
-	// for j := 0; j < opt.ParallelWorkers(); j++ {
 	for j := 0; j < nworkers; j++ {
 		newIter.Add(1)
 		go _ParseGenbankFile(
@@ -249,8 +507,6 @@ func ReadGenbank(reader io.Reader, options ...WithOption) (obiiter.IBioSequence,
 		)
 	}
 
-	// go _ReadFlatFileChunk(reader, entry_channel)
-
 	go func() {
 		newIter.WaitAndClose()
 		log.Debug("End of the genbank file ", opt.Source())

pkg/obiformats/rope_scanner.go

@@ -0,0 +1,77 @@
+package obiformats
+
+import "bytes"
+
+// ropeScanner reads lines from a PieceOfChunk rope.
+// The carry buffer handles lines that span two rope nodes; it grows as needed.
+type ropeScanner struct {
+	current *PieceOfChunk
+	pos     int
+	carry   []byte
+}
+
+func newRopeScanner(rope *PieceOfChunk) *ropeScanner {
+	return &ropeScanner{current: rope}
+}
+
+// ReadLine returns the next line without the trailing \n (or \r\n).
+// Returns nil at end of rope. The returned slice aliases carry[] or the node
+// data and is valid only until the next ReadLine call.
+func (s *ropeScanner) ReadLine() []byte {
+	for {
+		if s.current == nil {
+			if len(s.carry) > 0 {
+				line := s.carry
+				s.carry = s.carry[:0]
+				return line
+			}
+			return nil
+		}
+
+		data := s.current.data[s.pos:]
+		idx := bytes.IndexByte(data, '\n')
+
+		if idx >= 0 {
+			var line []byte
+			if len(s.carry) == 0 {
+				line = data[:idx]
+			} else {
+				s.carry = append(s.carry, data[:idx]...)
+				line = s.carry
+				s.carry = s.carry[:0]
+			}
+			s.pos += idx + 1
+			if s.pos >= len(s.current.data) {
+				s.current = s.current.Next()
+				s.pos = 0
+			}
+			if len(line) > 0 && line[len(line)-1] == '\r' {
+				line = line[:len(line)-1]
+			}
+			return line
+		}
+
+		// No \n in this node: accumulate into carry and advance
+		s.carry = append(s.carry, data...)
+		s.current = s.current.Next()
+		s.pos = 0
+	}
+}
+
+// skipToNewline advances the scanner past the next '\n'.
+func (s *ropeScanner) skipToNewline() {
+	for s.current != nil {
+		data := s.current.data[s.pos:]
+		idx := bytes.IndexByte(data, '\n')
+		if idx >= 0 {
+			s.pos += idx + 1
+			if s.pos >= len(s.current.data) {
+				s.current = s.current.Next()
+				s.pos = 0
+			}
+			return
+		}
+		s.current = s.current.Next()
+		s.pos = 0
+	}
+}

pkg/obioptions/version.go

@@ -3,7 +3,7 @@ package obioptions
 // Version is automatically updated by the Makefile from version.txt
 // The patch number (third digit) is incremented on each push to the repository
 
-var _Version = "Release 4.4.13"
+var _Version = "Release 4.4.21"
 
 // Version returns the version of the obitools package.
 //

pkg/obiseq/biosequence.go

@@ -120,6 +120,19 @@ func NewBioSequence(id string,
 	return bs
 }
 
+// NewBioSequenceOwning creates a BioSequence taking ownership of the sequence
+// slice without copying it. The caller must not use the slice after this call.
+// Use this when the slice was allocated specifically for this sequence.
+func NewBioSequenceOwning(id string,
+	sequence []byte,
+	definition string) *BioSequence {
+	bs := NewEmptyBioSequence(0)
+	bs.SetId(id)
+	bs.TakeSequence(sequence)
+	bs.SetDefinition(definition)
+	return bs
+}
+
 // NewBioSequenceWithQualities creates a new BioSequence object with the given id, sequence, definition, and qualities.
 //
 // Parameters:
@@ -444,6 +457,12 @@ func (s *BioSequence) SetSequence(sequence []byte) {
 	s.sequence = obiutils.InPlaceToLower(CopySlice(sequence))
 }
 
+// TakeSequence stores the slice directly without copying, then lowercases in-place.
+// The caller must not use the slice after this call.
+func (s *BioSequence) TakeSequence(sequence []byte) {
+	s.sequence = obiutils.InPlaceToLower(sequence)
+}
+
 func (s *BioSequence) HasValidSequence() bool {
 	for _, c := range s.sequence {
 		if !((c >= 'a' && c <= 'z') || c == '-' || c == '.' || c == '[' || c == ']') {
@@ -461,6 +480,15 @@ func (s *BioSequence) SetQualities(qualities Quality) {
 	s.qualities = CopySlice(qualities)
 }
 
+// TakeQualities stores the slice directly without copying.
+// The caller must not use the slice after this call.
+func (s *BioSequence) TakeQualities(qualities Quality) {
+	if s.qualities != nil {
+		RecycleSlice(&s.qualities)
+	}
+	s.qualities = qualities
+}
+
 // A method that appends a byte slice to the qualities of the BioSequence.
 func (s *BioSequence) WriteQualities(data []byte) (int, error) {
 	s.qualities = append(s.qualities, data...)

pkg/obiseq/biosequenceslice.go

@@ -195,7 +195,7 @@ func (s *BioSequenceSlice) ExtractTaxonomy(taxonomy *obitax.Taxonomy, seqAsTaxa
 				return nil, fmt.Errorf("sequence %v has no path", s.Id())
 			}
 			last := path[len(path)-1]
-			taxname, _ := obiutils.SplitInTwo(last, ':')
+			taxname, _ := obiutils.LeftSplitInTwo(last, ':')
 			if idx, ok := s.GetIntAttribute("seq_number"); !ok {
 				return nil, errors.New("sequences are not numbered")
 			} else {

pkg/obitax/taxid.go

@@ -31,7 +31,7 @@ func NewTaxidFactory(code string, alphabet obiutils.AsciiSet) *TaxidFactory {
 // It extracts the relevant part of the string after the first colon (':') if present.
 func (f *TaxidFactory) FromString(taxid string) (Taxid, error) {
 	taxid = obiutils.AsciiSpaceSet.TrimLeft(taxid)
-	part1, part2 := obiutils.SplitInTwo(taxid, ':')
+	part1, part2 := obiutils.LeftSplitInTwo(taxid, ':')
 	if len(part2) == 0 {
 		taxid = part1
 	} else {

pkg/obitools/obiclean/graph.go

@@ -64,7 +64,7 @@ func EmpiricalDistCsv(filename string, data [][]Ratio, compressed bool) {
 		fmt.Println(err)
 	}
 
-	destfile, err := obiutils.CompressStream(file, true, true)
+	destfile, err := obiutils.CompressStream(file, compressed, true)
 	if err != nil {
 		fmt.Println(err)
 	}

pkg/obitools/obiconvert/sequence_reader.go

@@ -68,6 +68,8 @@ func ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
 						strings.HasSuffix(path, "seq.gz") ||
 						strings.HasSuffix(path, "gb") ||
 						strings.HasSuffix(path, "gb.gz") ||
+						strings.HasSuffix(path, "gbff") ||
+						strings.HasSuffix(path, "gbff.gz") ||
 						strings.HasSuffix(path, "dat") ||
 						strings.HasSuffix(path, "dat.gz") ||
 						strings.HasSuffix(path, "ecopcr") ||
@@ -204,7 +206,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 					iterator = iterator.PairTo(ip)
 				}
 			} else {
-				iterator = obiiter.NilIBioSequence
+				return obiiter.NilIBioSequence, fmt.Errorf("no sequence files found in the provided paths")
 			}
 		}
 

pkg/obiutils/strings.go

@@ -144,7 +144,7 @@ func (r *AsciiSet) TrimLeft(s string) string {
 	return s[i:]
 }
 
-func SplitInTwo(s string, sep byte) (string, string) {
+func LeftSplitInTwo(s string, sep byte) (string, string) {
 	i := 0
 	for ; i < len(s); i++ {
 		c := s[i]
@@ -157,3 +157,17 @@ func SplitInTwo(s string, sep byte) (string, string) {
 	}
 	return s[:i], s[i+1:]
 }
+
+func RightSplitInTwo(s string, sep byte) (string, string) {
+	i := len(s) - 1
+	for ; i >= 0; i-- {
+		c := s[i]
+		if c == sep {
+			break
+		}
+	}
+	if i == len(s) {
+		return s, ""
+	}
+	return s[:i], s[i+1:]
+}

release_notes.sh

@@ -0,0 +1,294 @@
+#!/bin/bash
+
+# Generate GitHub-compatible release notes for an OBITools4 version.
+#
+# Usage:
+#   ./release_notes.sh                 # latest version
+#   ./release_notes.sh -v 4.4.15       # specific version
+#   ./release_notes.sh -l              # list available versions
+#   ./release_notes.sh -r              # raw commit list (no LLM)
+#   ./release_notes.sh -c -v 4.4.16   # show LLM context for a version
+
+GITHUB_REPO="metabarcoding/obitools4"
+GITHUB_API="https://api.github.com/repos/${GITHUB_REPO}"
+VERSION=""
+LIST_VERSIONS=false
+RAW_MODE=false
+CONTEXT_MODE=false
+LLM_MODEL="ollama:qwen3-coder-next:latest"
+
+# ── Helpers ──────────────────────────────────────────────────────────────
+
+die() { echo "Error: $*" >&2; exit 1; }
+
+next_patch() {
+  local v="$1"
+  local major minor patch
+  major=$(echo "$v" | cut -d. -f1)
+  minor=$(echo "$v" | cut -d. -f2)
+  patch=$(echo "$v" | cut -d. -f3)
+  echo "${major}.${minor}.$(( patch + 1 ))"
+}
+
+# Strip "pre-" prefix to get the bare version number for installation section
+bare_version() {
+  echo "$1" | sed 's/^pre-//'
+}
+
+installation_section() {
+  local v
+  v=$(bare_version "$1")
+  cat <<INSTALL_EOF
+
+## Installation
+
+### Pre-built binaries
+
+Download the appropriate archive for your system from the
+[release assets](https://github.com/metabarcoding/obitools4/releases/tag/Release_${v})
+and extract it:
+
+#### Linux (AMD64)
+\`\`\`bash
+tar -xzf obitools4_${v}_linux_amd64.tar.gz
+\`\`\`
+
+#### Linux (ARM64)
+\`\`\`bash
+tar -xzf obitools4_${v}_linux_arm64.tar.gz
+\`\`\`
+
+#### macOS (Intel)
+\`\`\`bash
+tar -xzf obitools4_${v}_darwin_amd64.tar.gz
+\`\`\`
+
+#### macOS (Apple Silicon)
+\`\`\`bash
+tar -xzf obitools4_${v}_darwin_arm64.tar.gz
+\`\`\`
+
+All OBITools4 binaries are included in each archive.
+
+### From source
+
+You can also compile and install OBITools4 directly from source using the
+installation script:
+
+\`\`\`bash
+curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --version ${v}
+\`\`\`
+
+By default binaries are installed in \`/usr/local/bin\`. Use \`--install-dir\` to
+change the destination and \`--obitools-prefix\` to add a prefix to command names:
+
+\`\`\`bash
+curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | \\
+  bash -s -- --version ${v} --install-dir ~/local --obitools-prefix k
+\`\`\`
+INSTALL_EOF
+}
+
+display_help() {
+  cat <<EOF
+Usage: $(basename "$0") [OPTIONS]
+
+Generate GitHub-compatible Markdown release notes for an OBITools4 version.
+
+Options:
+  -v, --version VERSION   Target version (e.g., 4.4.15). Default: latest.
+  -l, --list              List all available versions and exit.
+  -r, --raw               Output raw commit list without LLM summarization.
+  -c, --context           Show the exact context (commits + prompt) sent to the LLM.
+  -m, --model MODEL       LLM model for orla (default: $LLM_MODEL).
+  -h, --help              Display this help message.
+
+Examples:
+  $(basename "$0")                  # release notes for the latest version
+  $(basename "$0") -v 4.4.15       # release notes for a specific version
+  $(basename "$0") -l              # list versions
+  $(basename "$0") -r -v 4.4.15    # raw commit log for a version
+  $(basename "$0") -c -v 4.4.16    # show LLM context for a version
+EOF
+}
+
+# Fetch all Release tags from GitHub API (sorted newest first)
+fetch_versions() {
+  curl -sf "${GITHUB_API}/releases" \
+    | grep '"tag_name":' \
+    | sed -E 's/.*"tag_name": "Release_([0-9.]+)".*/\1/' \
+    | sort -V -r
+}
+
+# ── Parse arguments ──────────────────────────────────────────────────────
+
+while [ "$#" -gt 0 ]; do
+  case "$1" in
+    -v|--version)  VERSION="$2"; shift 2 ;;
+    -l|--list)     LIST_VERSIONS=true; shift ;;
+    -r|--raw)      RAW_MODE=true; shift ;;
+    -c|--context)  CONTEXT_MODE=true; shift ;;
+    -m|--model)    LLM_MODEL="$2"; shift 2 ;;
+    -h|--help)     display_help; exit 0 ;;
+    *)             die "Unsupported option: $1" ;;
+  esac
+done
+
+# ── List mode ────────────────────────────────────────────────────────────
+
+if [ "$LIST_VERSIONS" = true ]; then
+  echo "Available OBITools4 versions:" >&2
+  echo "==============================" >&2
+  fetch_versions
+  exit 0
+fi
+
+# ── Resolve versions ─────────────────────────────────────────────────────
+
+all_versions=$(fetch_versions)
+[ -z "$all_versions" ] && die "Could not fetch versions from GitHub"
+
+if [ -z "$VERSION" ]; then
+   # ── Pre-release mode: local HEAD vs latest GitHub tag ──────────────────
+   PRE_RELEASE=true
+   previous_tag="Release_${latest_version}"
+   VERSION="pre-$(next_patch "$latest_version")"
+
+   echo "Pre-release mode: $previous_tag -> HEAD (as $VERSION)" >&2
+
+   # Need to be in a git repo
+   if ! git rev-parse --is-inside-work-tree >/dev/null 2>&1; then
+     die "Not inside a git repository. Pre-release mode requires a local git repo."
+   fi
+
+   # Check that the previous tag exists locally
+   if ! git rev-parse "$previous_tag" >/dev/null 2>&1; then
+     echo "Tag $previous_tag not found locally, fetching..." >&2
+     git fetch --tags 2>/dev/null || true
+     if ! git rev-parse "$previous_tag" >/dev/null 2>&1; then
+       die "Tag $previous_tag not found locally or remotely"
+     fi
+   fi
+
+  # Get local commits from the tag to HEAD (full messages)
+  commit_list=$(git log --format="%h %B" "${previous_tag}..HEAD" 2>/dev/null)
+
+   if [ -z "$commit_list" ]; then
+     die "No local commits found since $previous_tag"
+   fi
+ else
+   # ── Published release mode: between two GitHub tags ────────────────────
+   PRE_RELEASE=false
+   tag_name="Release_${VERSION}"
+
+   # Verify the requested version exists
+   if ! echo "$all_versions" | grep -qx "$VERSION"; then
+     die "Version $VERSION not found. Use -l to list available versions."
+   fi
+
+   # Find the previous version
+   previous_version=$(echo "$all_versions" | grep -A1 -x "$VERSION" | tail -1)
+
+   if [ "$previous_version" = "$VERSION" ] || [ -z "$previous_version" ]; then
+     previous_tag=""
+     echo "No previous version found -- will include all commits for $tag_name" >&2
+   else
+     previous_tag="Release_${previous_version}"
+     echo "Generating notes: $previous_tag -> $tag_name" >&2
+   fi
+
+   # Fetch commit messages between tags via GitHub compare API
+   if [ -n "$previous_tag" ]; then
+     commits_json=$(curl -sf "${GITHUB_API}/compare/${previous_tag}...${tag_name}")
+     if [ -z "$commits_json" ]; then
+       die "Could not fetch commit comparison from GitHub"
+     fi
+     commit_list=$(echo "$commits_json" \
+      | jq -r '.commits[] | (.sha[:8] + " " + .commit.message)' 2>/dev/null)
+   else
+     commits_json=$(curl -sf "${GITHUB_API}/commits?sha=${tag_name}&per_page=50")
+     if [ -z "$commits_json" ]; then
+       die "Could not fetch commits from GitHub"
+     fi
+     commit_list=$(echo "$commits_json" \
+      | jq -r '.[] | (.sha[:8] + " " + .commit.message)' 2>/dev/null)
+   fi
+
+   if [ -z "$commit_list" ]; then
+     die "No commits found between $previous_tag and $tag_name"
+   fi
+fi
+
+# ── LLM prompt (shared by context mode and summarization) ────────────────
+
+LLM_PROMPT="Summarize the following commits into a GitHub release note for version ${VERSION}. \
+Ignore commits related to version bumps, .gitignore changes, or any internal housekeeping \
+that is irrelevant to end users. Describe each user-facing change precisely without exposing \
+code. Eliminate redundancy. Output strictly valid JSON with no surrounding text, using this \
+exact schema: {\"title\": \"<short release title>\", \"body\": \"<detailed markdown release notes>\"}"
+
+# ── Raw mode: just output the commit list ────────────────────────────────
+
+if [ "$RAW_MODE" = true ]; then
+  echo "# Release ${VERSION}"
+  echo ""
+  echo "## Commits"
+  echo ""
+  echo "$commit_list" | while IFS= read -r line; do
+    echo "- ${line}"
+  done
+  installation_section "$VERSION"
+  exit 0
+fi
+
+# ── Context mode: show what would be sent to the LLM ────────────────────
+
+if [ "$CONTEXT_MODE" = true ]; then
+  echo "=== LLM Model ==="
+  echo "$LLM_MODEL"
+  echo ""
+  echo "=== Prompt ==="
+  echo "$LLM_PROMPT"
+  echo ""
+  echo "=== Stdin (commit list) ==="
+  echo "$commit_list"
+  exit 0
+fi
+
+# ── LLM summarization ───────────────────────────────────────────────────
+
+if ! command -v orla >/dev/null 2>&1; then
+  die "orla is required for LLM summarization. Use -r for raw output."
+fi
+
+if ! command -v jq >/dev/null 2>&1; then
+  die "jq is required for JSON parsing. Use -r for raw output."
+fi
+
+echo "Summarizing with LLM ($LLM_MODEL)..." >&2
+
+raw_output=$(echo "$commit_list" | \
+  ORLA_MAX_TOOL_CALLS=50 orla agent -m "$LLM_MODEL" \
+  "$LLM_PROMPT" \
+  2>/dev/null) || true
+
+if [ -z "$raw_output" ]; then
+  echo "Warning: LLM returned empty output, falling back to raw mode" >&2
+  exec "$0" -r -v "$VERSION"
+fi
+
+# Sanitize: extract JSON object, strip control characters
+sanitized=$(echo "$raw_output" | sed -n '/^{/,/^}/p' | tr -d '\000-\011\013-\014\016-\037')
+
+release_title=$(echo "$sanitized" | jq -r '.title // empty' 2>/dev/null)
+release_body=$(echo "$sanitized" | jq -r '.body // empty' 2>/dev/null)
+
+if [ -n "$release_title" ] && [ -n "$release_body" ]; then
+  echo "# ${release_title}"
+  echo ""
+  echo "$release_body"
+  installation_section "$VERSION"
+else
+  echo "Warning: JSON parsing failed, falling back to raw mode" >&2
+  exec "$0" -r -v "$VERSION"
+fi

tools/json2md.py

@@ -0,0 +1,36 @@
+#!/usr/bin/env python3
+"""
+Read potentially malformed JSON from stdin (aichat output), extract title and
+body, and print them as plain text: title on first line, blank line, then body.
+Exits with 1 on failure (no output).
+"""
+
+import sys
+import json
+import re
+
+text = sys.stdin.read()
+
+m = re.search(r'\{.*\}', text, re.DOTALL)
+if not m:
+    sys.exit(1)
+
+s = m.group()
+obj = None
+
+try:
+    obj = json.loads(s)
+except Exception:
+    s2 = re.sub(r'(?<!\\)\n', r'\\n', s)
+    try:
+        obj = json.loads(s2)
+    except Exception:
+        sys.exit(1)
+
+title = obj.get('title', '').strip()
+body  = obj.get('body', '').strip()
+
+if not title or not body:
+    sys.exit(1)
+
+print(f"{title}\n\n{body}")

version.txt

@@ -1 +1 @@
-4.4.13
+4.4.21