- Ajout de prompt_documentation_globale.md décrivant les trois phases d'écriture de la documentation (fichier → package → outil)
- Présence de fichiers .DS_Store non significatifs (à ignorer)
This release introduces dynamic batch flushing in the Distribute component, replacing the previous fixed-size batching with a memory- and count-aware strategy. Batches now flush automatically when either the maximum sequence count (BatchSizeMax()) or memory threshold (BatchMem()) per key is reached, ensuring more efficient resource usage and consistent behavior with the RebatchBySize strategy. The optional sizes parameter has been removed, and related code—including the Lua wrapper and worker buffer handling—has been updated for correctness and simplicity. Unused BatchSize() references have been eliminated from obidistribute.
Additionally, this release includes improvements to static Linux builds and overall build stability, enhancing reliability across deployment environments.
Replace the old fixed batch-size mechanism in Distribute with a dynamic strategy that flushes batches when either BatchSizeMax() sequences or BatchMem() bytes are reached per key. This aligns with the RebatchBySize strategy and removes the optional sizes parameter. Also update related code: simplify Lua wrapper to accept optional capacity, and fix buffer growth logic in worker.go using slices.Grow correctly. Remove unused BatchSize() usage from obidistribute.
This release focuses on improving build reliability, memory efficiency for large datasets, and portability of Linux binaries.
### Static Linux Binaries
- Linux binaries are now built with static linking using musl, eliminating external runtime dependencies and ensuring portability across distributions.
### Memory-Aware Batching
- Users can now control memory usage during processing with the new `--batch-mem` option, specifying limits such as 128K, 64M, or 1G.
- Batching logic now respects both size and memory constraints: batches are flushed when either threshold is exceeded.
- Conservative memory estimation for sequences helps avoid over-allocation, and explicit garbage collection after large batch discards reduces memory spikes.
### Build System Improvements
- Upgraded to Go 1.26 for improved performance and toolchain stability.
- Fixed cross-compilation issues by replacing generic include paths with architecture-specific ones (x86_64-linux-gnu and aarch64-linux-gnu).
- Streamlined macOS builds by removing special flags, using standard `make` targets.
- Enhanced error reporting during build failures: logs are now shown before cleanup and exit.
- Updated install script to correctly configure GOROOT, GOPATH, and GOTOOLCHAIN, with visual progress feedback for downloads.
All batching behavior is non-breaking and maintains backward compatibility while offering more predictable resource usage on large datasets.
Update version to 4.4.27 in version.txt and pkg/obioptions/version.go.
Add zlib-static package to release workflow to ensure static linking of zlib, resolving potential runtime dependency issues with the external link mode.
- Upgrade Go version from 1.23 to 1.26 in release.yml
- Remove CGO_CFLAGS from cross-compilation matrix entries
- Replace Linux build tools installation with Docker-based static build using golang:1.26-alpine
- Simplify macOS build to use standard make without special flags
- Increment version to 4.4.26
Update version to 4.4.25 in version.txt and pkg/obioptions/version.go.
Fix CGO_CFLAGS in release.yml by replacing generic '-I/usr/include' with architecture-specific paths (x86_64-linux-gnu and aarch64-linux-gnu) to ensure correct header inclusion during cross-compilation on Linux.
- Add CGO_CFLAGS environment variable to release workflow for Linux builds
- Update go.work.sum with new golang.org/x/net v0.38.0 entry
- Remove obsolete logs archive file
This release includes a critical bug fix for the file synchronization module that could cause data corruption under high I/O load. Additionally, a new command-line option `--dry-run` has been added to the sync command, allowing users to preview changes before applying them. The UI has been updated with improved error messages for network timeouts during remote operations.
- Update version from 4.4.22 to 4.4.23 in version.txt and pkg/obioptions/version.go
- Add zlib1g-dev dependency to Linux release workflow for potential linking requirements
- Improve tag creation in Makefile by resolving commit hash with `jj log` for better CI/CD integration
### Memory-Aware Batching
- Introduced configurable min/max batch size bounds and memory limits for precise resource control.
- Added `--batch-mem` CLI option to enable adaptive batching based on estimated sequence memory footprint (e.g., 128K, 64M, 1G).
- Implemented `RebatchBySize()` to handle both byte and count limits, flushing when either threshold is exceeded.
- Added conservative memory estimation via `BioSequence.MemorySize()` and enhanced garbage collection for explicit cleanup after large batch discards.
- Updated internal batching logic across core modules to consistently apply default memory (128 MB) and size (min: 1, max: 2000) bounds.
### Linux Build Enhancements
- Enabled static linking for Linux binaries using musl, producing portable, self-contained executables without external dependencies.
### Build System & Toolchain Improvements
- Updated Go toolchain to 1.26.1 with corresponding dependency bumps (e.g., go-getoptions, gval, regexp2, go-json, progressbar, logrus, testify).
- Fixed Makefile to safely quote LDFLAGS for paths with spaces.
- Improved build error handling: on failure, logs are displayed before cleanup and exit.
- Updated install script to correctly set GOROOT, GOPATH, and GOTOOLCHAIN, ensuring GOPATH directory creation.
- Added progress bar to curl downloads in the install script for visual feedback during Go and OBITools4 downloads.
All batching behavior remains non-breaking, with consistent constraints improving predictability during large dataset processing.
- Update Go version from 1.25.0 to 1.26.1 in go.mod and go.work
- Fix Makefile: quote LDFLAGS to handle spaces safely in -ldflags
- Improve build error handling: on failure, cat log then cleanup and exit with error code
- Update install_obitools.sh: properly set GOROOT, GOPATH, and GOTOOLCHAIN; ensure GOPATH directory is created
Replace silent curl commands with --progress-bar option to provide visual feedback during Go and OBITools4 downloads, improving user experience without changing download logic.
Update go.mod and go.work to Go 1.25.0, bump several direct dependencies (e.g., go-getoptions, gval, regexp2, go-json, progressbar, logrus, testify), update indirect dependencies accordingly, and remove obsolete toolchain directive.
### Memory-Aware Batching
- Replaced single batch size limits with configurable min/max bounds and memory limits for more precise control over resource usage.
- Added `--batch-mem` CLI option to enable adaptive batching based on estimated sequence memory footprint (e.g., 128K, 64M, 1G).
- Introduced `RebatchBySize()` with explicit support for both byte and count limits, flushing when either threshold is exceeded.
- Implemented conservative memory estimation via `BioSequence.MemorySize()` and enhanced garbage collection to trigger explicit cleanup after large batch discards.
- Updated internal batching logic across `batchiterator.go`, `fragment.go`, and `obirefidx.go` to consistently use default memory (128 MB) and size (min: 1, max: 2000) bounds.
### Linux Build Enhancements
- Enabled static linking for Linux binaries using musl, producing portable, self-contained executables without external dependencies.
### Notes
- This release consolidates and improves batching behavior introduced in 4.4.20, with no breaking changes to the public API.
- All user-facing batching behavior is now governed by consistent memory and count constraints, improving predictability and stability during large dataset processing.
Replace calls to Rebatch(size) with RebatchBySize(obidefault.BatchMem(), obidefault.BatchSizeMax()) in batchiterator.go, fragment.go, and obirefidx.go to ensure consistent use of default memory and size limits for batch rebatching.
Introduce separate _BatchSize (min) and _BatchSizeMax (max) constants to replace the single _BatchSize variable. Update RebatchBySize to accept both maxBytes and maxCount parameters, flushing when either limit is exceeded. Set default batch size min to 1, max to 2000, and memory limit to 128 MB. Update CLI options and sequence_reader.go accordingly.
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
Enable static linking for Linux binaries by installing musl-tools and passing appropriate LDFLAGS during build. This ensures portable, self-contained executables for Linux targets.
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.
- Add .DEFAULT_GOAL := all to Makefile for consistent default target
- Document -j/--jobs option in README.md to allow parallel compilation
- Add JOBS variable and -j/--jobs argument to install script (default: 1)
- Replace fragile mkdir/cp commands with robust error handling and clear diagnostics
- Add build directory preservation on copy failure for manual recovery
- Pass -j option to make during compilation to enable parallel builds
### Enhancements
- **Rope-based parsing**: Added direct rope parsing for FASTA, EMBL, and FASTQ formats via `FastaChunkParserRope`, `EmblChunkParserRope`, and `FastqChunkParserRope`. Sequence extraction now supports U→T conversion and improved line ending detection.
- **Rope scanner refactoring**: Unified rope scanning logic under a new `ropeScanner`, improving maintainability and consistency.
- **Sequence handling**: Added `TakeQualities()` method to BioSequence for more efficient quality data handling.
### Bug Fixes
- **Compression behavior**: Fixed `CompressStream` to correctly use the `compressed` variable instead of a hardcoded boolean.
- **String splitting**: Replaced ambiguous `SplitInTwo` calls with precise `LeftSplitInTwo` or `RightSplitInTwo`, and added dedicated right-split utility.
### Tooling & Workflow Improvements
- **Makefile enhancements**: Added colored terminal output, a `help` target for documenting all targets, and improved release workflow automation.
- **Release process**: Refactored `jjpush` into modular targets (`jjpush-notes`, `jjpush-push`, `jjpush-tag`), replaced `orla` with `aichat` for AI-assisted release notes, and introduced robust JSON parsing using Python. Release notes are now generated and stored in temp files for tag creation.
- **Versioning**: `bump-version` now supports the VERSION environment variable for manual version setting.
- **Submission**: Switched from raw `jj git push` to `stakk` for PR submission.
### Internal Notes
- Installation instructions are now included in release tags.
- Fixed-size carry buffer replaced with dynamic slice for arbitrarily long line support without extra allocations.
- Add colored terminal output support (GREEN, YELLOW, BLUE, NC)
- Introduce `help` target to document all Makefile targets
- Enhance `bump-version` to accept VERSION env var for manual version setting
- Refactor jjpush: split into modular targets (jjpush-notes, jjpush-push, jjpush-tag)
- Replace orla with aichat for AI-powered release notes generation
- Add robust JSON parsing using Python for release notes extraction
- Use stakk for PR submission (replacing raw `jj git push`)
- Generate and store release notes in temp files for tag creation
- Add installation instructions to release tags
- Update .PHONY with new targets
4.4.20: Rope-based parsing, improved release tooling, and bug fixes
### Enhancements
- **Rope-based parsing**: Added direct rope parsing for FASTA, EMBL, and FASTQ formats via `FastaChunkParserRope`, `EmblChunkParserRope`, and `FastqChunkRope` functions, eliminating unnecessary memory allocation via Pack(). Sequence extraction now supports U→T conversion and improved line ending detection.
- **Rope scanner refactoring**: Unified rope scanning logic under a new `ropeScanner`, improving maintainability and consistency across parsers.
- **Sequence handling**: Added `TakeQualities()` method to BioSequence for more efficient quality data handling.
### Bug Fixes
- **Compression behavior**: Fixed CompressStream to correctly use the `compressed` variable instead of a hardcoded boolean.
- **String splitting**: Replaced ambiguous `SplitInTwo` calls with precise `LeftSplitInTwo` or `RightSplitInTwo`, and added dedicated right-split utility.
### Tooling & Workflow Improvements
- **Makefile enhancements**: Added colored terminal output, a `help` target for documenting all targets, and improved release workflow automation.
- **Release process**: Refactored `jjpush` into modular targets (`jjpush-notes`, `jjpush-push`, `jjpush-tag`), replaced `orla` with `aichat` for AI-assisted release notes, and introduced robust JSON parsing using Python. Release notes are now generated and stored in temp files for tag creation.
- **Versioning**: `bump-version` now supports the VERSION environment variable for manual version setting.
- **Submission**: Switched from raw `jj git push` to `stakk` for PR submission.
### Internal Notes
- Installation instructions are now included in release tags.
- Fixed-size carry buffer replaced with dynamic slice for arbitrarily long line support without extra allocations.
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.
Split the jjpush target into multiple sub-targets (jjpush-describe, jjpush-bump, jjpush-push, jjpush-tag) for better modularity and control.
Enhance release notes generation by:
- Using git log with full commit messages instead of GitHub API for pre-release mode
- Adding robust JSON parsing with fallbacks for release notes
- Including detailed installation instructions in release notes
- Supporting both pre-release and published release modes
Update release_notes.sh to handle pre-release mode, improve commit message fetching, and add installation section to release notes.
Add .PHONY declarations for new sub-targets.
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.
Add support for .gbff and .gbff.gz file extensions in sequence reader.
Update the logic to return an error instead of using NilIBioSequence when no sequence files are found, improving the error handling and user feedback.
Update test script name from obisuperkmer to obik-super and adjust all command references accordingly.
- Changed TEST_NAME from 'obisuperkmer' to 'obik-super'
- Changed CMD from 'obisuperkmer' to 'obik'
- Updated MCMD to 'OBIk-super'
- Modified command calls to use '$CMD super' instead of direct command names
- Updated help test to use '$CMD super -h'
- Updated all test cases to use the new command format
Refactor k-mer matching to use a pipeline architecture with improved concurrency and memory management:
- Replace sort.Slice with slices.SortFunc and cmp.Compare for better performance
- Introduce PreparedQueries struct to encapsulate query buckets with metadata
- Implement MergeQueries function to merge query buckets from multiple batches
- Rewrite MatchBatch to use pre-allocated results and mutexes instead of map-based accumulation
- Add seek optimization in matchPartition to reduce linear scanning
- Refactor match command to use a multi-stage pipeline with proper batching and merging
- Add index directory option for match command
- Improve parallel processing of sequence batches
This refactoring improves performance by reducing memory allocations, optimizing k-mer lookup, and implementing a more efficient pipeline for large-scale k-mer matching operations.
This commit introduces entropy-based filtering for k-mers to remove low-complexity sequences. It adds:
- New KmerEntropy and KmerEntropyFilter functions in pkg/obikmer/entropy.go for computing and filtering k-mer entropy
- Integration of entropy filtering in the k-mer set builder (pkg/obikmer/kmer_set_builder.go)
- A new 'filter' command in obik tool (pkg/obitools/obik/filter.go) to apply entropy filtering on existing indices
- CLI options for configuring entropy filtering during index building and filtering
The entropy filter helps improve the quality of k-mer sets by removing repetitive sequences that may interfere with downstream analyses.
This commit introduces sparse index support for KDI files to enable fast random access during k-mer matching. It adds a new .kdx index file format and updates the KDI reader and writer to handle index creation and seeking. The changes include:
- New KdxIndex struct and related functions for loading, searching, and writing .kdx files
- Modified KdiReader to support seeking with the new index
- Updated KdiWriter to create .kdx index files during writing
- Enhanced KmerSetGroup.Contains to use the new index for faster lookups
- Added a new 'match' command to annotate sequences with k-mer match positions
The index is created automatically during KDI file creation and allows for O(log N / stride) binary search followed by at most stride linear scan steps, significantly improving performance for large datasets.
Refactor lowmask options to use shared kmer options and CLI getters
This commit refactors the lowmask subcommand to use shared kmer options and CLI getters instead of local variables. It also moves the kmer size and minimizer size options to a shared location and adds new CLI getters for the lowmask options.
- Move kmer size and minimizer size options to shared location
- Add CLI getters for lowmask options
- Refactor lowmask to use CLI getters
- Remove unused strings import
- Add MaskingMode type and related functions
Add a new boolean option 'keep-shorter' to preserve fragments shorter than kmer-size during split/extract mode.
This change introduces a new flag _lowmaskKeepShorter that controls whether fragments
shorter than the kmer size should be kept during split/extract operations.
The implementation:
1. Adds the new boolean variable _lowmaskKeepShorter
2. Registers the command-line option "keep-shorter"
3. Updates the lowMaskWorker function signature to accept the keepShorter parameter
4. Modifies the fragment selection logic to check the keepShorter flag
5. Updates the worker creation to pass the global flag value
This allows users to control the behavior when dealing with short sequences in
split/extract modes, providing more flexibility in low-complexity masking.
This commit introduces max frequency filtering to limit k-mer occurrences and adds functionality to save the N most frequent k-mers per set to CSV files. It also includes the ability to output k-mer frequency spectra as CSV and updates the CLI options accordingly.
This commit refactors the k-mer index management tools to use a unified subcommand structure with obik, adds support for per-set metadata and ID management, enhances the k-mer set group builder to support appending to existing groups, and improves command-line option handling with a new global options registration system.
Key changes:
- Introduce obik command with subcommands (index, ls, summary, cp, mv, rm, super, lowmask)
- Add support for per-set metadata and ID management in kmer set groups
- Implement ability to append to existing kmer index groups
- Refactor option parsing to use a global options registration system
- Add new commands for listing, copying, moving, and removing sets
- Enhance low-complexity masking with new options and output formats
- Improve kmer index summary with Jaccard distance matrix support
- Remove deprecated obikindex and obisuperkmer commands
- Update build process to use the new subcommand structure
Refactor k-mer index building to use the new disk-based KmerSetGroupBuilder instead of the old KmerSet and FrequencyFilter approaches. This change introduces a more efficient and scalable approach to building k-mer indices by using partitioned disk storage with streaming operations.
- Replace BuildKmerIndex and BuildFrequencyFilterIndex with KmerSetGroupBuilder
- Add support for frequency filtering via WithMinFrequency option
- Remove deprecated k-mer set persistence methods
- Update CLI to use new builder approach
- Add new disk-based k-mer operations (union, intersect, difference, quorum)
- Introduce KDI (K-mer Delta Index) file format for efficient storage
- Add K-way merge operations for combining sorted k-mer streams
- Update documentation and examples to reflect new API
This refactoring provides better memory usage, faster operations on large datasets, and more flexible k-mer set operations.
Refactor kmer index package to use disk-based partitioning with minimizer
- Replace roaring64 bitmaps with disk-based kmer index
- Implement partitioned kmer sets with delta-varint encoding
- Add support for frequency filtering during construction
- Introduce new builder pattern for index construction
- Add streaming operations for set operations (union, intersect, etc.)
- Add support for super-kmer encoding during construction
- Update command line tool to use new index format
- Remove dependency on roaring bitmap library
This change introduces a new architecture for kmer indexing that is more memory efficient and scalable for large datasets.
Update version from 4.4.11 to 4.4.12
- Bump version in version.go
- Enhance release note generation in Makefile to use JSON output from orla and fallback to raw output if JSON parsing fails
- Improve test script to verify minimum super k-mer length is >= k (default k=31)
This commit optimizes the low-complexity masking algorithm by:
1. Precomputing logarithm values and normalization tables to avoid repeated calculations
2. Replacing the MinMultiset-based sliding minimum with a more efficient deque-based implementation
3. Improving entropy calculation by using precomputed n*log(n) values
4. Simplifying the circular normalization process with precomputed tables
5. Removing unused imports and log statements
The changes significantly improve performance while maintaining the same masking behavior.
This commit fixes minor whitespace issues in the test script and adds new tests to ensure merge attribute consistency between in-memory and on-disk paths.
- Removed trailing spaces in log messages
- Added tests for merge consistency between in-memory and on-disk paths
- These tests catch a bug where shared classifier in on-disk dereplication path caused incorrect merged attributes
This commit introduces a new configuration module `obidefault` to manage progress bar settings, allowing users to disable progress bars via a `--no-progressbar` option. It updates various packages to conditionally display progress bars based on this new configuration, improving user experience by providing control over progress bar output. The changes also include improvements to progress bar handling in several packages, ensuring they are only displayed when appropriate (e.g., when stderr is a terminal and stdout is not piped).
This commit fixes an issue in the chunk processing logic where the wrong classifier instance was being reset and used for code generation. A local clone of the classifier is now created and used to ensure correct behavior during dereplication.
Modify CLIProgressBar function to check if stdout is a named pipe and disable the progress bar accordingly. This prevents the progress bar from being displayed when the output is redirected or piped to another command.
This commit addresses a bug in the super k-mer implementation where the minimizer bijection property was not properly enforced. The fix ensures that:
1. All k-mers within a super k-mer share the same minimizer
2. Identical super k-mer sequences have the same minimizer
The changes include:
- Fixing the super k-mer iteration logic to properly validate the minimizer bijection property
- Adding a comprehensive test suite (TestSuperKmerMinimizerBijection) that validates the intrinsic property of super k-mers
- Updating the .gitignore file to properly track relevant files
This resolves issues where the same sequence could be associated with different minimizers, violating the super k-mer definition.
This commit adds the implementation of the obisuperkmer command, including:
- The main command in cmd/obitools/obisuperkmer/
- The package implementation in pkg/obitools/obisuperkmer/
- Automated tests in obitests/obitools/obisuperkmer/
- Documentation for the implementation and tests
The obisuperkmer command extracts super k-mers from DNA sequences, following the standard OBITools architecture. It includes proper CLI option handling, validation of parameters, and integration with the OBITools pipeline system.
Tests cover basic functionality, parameter validation, output format, metadata preservation, and file I/O operations.
Ajout d'une documentation détaillée sur l'architecture des commandes OBITools, incluant la structure modulaire, les patterns architecturaux et les bonnes pratiques pour la création de nouvelles commandes.
This commit refactors the SuperKmer extraction functionality to use Go's new iterator pattern. The ExtractSuperKmers function is now implemented as a wrapper around a new IterSuperKmers iterator function, which yields results one at a time instead of building a complete slice. This change provides better memory efficiency and more flexible consumption of super k-mers. The functionality remains the same, but the interface is now more idiomatic and efficient for large datasets.
Mise à jour du Makefile pour améliorer le processus de version bump et de création de tag.
- Utilisation de variables pour stocker les versions précédente et actuelle
- Ajout de la génération automatique des notes de version à partir des commits entre les tags
- Intégration d'une logique de fallback si orla n'est pas disponible
- Amélioration de la documentation des étapes du processus de release
- Mise à jour de la commande de création du tag avec le message généré
Update installation script to support specific version installation, list available versions, and improve documentation.
- Add support for installing specific versions with -v/--version flag
- Add -l/--list flag to list all available versions
- Improve help message with examples
- Update README.md to reflect new installation options and examples
- Add note on version compatibility between OBITools2 and OBITools4
- Remove ecoprimers directory
- Improve error handling and user feedback during installation
- Add version detection and download logic from GitHub releases
- Update installation process to use tagged releases instead of master branch
This commit simplifies the artifact packaging process by creating a single tar.gz file containing all binaries for each platform, instead of individual files. It also updates the release notes to reflect the new packaging approach and corrects the documentation to use the new naming convention 'obitools4' instead of '<tool>'.
Mise à jour du workflow de release pour utiliser ubuntu-24.04-arm au lieu de ubuntu-latest pour ARM64, et macos-15-intel au lieu de macos-latest pour macOS. Suppression de la compilation croisée pour ARM64 et ajustement de l'installation des outils de build pour macOS.
This commit introduces a new build job that compiles binaries for multiple platforms (Linux, macOS) and architectures (amd64, arm64). It also refactors the release process to download pre-built artifacts and simplify the release directory preparation. The workflow now uses matrix strategy for building binaries and downloads all artifacts for the final release, removing the previous manual build steps for each platform.
Modification du fichier de workflow de release pour compiler uniquement les outils obitools lors de la construction des binaires pour chaque plateforme (Linux AMD64, Linux ARM64, macOS AMD64, macOS ARM64, Windows AMD64). Cela permet d'optimiser le processus de build en ne générant que les binaires nécessaires.
This commit introduces a new GitHub Actions workflow to automatically create releases when tags matching the pattern 'Release_*' are pushed. It also updates the Makefile to use the new tag format 'Release_<version>' for tagging commits, ensuring consistency with the new release automation.
Add Jaccard distance and similarity computations for KmerSet and KmerSetGroup
This commit introduces Jaccard distance and similarity methods for KmerSet and KmerSetGroup.
For KmerSet:
- Added JaccardDistance method to compute the Jaccard distance between two KmerSets
- Added JaccardSimilarity method to compute the Jaccard similarity between two KmerSets
For KmerSetGroup:
- Added JaccardDistanceMatrix method to compute a pairwise Jaccard distance matrix
- Added JaccardSimilarityMatrix method to compute a pairwise Jaccard similarity matrix
Also includes:
- New DistMatrix implementation in pkg/obidist for storing and computing distance/similarity matrices
- Updated version handling with bump-version target in Makefile
- Added tests for all new methods
This commit refactors the k-mer normalization functions, renaming them from 'NormalizeKmer' to 'CanonicalKmer' to better reflect their purpose of returning canonical k-mers. It also introduces new quorum operations (AtLeast, AtMost, Exactly) for k-mer set groups, along with comprehensive tests and benchmarks. The version commit hash has also been updated.
This commit translates all French comments in the kmer filtering and set management code to English, improving code readability and maintainability for international collaborators.
Ajout de la fonctionnalité de sauvegarde et de chargement pour FrequencyFilter en utilisant le KmerSetGroup sous-jacent.
- Nouvelle méthode Save() pour enregistrer le filtre dans un répertoire avec formatage des métadonnées
- Nouvelle méthode LoadFrequencyFilter() pour charger un filtre depuis un répertoire
- Initialisation des métadonnées lors de la création du filtre
- Optimisation des méthodes Union() et Intersect() du KmerSetGroup
- Mise à jour du commit hash
This commit refactors all k-mer encoding and normalization functions to consistently use 'canonical' instead of 'normalized' terminology. This includes renaming functions like EncodeNormalizedKmer to EncodeCanonicalKmer, IterNormalizedKmers to IterCanonicalKmers, and NormalizeKmer to CanonicalKmer. The change aligns the API with biological conventions where 'canonical' refers to the lexicographically smallest representation of a k-mer and its reverse complement. All related documentation and examples have been updated accordingly. The commit also updates the version file with a new commit hash.
This commit introduces new functions for encoding and decoding k-mers, including support for normalized k-mers. It also updates the frequency filter and k-mer set implementations to use the new encoding functions, providing zero-allocation encoding for better performance. The commit hash has been updated to reflect the latest changes.
This commit refactors the KmerSet and related structures to use an immutable K parameter and introduces consistent Copy methods instead of Clone. It also adds attribute API support for KmerSet and KmerSetGroup, and updates persistence logic to handle IDs and metadata correctly.
Cette modification ajoute la capacité de stocker et de persister des métadonnées utilisateur dans les structures KmerSet et KmerSetGroup. Les changements incluent l'ajout d'un champ Metadata dans KmerSet et KmerSetGroup, ainsi que la mise à jour des méthodes de clonage et de persistance pour gérer ces métadonnées. Cela permet de conserver des informations supplémentaires liées aux ensembles de k-mers tout en maintenant la compatibilité avec les opérations existantes.
This commit adds support for saving and loading KmerSet and KmerSetGroup structures using TOML, YAML, and JSON formats for metadata. It includes:
- Added github.com/pelletier/go-toml/v2 dependency
- Implemented Save and Load methods for KmerSet and KmerSetGroup
- Added metadata persistence with support for multiple formats (TOML, YAML, JSON)
- Added helper functions for format detection and metadata handling
- Updated version commit hash
Refactor FrequencyFilter to inherit from KmerSetGroup for better code organization and maintainability. This change replaces the direct bitmap management with a group-based approach, simplifying the implementation and improving readability.
This commit refactors the k-mer encoding logic to handle ambiguous bases more consistently and introduces a KmerSet type for better management of k-mer collections. The frequency filter now works with KmerSet instead of roaring bitmaps directly, and the API has been updated to support level-based frequency queries. Additionally, the commit updates the version and commit hash.
This commit introduces error handling for ambiguous DNA bases (N, R, Y, W, S, K, M, B, D, H, V) in k-mer encoding. It adds new functions IterNormalizedKmersWithErrors and EncodeNormalizedKmersWithErrors that track and encode the number of ambiguous bases in each k-mer using error markers in the top 2 bits. The commit also updates the version string to reflect the latest changes.
Implémentation complète du filtre de fréquence utilisant v niveaux de Roaring Bitmaps pour éliminer efficacement les erreurs de séquençage.
- Ajout de la logique de filtrage par fréquence avec v niveaux
- Intégration des bibliothèques RoaringBitmap et bitset
- Ajout d'exemples d'utilisation et de documentation
- Implémentation de l'itérateur de k-mers pour une utilisation mémoire efficace
- Optimisation pour les distributions skewed typiques du séquençage
Ce changement permet de filtrer les k-mers par fréquence minimale avec une utilisation mémoire optimale et une seule passe sur les données.
This commit introduces error marker functionality for k-mers with odd lengths up to 31. The top 2 bits of each k-mer are now reserved for error coding (0-3), allowing for error detection and correction capabilities. Key changes include:
- Added constants KmerErrorMask and KmerSequenceMask for bit manipulation
- Implemented SetKmerError, GetKmerError, and ClearKmerError functions
- Updated EncodeKmers, ExtractSuperKmers, EncodeNormalizedKmers functions to enforce k ≤ 31
- Enhanced ReverseComplement to preserve error bits during reverse complement operations
- Added comprehensive tests for error marker functionality including edge cases and integration tests
The maximum k-mer size is now capped at 31 to accommodate the error bits, ensuring that k-mers with odd lengths ≤ 31 utilize only 62 bits of the 64-bit uint64, leaving the top 2 bits available for error coding.
Eric Coissac