cdc72c5346
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.
obitools V4
OBITools V4 is the new version of OBITools. They are closer to OBITools2 than to OBITools3. They are implemented in GO and are tens of times faster than OBITools2.
The git for OBITools4 is available at :
Installing OBITools V4
An installation script that compiles the new OBITools on your Unix-like system is available online. The easiest way to run it is to copy and paste the following command into your terminal
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash
By default, the script installs the latest version of OBITools commands and other associated files into the /usr/local directory.
Installation Options
The installation script offers several options:
-l, --list List all available versions and exit.
-v, --version Install a specific version (e.g.,
-v 4.4.3). By default, the latest version is installed.-i, --install-dir Directory where obitools are installed (as example use
/usr/localnot/usr/local/bin).-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 gwill producegobigrepcommand instead ofobigrep).-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
List all available versions:
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --list
Install a specific version:
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --version 4.4.3
Install in a custom directory with command prefix:
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | \
bash -s -- --install-dir test_install --obitools-prefix k
In this last example, the binaries will be installed in the test_install directory and all command names will be prefixed with the letter k. Thus, obigrep will be named kobigrep.
Note on Version Compatibility
The names of the commands in the new OBITools4 are mostly identical to those in OBITools2.
Therefore, installing the new OBITools may hide or delete the old ones. If you want both versions to be
available on your system, use the --install-dir and --obitools-prefix options as shown above.
Continuing the analysis...
Before with OBITools2 to continue the analysis, obitab was used as last command to produce a tab delimited file that was loadable in R or in any spreadsheet. The generated file was huge and required to load the full dataset in memory to be produced. Hereby OBITools4 proposes to substitute the obitab usage by the ROBIFastRead R module.