cd0c525f50
### 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.
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).
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.