05de9ca58e
This commit introduces the ExtractSuperKmers function which identifies maximal subsequences where all consecutive k-mers share the same minimizer. It includes: - SuperKmer struct to represent the maximal subsequences - dequeItem struct for tracking minimizers in a sliding window - Efficient algorithm using monotone deque for O(1) amortized minimizer tracking - Comprehensive parameter validation - Support for buffer reuse for performance optimization - Extensive test cases covering basic functionality, edge cases, and performance benchmarks The implementation uses simultaneous forward/reverse m-mer encoding for O(1) canonical m-mer computation and maintains a monotone deque to track minimizers efficiently.
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 OBITools commands and other associated files into the /usr/local directory.
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, the installation script offers two options:
-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).
You can use these options by following the installation command:
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | \
bash -s -- --install-dir test_install --obitools-prefix k
In this case, 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.
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.