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btllib
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Bioinformatics Technology Lab common code library in C++ with Python wrappers.
The recommended way is to download using Conda package manager:
conda install -c bioconda btllib
Alternatively, you can compile the code from source. Download btllib-$VERSION.tar.gz from the GitHub latest release where $VERSION is the latest btllib version and do the following:
tar xzf btllib-$VERSION.tar.gz to extract the source code.btllib/compilebtllib/install directory. You can provide the --prefix parameter to change this.CXX environment variable to point to the compiler before running btllib/compile.python3 -m pip install $PREFIX/lib/btllib/python afterwards to install the Python package. The Python wrappers are usable even without this step. $PREFIX is the path where btllib is installed.$PREFIX is the path where btllib is installed):$PREFIX/lib/libbtllib.a (pass -L $PREFIX/lib -l btllib flags to the compiler).#include any header from the $PREFIX/include directory (pass -I $PREFIX/include flag to the compiler).btllib uses C++11 features, so that standard should be enabled at a minimum.python3-config to determine the flags used for compilation. Running python3-config --exec-prefix will give the path to the Python installation that needs to be used. The python3 executable can be found at $(python3-config --exec-prefix)/bin/python3.btllib::SeqReader::Flag in C++ versus btllib.SeqReaderFlag in Python).PYTHONPATH environment variable or sys.path.append() in your Python code to include $PREFIX/lib/btllib/python/btllib directory to make btllib available to the interpreter.import btllib$PREFIX/bin directory. Append that path to the PATH environment variable to make it available to your shell.git clone --recurse-submodules https://github.com/bcgsc/btllib in order to obtain all the code.btllib dir, run meson build to create a build directory.build dir:ninja wrap to regenerate wrappers.ninja test to build wrappers and tests, and run tests.build dir:ninja quality-assurance to make sure all CI tests pass.sdsl-lite subproject. Meson config file adjusts the sdsl-lite config in order for it to work for btllib, but this is done ad hoc and is not necessary to be committed. By doing it ad hoc we keep a list of differences compared to the upstream repository.build dir:ninja docs to regenerate docs to reflect the release and then commit the changes.meson dist --allow-dirty to generate a self-contained package based on the last commit. --allow-dirty permits making a distributable with uncommited changes. This is necessary as sdsl-lite dependency has ad hoc changes made during the build process. The resulting distributable will be compressed with xz. For easier use, decompress it and then compress with gzip. Attach the resulting file to the release.The following are all the available ninja commands which can be run within build directory:
ninja format formats the whitespace in code (requires clang-format 8+).ninja wrap wraps C++ code for Python (requires SWIG 4.0+).ninja clang-tidy runs clang-tidy on C++ code and makes sure it passes (requires clang-tidy 8+).ninja builds the tests and wrapper libraries / makes sure they compile.ninja test runs the tests.ninja sanitize-undefined runs undefined sanitization.ninja test-wrappers tests whether wrappers work.ninja docs generates code documentation from comments (requires Doxygen).ninja quality-assurance runs clang-format, wrap, clang-tidy, test, sanitize-undefined, and test-wrappers. These are all checked at the CI test.