LCP for Succinct k-Spectra

This is the code for the paper Longest Common Prefix Arrays for Succinct k-Spectra by J. N. Alanko, E. Biagi, S. J. Puglisi, SPIRE 2023.

Building

git submodule update --init --recursive
cd SBWT/build

# Here we are compiling with gcc-10 and g++-10. Replace these with whatever
# version of g++ you have. Clang will not work.
cmake .. -DCMAKE_C_COMPILER=$(which gcc-10) -DCMAKE_CXX_COMPILER=$(which g++-10)
make -j4

cd ../..
make benchmark --always-make CXX=g++-10

Running

The code takes a plain-matrix sbwt file as input. You can generate one by running:

./SBWT/build/bin/sbwt build -i SBWT/example_data/coli3.fna -o index.sbwt -k 30

Then, you can run the benchmark with:

./benchmark index.sbwt linear out.txt

where linear is one of: naive, basic, superalphabet-2, superalphabet-4, linear.