🗂️ Accessing the Suffix Array via Φ−1 Forest

✔️ Prerequisites

• libdivsufsort
• g++

🚀 Complete Test Run

git clone https://github.com/koeppl/randSAbench.git
cd randSAbench
submodule update --init --recursive

In the file bench.sh, you have to adjust the variable kFullFasta for the path to the FASTA file you want to index, and sequences for the number of sequences you want to extract from this file. Then you can run bench.sh measuring the query time for suffix array access with our proposed method and the standard method of the r-index. Note that the default is to also build the plain suffix array to check whether the reported entry is correct. Building the plain suffix array will not work with large inputs and a modest amount of memory.