The input for this program should be a FASTA file on the alphabet {A, C, G, T}.
Some examples are provided in the directory tests/.
The output of the program are the BWT and the LCP array of the collection of strings in the input file.
After the main command execution, the binary-encoded BWT is contained in the file tests/BWTbin,
while the binary LCP array is contained in the file tests/LCP.
Each entry of the latter file is a 8-bit unsigned integer with the only exception of -1 encoded as 0xFF.
Both files can be decoded into human-readable files with the commands decode_bwt and decode_lcp.
After cloning the repository:
cd bwt-lcp-em
make subdirs bin
Now it is possible to run the program as follows:
./bwt_lcp <path to the FASTA file>
./decode_bwt tests/BWTbin > <path where to save readable BWT>
./decode_lcp tests/LCP > <path where to save readable LCP>
For example, for invoking the program on one of the provided examples, we can enter the following commands:
make subdirs bin
./bwt_lcp tests/uploaded_test.fasta
# Optionally, to obtain the results in a human-readable format:
./decode_bwt tests/BWTbin > BWT.txt
./decode_lcp tests/LCP > LCP.txt
Some test instances are provided in the repository.
To run them, one can issue the command make test.
The algorithm is described in:
Computing the BWT and LCP array of a Set of Strings in External Memory.
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi.
arXiv:1705.07756, 2017.