zjurelinac / fer.LCP-BWT

Bioinformatics course project: Computing the LCP array based on BWT

LCP-BWT

Computing the LCP array based on BWT

Bioinformatics course project at FER, University of Zagreb

Installation

1. Clone this repo to your computer (git clone https://github.com/zjurelinac/LCP_BWT), or download it as a zip archive and unpack it.
2. Open terminal in the root directory of the project (LCP-BWT) and run make.
3. If everything proceeds without error, the executable program should be located at build/lcp-bwt.
4. If any errors occurred in the previous step, try changing the compiler (on the first line of the Makefile). All modern versions of GCC and Clang should be supported (compilation requires some advanced C++ features from recent standards (C++11 and C++14)).

Usage

To run the program, type ./build/lcp-bwt input_file output_file. The input should be in the FASTA format, with only one sequence per file.

Testing

To run automatic tests, position yourself in the tests directory, and type ./test_runner.py (This requires Python 3 to be installed on the computer).

To generate additional tests, type ./test_runner.py -g SIZE1[,SIZE2,...] [-p], which will generate random DNA (or protein, if -p flag is given) sequences of a given length. If the size of test case is less than 25000, it will also generate the expected output file (using brute-force algorithm).