generate_haplotypes SAMPLPE_SIZE=<?> REGION_IN_BASE_PAIRS=<?> OUTPUTFILE=<?>
It generates haplotypes with help of MaCS project. To run this you have to download MaCS and setup it. After that, you need to set MACS_PATH variable in the Makefile.
encode_haplotypes input.txt output.txt
It encodes haplotypes from an input file and outputs it as a separate file.
create_wg input.txt output.wg
It creates a wheeler graph from a file with help of pfp_wg repository. Before running, you need to set PFP_WG_PATH variable in the Makefile.
visualize_haplotypes_sizes
Outputs a graph in .png which shows the sizes of haplotypes represented as wheeler graph.