This code is provided as Supplemental code to the paper "Minimal Positional Substring Cover Is a Haplotype Threading Alternative to Li & Stephens Model" by Ahsan Sanaullah, Deguiz Zhi, and Shaojie Zhang.

There are two versions of code available here. Firstly, a user code is provided to allow an interested reader to obtain MPSC statistics and results for a reference panel and query haplotypes. The second version is the benchmark code. This is the code that was run to obtain the results in the paper. It is provided for posterity.

