Source files to create linkage calc, a program that determines if haploid samples in a multi-sample vcf have alleles that are linked, by using a gamitic linkage calculation then permitation tests. Developed initioly for use with the NOTCH2NL genes, but is fully generalized.
Installation: make sure you have the required dependincies for htslib (pthread lzip)
make sure you have cmake 3.10.0 or higher installed
run the command "cmake CMakeLists.txt && make "
then move the binary "linkage" into your path.