How to run:
Make sure genotypes.csv exists in the current folder,. run make and run ./fast-ibd1-set-intersection-scanner.
Overview:
class Set : a bit vector ( 1 bit per individual). In the algorithms the ones are compatible people (matches) with the current one.
CollectionOfPacked12s : A list of m sets S_i (m: number of markers) sets with 1 bit per individual. For each marker position and individual, a bit is 1 if they individual has a genotype of 1 or 2. That means that set S_i contains the individuals that are compatible with a 2 at position i.
Functions: find_matches_single_window: find matches for a single window and a single individual. scanner_v1: first implementation of the whole chromosome scanner.
To switch between the implementations, change function scan_matches.
Run python3 partitions.py 3
where 3 is the index of the invididual which is the query.