Your right. I tried to provide checkpoints so that I wouldn't have to crawl through all the data (aka, making sure the chromosomes considered match, etc.), but even then there is a lot to go through. Heck, I even tried to write a multi threaded version of this program, but it has a few bugs still. Should it really take this long though? I don't have any benchmarks written in, so that will probably be my next step. I'll look into putting this into a database to do some of this for me, but sql is still a bit of a learning curve for me.