If you want input from everyone instead of only the biologists you probably have to describe your data and what '50 base-pairs away' means in the context of that data.
Comment on Re: A more efficient sort or heap algorithm...
Point well taken. The gist of the problem is that I have two large integers that I need to parse from each line in a file, and then compare the integers from each file. The base-pair comment denoted (in my head anyway) that these integers reference a position in the genome.