Previously used time() which has 1 second precision.
Now use gettimeofday() which has millisecond precision.

complementBed now reports chromosomes that were not present in the BED file,
yet were in the genome file.  Thanks to Michael Hoffman for reporting this.

Fixed casting issue in windowBed.AddWindow() that cuased slop positions to run off the end of the chromosome.

This will eliminate the oft-reported compilation issue.