def read_coverage(cov_file):
    """Determine the total number of bases covered.

    Reads in the given coverage file and computes the total number of
    bases covered, returning that value as an int.
    """
    header = cov_file.next()
    footprint = 0
    for line in cov_file:
        (chromosome, start, end, cov) = line.split("\t")
        start = int(start)
        end   = int(end)
        footprint += end - start
    return footprint