Sorted order was defined as ascending lexicographical chromosome order first, ascending integer order using the start coordinate next, and ascending integer order using the end coordinate last. Other fields are retained but ignored by the sort-bed and the bbms implementations.
The advantages to using lexicographical chromosome ordering were that no source code required hardcoded chromosome names for a given species, and there was no reason to limit the first field to only those names that begin with 'chr'. The design choice allows the software to work with any species' data without modification. The ordering established by using both the start and end coordinates in addition to chromosome names helped to simplify operations in the bedops, bedmap, and closest-features utilities, and led to smaller runtime memory requirements and generally improved time performance.
