make use of two genome region annotations
read_cages from file should automatically recognize extension (.gz or not); make use of OptionParser
move GenomeRegion.new_by_bed_line
make bed chunk scissors customizable; move some logic to lib/cage
make order of command line arguments for cut_cages more convenient
make var names more universal (complying BED file format specification: http://genome.ucsc.edu/FAQ/FAQformat.html)
rename part_of_cages to bed_scissors
rename cut_cages --> expand_cages; made tool descriptions