Program			Function	
-------			--------
gmapper-cs		colourspace mapper
gmapper-ls		letterspace mapper
prettyprint-cs		pretty print alignments from rmapper/probcalc (c. space)
prettyprint-ls		pretty print alignments from rmapper/probcalc (l. space)
probcalc		parse rmapper output (non-pretty-printed output)
probcalc_mp		combine read mappings from probalc into mate pairs
shrimp_var		list detailed hit variations in rmapper/probcalc results
