The latest version of GNUMAP (version 2.6.0) has just bee uploaded to the website. You can download by going here: http://dna.cs.byu.edu/gnumap/download.cgi, or straight to the link at http://dna.cs.byu.edu/gnumap/gnumap-2.6.0.tgz.
Most important, this release made significant improvements to bisulfite mapping to include BSW, BSWR, BSC, and BSCR reads (for a full description of these sequence types and flags for mapping them, please see http://dna.cs.byu.edu/gnumap/parameters.shtml#bisulfite).
Nathan