Also, broke the Options.pm's feature() method into multiple methods because it was trying to do to much. Fixed track selection.
This set of changes is paralleling the 220.127.116.11 version of gbrowse.PLS. Not quite done, there is no mechanism yet for reading the cookie and I'm not really sure that the cookie naming and expiration are done correctly.
-Numerous changes to minimize GD.pm color and tile overflow problems. Still needs rewrite to use Bio::Graphics::Glyph built-in methods to draw stuff -Replaced NCBI-2-GFF conversion script with UCSC-2-GFF3 script. NCBI annotations proved hard to work with due to to ever-changing download dir layout, hence the switch
…dvertently backed out updates from a few weeks ago. I think these will work :-)
… DAS-only operation
…stall tree and stripping out prefix path from generated PLS->pl scripts. appears to work for all use cases given by Makefile.PL --help, although i'm sure i'll hear about it if something is broken!