Add inMemory option to hdf5 alignment interface.  this option will store all arrays entirely in memory and disable the hdf5 cache.
add check for unrecognized option without parameter.  cant believe that was missing until now
add a few heuristics to cut down on lookup times in position cache
fix bug setting updateFlag where it was getting true almost all the time
change to version 1.3 and update doc
Try to fix linewrapping in options help display
add discription to halliftover
fix indent