
LOG: 2010-12-16 10:30:11 Thursday  Week 50 <nanjiang@illergard>
    1. The "EXTRA 1" output is removed when the "-q" option is on
    2. Change the kalign position specific gap penalty scheme. 
    Two modes:
    (1). {gpo: 1 2 0.5 0.6}
    (2). {gpo: 1-43:1 55:0.5 43:-3}
    Here the value is not the direct gap penalty, but the multiplication value
    the real gpo[i] = m(i)*default_gpo      
    3. when no PSGP are supplied, call the original kalign function
