added documentation
added detection of "blank" fragments

these are fragments that don't harbor a secondary RE site.  fragment
output now contains another column that indicates the distance between
the left and the right primary RE sites (or -1,-1 if there is no
secondary site; ND if it was not tested).
bug fixes (e.g. division by null length for N frequency)
modified the criterion for excluding short fragments

instead of 2 * flank_len it's not flank_len + 10.
Merge branch 'blind' into develop