Put back the line of code to output BAM_FPROPER_PAIR flag for reads in
---> <--- paired orientation.

While this isn't strictly correct for all library types, making this
assumption is still usually correct and far better than simply never
setting this flag at all.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3702 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1