InputUtilities: fix alignment consistency check
InputUtilities: fix alignment consistency check

We need to reverse the source and target sentences if the alignment is
also being reversed.

tdomhan/thrax,tdomhan/thrax,joshua-decoder/thrax,jweese/thrax,jweese/thrax,joshua-decoder/thrax,joshua-decoder/thrax,tdomhan/thrax,jweese/thrax,joshua-decoder/thrax