Fixed write_crunch()/write_line()
Fixed write_crunch()/write_line()

This was not correctly inverting subject sequence locations, when
preparing the .crunch file output.

widdowquinn/Teaching-Dundee-BS32010,widdowquinn/Teaching-Dundee-BS32010,widdowquinn/Teaching-2015-03-17-UoD_compgenvis,widdowquinn/Teaching-2015-03-17-UoD_compgenvis,widdowquinn/Teaching-Dundee-BS32010,widdowquinn/Teaching-2015-03-17-UoD_compgenvis