 ~/git/BEETL_DEV/Beetl ext -i ../../test.seq -a -p fred -sap and  ~/git/BEETL_DEV/Beetl ext -i ../../test.seq -a -p fred work and give correct output.
 ~/git/BEETL_DEV/Beetl ext -i ../../test.seq -a -p fred -sap
and
 ~/git/BEETL_DEV/Beetl ext -i ../../test.seq -a -p fred
work and give correct output.

 ~/git/BEETL_DEV/Beetl ext -i ../../test.seq -r -p fred -sap
and
 ~/git/BEETL_DEV/Beetl ext -i ../../test.seq -r -p fred
work and give same output.

TBDs
-i option does not work (everything called BCRext*)
-sap mode needs to actually do SAP-sorting

BEETL/BEETL,BEETL/BEETL,BEETL/BEETL,BEETL/BEETL