Add --both option

[iimog]

Usually the orientation of LSC relative to SSC can not be resolved with short reads only (due to the length of the IR). Therefore the assembly graph will support both solutions equally. I think it is ok for the chloroExtractor to pick one arbitrarily and print a warning about it. However, there should be an option for the perl script of this step to extract both or all possible solutions.

[greatfireball]

Filed for version 2.0.0