Working on extend-orf
Added genetic-code option to specify the genetic code. Affects translation in analyzer and Exonerate in reporter.
Added --genetic-code to manual
Fixed a bug with the genetic-code option
Fixed bugs concerning --genetic-code
ORF extension with correct overlap calculation
Fixed minor bug and improved output
Added documentation for --extend-orf
Added two-pass ORF prediction for extend-orf
Minor changes
Merged extend-orf story from devel