Changed TranscriptUtils.pm and WGA2GenesDirect.pm
Changed the logic in TranscriptUtils for the replace_stops sub. The logic now states that if the edited
translation is longer than the original, then throw. If the edited translation is shorter than the max
allowed removals, then throw. If the max_stops parameter is not defined and the number of stops removed
is greater than one, then throw. Otherwise it's okay.

For WGA2GenesDirect.pm I have set the max allowed removals to 10, however this might change in future.