Change to TranscriptUtils.pm and WGA2GenesDirect.pm
In TranscriptUtils.pm, in the replace_stops_with_introns function there was the assumption that any transcript
passed in will have at least one internal stop. This is not always the case as WGA2GenesDirect.pm uses this
function to check all transcripts. Now a flag can be passed in, that allows multiple stops to be processed.
For the moment this flag is experimental, so if you're using it you should check the results. The function
will now no longer throw on transcripts that have no internal stops.

In addition I changed WGA2GenesDirect.pm to do a check on the peptide sequence of a transcript to see if there
are any internal stops present. This way the code should never call replace_stops_with_introns unless there is
a reason to begin with.