Change to GeneScaffold.pm
The projected transcript will now take in the stable id of the parent transcript.
This will be useful for the hive pipeline and should not affect the old code.
Changes to ProjectionCandidates and HiveWGA2GenesDirect
ProjectionCandidates now takes in a hash of allowed biotypes to select transcripts from.
HiveWGA2GenesDirect has mainly just had a call to empty_Gene added to stop it going insane
when storing genes
Change to TranscriptUtils.pm
I was convinced I had committed this fix before but can't find it. I've commented out
some code in replace_stops_with_introns as there is no need to do the swap since the
code is working on a translation and thus is already working in a stranded manner.
Before this fix we were swapping the split features on any stop replaced in a gene
on the minus strand and assigning them to the incorrect exon
Changes to TranscriptUtils.pm
Some changes to replace_stops_with_introns to deal with various issues. Some debugging
code present, will remove in a later commit