GitLab

where all my transcripts were disappearing to.

I'm assuming it still works for slices.  I don't have slice tests yet.

Refactored PredictionTranscriptAdaptor to inherit from BaseAlignFeature (and fixed some bugs)
Altered RepeatFeatureAdaptor slightly for changed BaseAlignFeature implementation

StickyExon now handles negative strand slices (forgot to add this before), renamed StickyExon::each_component_Exon to get_all_component_Exons

fixed genes calls - and added deprecated warnings, change get KBs calls to get_all_KBs, minor fixes to DAS code

     $str = substr($str, $start -1, $end -1);
to
     $str = substr($str, $start -1, $end - $start + 1);

add_supporting_features - before supporting features are added a check is made whether they are from the same contig.

RepeatFeatureAdaptor - only one match returned.  (I think I stomped on Arne's fix here
all ok now)

Exon - checks phase is defined before comparison
PredictionTranscript - checks phase is defined.  Commented out LOG print statements
TranscriptFactory - start_exon end_exon same old thang
ExonAdaptor - hmm.

Updates so slices can handle negative strand, not finished yet, and not tested

method name changes and list to listref stuff