GitLab

_transform_to_RawSlice was not aware of reverse slices, but it is now thanks to Graham.  Cleaned up a few other things.

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.

bug fix to ensure supporting features are being passed properly

removed _transform_to_slice as should use one in SeqFeature and added a check so if features are split and second half has 0 length it is skipped

In _parse_features, making better use of strandedness information to make sure query and hit start and end coordinates are turned the right way around.

Removed deprecated Repeat, RepeatI modules
Added a few more PODs

These were causing infinite recursion due to new superclass implementation of entire_seq, attach_seq, and contig methods

BaseAlignFeature - fixed a horrible rounding error caused by features being split across contigs with lot of help from graham

ExonAdaptor altered the way some adaptors are called

-'Flatening' FeaturePair object so that it no longer contains 2 SeqFeatures; It is now isa SeqFeature with some additional Hit attributes (object still bhaves as if it contained two features
-Adding 'fast' constructors to DnaDnaAlignFeatures and PepDnaAlignFeatures
-Some other minor tweaks such as using bind columns instead of fetchrow_hashref

transform functionality in BaseAlignFeature should now work for slice -> raw contig other way still need implementing should also now split cigarlines nice where necessary

made sure end_phase was set explicitly when transforming sticky exons in Exon.pm

moved around some of the feature pair stuff again.  RepeatFeature now inherits from RepeatFeatureI, BaseFeature now inherits from RepeatFeature

AssemblyMapper, altereed checking of seq->start to allow for negative numbers

AlignFeatures, added coordinate transforms, only slice->rawcontig implemented currently plus otehr methods to make new supportting feature storage work like dbID and contig

Exon, altered supporting feature storage

FeaturePair remove cigar accessor as it is just confusing!

AssemblyMapper - altered the way certain methods were called so arguments are passed in the correct order
BaseAlignFeature - added feature validation to _generic_parse_features method
SeqFeature removed checking for Source tag and Primary tag from feature validation method as these are now deprecited

deleted final else in new as this would throw even if the correct arguments had been specified

Some bugs with BaseAlign still there.