GitLab

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.