GitLab

ProteinAlignFeatureAdaptor should create DnaPepAlignFeatures not PepDnaAlignFeatures; hitstrand should always be 1

Changed the way exons handle supporting features a bit

Added new SupportingFeatureAdaptor

code review on Bio::EnsEMBL::Exon. Removed transform method, because already in Bio::EnsEMBL::SeqFeature. Changed naming of _tranform... methods. Make them aware of slice strand -1

and in Slice to make more consistant.

in get_repeatmasked_seq and _mask_features methods

overload get_repeatmasked_seq method, and _mask_feature as consequence to allow soft masking (replace repeat by their lower case equivalent, needed for blastz for example). BTW, fixed little bug, previously when a repeat was overlapping slice, but was partly out of range, no masking was done with it. Now it does.

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

use a consensus from the database if one exists