GitLab

use arg strand in Slice::subseq so that SequenceAdaptor does reverse complimenting (it has more complete transliteration) rather than exon code

changed add_sub_SeqFeature method so that it no longer expects passed in feature to implement contains() method
This should allow Features to be used instead of SeqFeatures

made sure seqname was maintained in alignfeatures and corrected an error message in SliceAdaptor

reduced number of function calls in add_map_coordinates, probably a little bit faster now in some situations

seq_region_start|end could have returned undef inappropraitely when one (but not both) of the features end|start was undefined

Updated it not to use anymore /tmp for temporary copy and knows now about the mysql new directory configuration standards