GitLab

* store method will store display_xref if it is set

* fetch methods correctly populate created display_xrefs now
* store method will store display_xref if it is set

Slice::project no longer forces projection to assembly_exception regions.  Not sure why it did this.

Updated to schema 20 and now gene descriptions are not uppercased anymore. They are kept as in the original source. Also added -port option and updated the help menu

Preprocess coordinates by merging adjacent inserts and deletes (mis-matches) so that they are treated like matches. Lose fewer exons this way.

Added methods: hseq_region_name, hseq_region_strand, hseq_region_start and hseq_region_end, that return something if hslice is defined

* store xrefs to human genes/transcripts/translations that chimp genes were generated from

moved routines related to storing of final genes into Gene package, added splitting of v. long introns, clustering of transcripts into genes, removal of duplicate transcripts and brinnging   across xrefs

addition of a $sth->finish

chained mapper was already being used even though faster regular mapper could usually have been used (accidentally commited with cache fix commit)

split input of seq_region files into seperate query/target seq_region files because the same names may be used on both sides

removed phase recalculation code, instead retain human phases which is the correct thing to do when exons are dropped