store each density feature as it is created rather than building a list per seq_region - smaller memory footprint (but repeats still leaking mem)

supercontig length should be max(superctg_end) not length because occasionally supercontigs do not start at 1

Added: AFFY_Rat230_2, AFFY_Zebrafish

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.

* 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

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

now gets protein_id vai previous dump's embl file; includes names, descriptions, Dros orhtologues; deals with bacterial genes; has comments