Tried to keep the format of the script the same and just add in the extra rows needed. The script should now do:

1. Set the canonical transcript to be the one with the longest CCDS translation
2. If no CCDS, set the canonical transcript to be the merged transcript with the longest translation
3. If no merged, set the canonical transcript to be the one with the longest translation
4. If no coding transcripts, choose the longest noncoding merged transcript
5. If no merged transcripts, choose the longest noncoding transcript

database, prefix each SQL line with the string "#HEADS_UP!#" to avoid
unnecessary suffering.

when the primary key exists in both database table and master table
(didn't do this before).

look for entries that are the same (sans private key) and report these
in the output and SQL.

Modify formatting of generated SQL.

fixed bug where the dbID of an xref that had already been stored was not set in the object when store was called

for origin overlapping genes take into account exons with negative start and with start greater then end

it looks like the features overlapping origin can be attached to a normal slice as well as to an overlapping origin

make sure the sequence is retrieved for both ends of the region overlapping circular chromosome origin

exons of the genes overlapping chromosome origin are attached to the normal slice, but with negative coordinates