GitLab

Added an additional check in the transform method. When testing exons, if consecutive exons in the old version of the transcript were on the same strand then the new versions should be on the same strand too. If not, returns undef. Prevents cases being transformed where the transcript's exons map as below:

1
------------------------------
-1        5  4  3  2  1

to

1      3  4  5
------------------------------
-1               2  1

Replace HGNC_ENSTParser.pm, GI_Vega_Parser.pm and ZFIN_DARTParser.pm parsers with VegaOfficialNameParser.pm

CV: ----------------------------------------------------------------------

changed the dumped databases entrys from int to enum so changed the values here to match those in the database

Add abillity to ignore a black list of genes for dumping. Also new methos to get a hash of the non reference alt_alleles

changed the dumped databases entrys form int to enum so changed the values here to match those in the database

New table alt_allele added and dumped in the xref table changed to an enum for ease of use/understabding

Changed order of vega xrefs to check and added a test that the transcript has a logic_name of havana.

Changed order of vega xrefs to check and added a test that the transcript has a logic_name of havana, plus made sql easier to read.

to ens-staging2.

Change one instance of $dbport to $mport to connect to the right port
on the master server.

server port.

for a few releases but that I've ignored.