Do not die when finding an InnoDB table, go on to the next database instead.

First pass attempt at a copy data command using sysread and syswrite to bypass buffers. Basic tests say that it works.

Patches for 67. Index addition on transcript, new status on transcript & gene and a new supporting evidence table for introns

new script to fix mapping coordinates in asm_start, asm_end columns; don't merge or bridge gaps as this is done ordering by cmp_start in fix_cmp_overlaps.pl

don't limit seq_region to chromosomes, so the script can be used to fix overlaps in mappings between other coord_systems

fact an IP address.

only one single database *instead* of an input file.

Format of arguments (for example):

  --source=ak4_chrysemys_picta_ref@genebuild1
  --target=ak4_test@ens-research


If a special port number needs to be specified:

  --source=ak4_chrysemys_picta_ref@genebuild1:3306
  --target=ak4_test@ens-research:3306

You still need to log in on the destination/target server and run the
script as the mysqlens user.

Do not re-set $executable{$key} = $key when we have worked so hard to
set it to something usable...

Correctness of classification may leave something to be desired.

Groupings are more or less complete, but there are still ambiguities over transcript biotypes.

Made the circular slice code compartmentalised to just SliceAdaptor (making cache initalisation code easier) and we now only build circular slices when the seqregion it is based off is flagged as circular

Attempting to fix the issues with too many KNOWN status genes appearing in species we should not be seeing them in. UniProtParser now limits to using ACs with an evidence of 1 and 2. We now do not assign KNOWN based upon a depdendent xref when we didn't trust the parent xref. Also the loader & SQL has been edited to allow for LOWEVIDENCE types of sources.