Only do block retrieval of repeats when we are caching our hits. Otherwise we're bringing back more data for no reason

added method fetch_all_by_display_label and changed fetch_by_display_label to return a gene on the reference slice if there is one

Removing the new_fast and replacing ISA with base. new_fast comes from Feature & should not be overriden. ISA is just nasty

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...