If the configuration parameter 'not_biotypes' is present, exclude all
  genes whose biotype is listed (but include all other genes).

  If the configuration parameter 'biotypes' is present, include all
  genes whose biotype is listed (as usual).

  It is an error to define both options in the configuration.

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.