Performance optimisation in fetch_all_by_feature_class method. Contributed by Shiran Pasternak at CSHL

load different Go sources as the same so that the xrefs are NOT treated as priority ones which only give one to one mappings, which is in approriate for GO

  The ranges in the registry are sorted by start position.  When
  calculating the overlap with a query range, a loop goes through the
  registered ranges and checks for overlaps between each range and the
  query.  This change will terminate this loop when all the remaining
  start positions are larger than the end position of the query range.

  This cuts the running time for this routine by 90% in some
  applications that registers a large number of ranges.

Tested.

existing database, save these values before wiping the table.  When
reading the new external_db table is read from file, instead of writing
the db_release column from the file, use the saved values.

Formatting.

  Add an optional fourth boolean argument, $ignore_release:

    If unset or zero, will require that the release string of the
    DBEntry object is identical to the release of the external database.
    If set and non-zero, will ignore the release information.

  Requiring that all of $a, $c, $t, and $g be non-zero is too strict
  when trying to avoid that $a+$c+$t+g be non-zero in division.  Just
  test the sum instead.  This would have generated the wrong results for
  sequences which lacked one of A, C, T, or G...

  tr/Aa// is theoretically quicker than tr/Aa/Aa/

  Formatting


Tested.