Fix to alignment regex
add test case for GenBank tests for bug #3448
clean up code
remove and refactor genbank CONTIG code, address part of bug #3448
fix NCBIHelper bug, vars => ours
add some additional comments
add support for a stricter standard codon table, for the MAKER folks
fix issue with seq_id when set to 0, patch courtesy of Benjamin Warren
Updating Bug address. Adding -w to perl invocation.
Adding script which runs deob_index to update the db. (prob Mauricio's code)
Bugfix: wasn't checking return value from _load_module, so when it failed we never knew. Documentation added for new error message and for requirement that BioPerl itself be in @INC. Bug reporting and email address also updated.
Better error message

When file was '', the message was pretty unclear
Math::Random does not seem to be used anywhere... removing it
BigInt and BigFloat commented out. Commenting them out in the POD as well
Bio/Factory/FTLocationFactory.pm: Refined logic for sublocations order
in complex locations like in trans-splicing
Bio/SeqFeatureI.pm: Changes to spliced_seq sequence handling in line
with sublocations changes
Bio/DB/Fasta.pm: Small Windows compatibility fix in header subroutine
Merge remote branch 'upstream/master' into test
Bio/SeqFeature/Generic.pm: Updated Start, End and Length subroutines
to handle circular sequences that have been cut by origin
(e.g., join(5075..5386,1..51))). It can be detected when a subloc ends
in the last nucleotide of the primary sequence and the next subloc starts
at the first nucleotide in the same strand
t/SeqFeature/Generic.t: Fixed a test of circular sequences with a wrong
end coordinate and deleted TODO since the circular tests now pass