add branch to track commits
PrimarySeqI.pm: Avoid using Bio::Root::clone when object
is 'Bio::Seq::LargePrimarySeq' or 'Bio::Seq::LargeSeq'.
This fix fails in t/Seq/LargePSeq.t and t/SeqIO/largefasta.t

Fix conflict:
	Bio/PrimarySeqI.pm
No, really, fix the conflict :P
forgot to be on topic
FTLocationFactory.pm: Fix in from_string() for some complex
location tests that failed in LocationFactory.t
Reformatting and editing
Fix typing errors
Bio/SeqUtils: trunc_with_features() and revcom_with_features()
now explicitly removes all annotations/features before adding some back,
so they don't conflict with trunc() and revcom() object cloning
Bio/PrimarySeq.pm: Fixed some 'uninitialized value' warnings

Fix minor conflicts:
	Bio/PrimarySeq.pm
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.