[Bioperl-l] GenBank references parsing bug, Bio::DB::GenBank

[Hilmar Lapp]

The GenBank format bug reported by Ed Green (#833) turned out to be a bug
in the section for parsing references. The method responsible for this
contained other bugs, too, which haven't been exposed yet.

These bugs are now fixed in the main trunk (along with some code polish).

In addition, the phenomenon reported by Ed that he wouldn't get the error
when he used Bio::DB::GenBank for retrieving the sequence entries instead
of a flatfile is due to the fact that Bio::DB::GenBank only retrieved the
sequences in Fasta format. This also means that there is no way to get
the feature table as annotated features, which is a pity I think.

I've therefore modified Bio::DB::GenBank so that there is now an option
for specifying the desired retrieval format (-format). This can also be
changed between retrievals by calling e.g. $db->request_format('Fasta').
The default is now GenBank format. 

	Hilmar
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Hilmar Lapp                                email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
A-1235 Vienna                                fax: +43 1 86634 727
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