Jbrowse JBrowse

make prepare-refseqs.pl warn about multiple matches, and use the first one.

motivated by
http://sourceforge.net/mailarchive/message.php?msg_id=28816994
(appended below)

=======================================================================

Re: [Gmod-ajax] setting up jbrowse with a bacterial reference genome
From: Heewook Lee heewlee@um... - 2012-02-10 18:32
I am actually looking at a document: Setting Up the JBrowse Genome Browser
that was published in Current Protocols in Bioinformatics in 2010 and there
is an example using NCBI gbk file. I tried that but I am getting the
following error:

[heewlee@... tmp]$ bin/prepare-refseqs.pl --conf docs/examples/config/yeast_genbank.json --refs NC_001133

-------------------- EXCEPTION -------------------- MSG: segment() called in a scalar context but multiple features match.
Either call in a list context or narrow your search using the -types or
-class arguments

STACK Bio::DB::SeqFeature::Store::segment
/usr/local/share/perl5/Bio/DB/SeqFeature/Store.pm:1359

STACK toplevel bin/prepare-refseqs.pl:156

Any idea how I can get around this? Thanks
https://github.com/GMOD/jbrowse/commit/3218f1c25e1d24d81c1ff8fd641d...