[Bioperl-l] Windows bug in Bio::DB::Fasta?

[Scott Cain]

Hello all,

I am investigating a bug in GBrowse that seems to only surface when
people are using the memory (ie, file) adaptor on Windows systems.
Here's the bug report:

https://sourceforge.net/tracker/?func=detail&atid=391291&aid=1256169&group_id=27707

I've tracked the problem down to Bio::DB::Fasta when the file is dos
formatted (that is, it has both line feeds and carriage returns), BDF
returns the wrong string when a subsequence is requested, but when the
file is unix formatted (ie only CR (or is it only LF?)), it returns the
right string.  I wrote the very simple test script below and stepped it
through the perl debugger.  It looks like the bug is in the caloffset
method, as it returns the same offsets regardless of the file type,
which then makes the subsequent seek into the file go to the wrong
coordinates of dos formatted files.

Unfortunately, I don't really know what is going on caloffset, so I
don't know how to fix it, but it presumably has to check the format of
the file somewhere and take that into account.

Thanks,
Scott

-- 
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Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory