[Bioperl-l] Bio::DB::Fasta bug

Chris Fields cjfields at illinois.edu
Wed Apr 6 16:10:40 UTC 2011


Okay, assuming this is kosher to be included in the next CPAN release.  I'll close the bug report out.


On Apr 4, 2011, at 2:05 PM, Chris Fields wrote:

> All,
> I just added a BioPerl bug fix for this issue:
> https://redmine.open-bio.org/issues/3172
> which catches cases where no match occurs in a sequence header for the regex '>(\S+)' and throws a proper exception (previously it treated the line as part of the sequence).  My concern is performance issues with the fix, particularly with regards to Bio::DB::Sam and other code using Bio::DB::Fasta.  If there is a significant performance issue let me know and I can revert those.
> chris
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