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

Chris Fields cjfields at illinois.edu
Mon Apr 4 19:05:15 UTC 2011


I just added a BioPerl bug fix for this issue:


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.


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