# $Id: BUGS,v 1.4 2002-12-31 13:09:05 birney Exp $

Known Bugs 

Bioperl 1.2
===========

 * The searchio.t test is failing on cygwin installations (and
   nowhere else). We need a developer who works with cygwin to
   help us out here. We suspect something to do with temporary file
   opening.


Bioperl 0.9.0 
=============
 * Bio::Tools::Blast continues to cause problems for some people.  As
   it is not actively maintained there are a slew of reported bugs for 
   it that have not been fixed.  

 * Bio::Tools::Run::Alignment::TCoffee - t_coffee binary does not get 
   all parameters it needs when aligning (two) two DNA sequences
   (jitterbug #966).

 * Bio::Tools::Run::ClustalW and t/ClustalW will report errors for
   clustalw versions 1.8x due to a bug in clustalw.

 * Bio::DB::GenBank continues to have intermittent errors.  Bio::DB::GDB 
   is also unreliable at times and one can safely ignore errors from
   these during a make test.  
   Bio::DB::GenBank is unable to download whole contig files as well
   as NCBI ref seqs like NT_* numbers unless the -format flag is
   passed in and specified as 'fasta' in the constructor.
   get_Stream_by_batch() also has intermittent errors which are being
   tracked down.

Bioperl 0.7.2
=============

 * NCBI has changed some of the cgi scripts for retrieving sequences
   online which as resulted in some of the DB methods from not working
   consistently.  We are addressing these in the 0.9.x and 1.0 series
   of releases.  We recommend using the Bio::DB::EMBL object that is
   part of the later releases. 
 
   Additionally RefSeq Contigs are not properly downloaded, please see
   the bioperl list archives for information about potential
   workarounds and ongoing development effort to address these.

Bioperl 0.7.1
=============
 * Bio::Tools::BPlite does not parse and set frame properly for
   tblastx reports (Jitterbug bug # 978).

 * Bio::Tools::BPlite interface needs to be updated to fix parsing
   more than bl2seq report report (Jitterbug bug #940), this has been
   fixed on the main code trunk and will be part of the next major
   bioperl release.
 
 * If File::Temp is not installed, tempdirs are not cleaned up
   properly.  This is fixed on main code trunk with the introduction
   of rmtree method in Bio::Root::IO, however, it is best to install
   File::Temp when running 0.7 branch code.
 
 * Bio::Tools::Blast does not allow users to run blast, instead use
   Bio::Tools::Run::StandAloneBlast to run local blasts.  To submit
   jobs to a remote blast server like NCBI a module
   Bio::Tools::Run::RemoteBlast has been written but is part of the
   main trunk code and must be obtained through CVS until the next
   major bioperl release.

Bioperl 0.7
===========
 * Bio::Tools::BPlite doc error lists
   code synopsis code as 
     my $parser = new BPlite(\*FH);  
   should be 
     my $parser = new Bio::Tools::BPlite(\*FH);