# $Id: BUGS,v 1.7 2006-11-16 10:51:50 sendu Exp $

Known Bugs

Bugs are tracked at this URL:
https://redmine.open-bio.org/projects/bioperl/

Bioperl 1.6 series
=============

Though a stable release, some bugs and enhancements remain for this series
that will be addressed in future point releases. For a full list please see:

https://redmine.open-bio.org/projects/bioperl/

Bug     Summary (additional info)

2247    Have Bio::SearchIO::blast methods available for other BLAST parsers
        (enhancement request)
2332    Software for analysis of redundant fragments of affys human mitochip v2
        (API hasn't stabilized, may appear in a 1.6 point release)
2439    multiple results HTMLResultWriter.pm and non-redundant entries in SearchIO
        (partially implemented)
2463    bp_seqconvert.pl & Bio::SeqIO code cleanup and user friendly interface
        (enhancement request)
2476    "Undefined sub-sequence" when processing tblastx output
        (related to HSP tiling)
2482    paml4 mlc file fails to parse
        (may require refactoring Bio::Tools::Phylo::PAML)
2492    Method "pi" in package Bio::PopGen::Statistics
        (awaiting comment from Jason)
2513    creating a Bio::SeqFeature::Annotation object downloads the entire so.obo
        (should allow local copies)
2594    Bio::Species memory leak
        (fix implemented, but additional leaks likely remain)
2673    original fields not inherited by seq objects in alignment slices
        (request for bequest/bequeath behavior for attribute carryover)
2686    WU-BLAST XML support
        (partially implemented, but issues remain)
2691    Bio::Microarray::Tools::ReseqChip depends on CPAN module Statistics::Frequency
        (related to bug 2332 above)
2696    global verbosity does not propagate to new objects post-set
        (requires more specific implementation details)
2700    Refactor Build.PL
        (some of the behind-the-scenes stuff is a little klunky)
2702    Scripts recopied upon each call to './Build test'
        (minor bug)
2703    Bio::Tools::GuessSeqFormat guesses SELEX as PHYLIP
        (minor bug that mistakes format)
2707    Bio::Tools::Run::StandAloneBlast does not quote shell metacharacters in
        filenames, but Bio::SearchIO::blast does
        (bug within StandAloneBlast)
2715    LocatableSeq symbols are globally set
        (bug related to sequence symbol issues; rarely surfaces but needs addressing)


Bioperl 1.5.2
=============

There are no known installation bugs in 1.5.2 per se, but issues with
external programs may cause problems. See the following URL for details:
http://www.bioperl.org/wiki/Release_1.5.2#Notes


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

 * The StandAloneBlast.t test is failing on cygwin installations (and
   nowhere else). We suspect something to do with temporary file
   opening. Fixed in 1.4 (set TMPDIR).


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);