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

Known Bugs

Bugs are tracked at this URL:
https://github.com/bioperl/bioperl-live/issues

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://github.com/bioperl/bioperl-live/issues

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