[Bioperl-announce-l] Bioperl 1.0.1 Released

Jason Stajich jason@cgt.mc.duke.edu
Tue, 11 Jun 2002 10:27:45 -0400 (EDT)

11 June 2002

I am happy to announce the release of Bioperl 1.0.1 - bugfix release.
This release contains several small bug fixes and enhancements.  No
changes have been made to the API established in the 1.0 release that
would prevent scripts written for 1.0 to be used with the 1.0.1 release.

Pdoc generated HTML documentation is available from http://doc.bioperl.org
under the 1.0.1 release link.

I have updated the PPM for those using ActiveState and you should be able
to follow the directions described in the README here:
Note that I did not have access to a windows machine so I couldn't test
this myself, please let me know if you have any problems.

A RedHat RPM will be arriving to the distribution site as well in the next
week or so.

The distribution will be available from CPAN in the next few days as it is
pushed out.  As usual the package is available for download from

See http://bio.perl.org/Core/Latest/ for more install and download

Attached below is the ChangeLog for this release.

Jason Stajich
on behalf of the Bioperl developers.

ChangeLog for this release.

1.0.1 Bug fix release

    o Minor bug fixes to Bio::DB:GFF.  Glyph sets improved.

    o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
      and mixed (3.3 - 3.4) versions of FASTA.

    o Small API change to add methods for completeness across
      implementations of Bio::Search objects.  These new methods
      in the interface are implemented by the GenericXX object as well
      as the BlastXX objects.
	* Bio::Search::Result::ResultI
	 - hits() method returns list of all Hits (next_hit is an
	   iterator method)

	* Bio::Search::Hit::HitI
	 - hsps() method returns list of all HSPs (next_hsp is an
           iterator method)

    o The Bio::SearchIO::Writer classes have been fixed to handle results
       created from either psiblast (Search::BlastXX objects) or
       blast|fasta|blastxml objects (Search::GenericXX objects).  More
	work has to be done here to make it work properly and will nee major
       API changes.

    o Bugs in Bio::Tools::HMMER fixed, including
       * #1178 - Root::IO destructor wasn't being called
       * #1034 - filter_on_cutoff now behaves properly

    o Bio::SeqFeature::Computation initialization args fixed and
      tests added.

    o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,

    o Updated FAQ with more example based answers to typical questions

    o Bug #1202 was fixed which would improperly join together qual values
      parsed by Bio::SeqIO::qual when a trailing space was not present before
      the newline.

Jason Stajich
Duke University
jason at cgt.mc.duke.edu