[Bioperl-announce-l] Bioperl 1.0.1 Released
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.
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.
- hits() method returns list of all Hits (next_hit is an
- hsps() method returns list of all HSPs (next_hsp is an
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
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
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
jason at cgt.mc.duke.edu