New version of Blast distribution

[Steve A. Chervitz]

A new version of my Blast package (0.06) is now available for downloading 
from the usual site:

 http://genome-www.stanford.edu/perlOOP/bioperl/blast/

Here's what's new (from the CHANGES file):

 - Fixed bug in HSP::_set_match_stats() that failed to recognize Frames
   on the + strand.
 - Added HSP::strand() method for retrieval of strand information for
   query and sbjct HSP sequences from nucleotide Blasts.
 - Changed calls to Perl's length() function to CORE::length()
   to avoid confusing the Perl 5.005_001 interpreter with
   Bio::Tools::HSP::length() and Bio::Tools::Sbjct::length(). 
   (Reported by Mike Cariaso).
 - Added column to the output of the Blast::table_tiled() method
   to include fraction-aligned of the sbjct sequence.
 - Uses new version of Bio::Root::Object.pm that has new exception
   handling policy: exceptions and warnings are no longer by default
   attached to the objects that threw them. See notes about this in 
   Bio::Root::Object.pm. (Main reason for 0.003-point jump in version).
 - Added some safety net methods in Sbjct.pm: frac_aligned_sbjct()
   and num_unaligned_sbjct(), which map to frac_aligned_hit() and 
   num_unaligned_hit(), respectively (API consistency issue).
 - Minor changes/fixes in some of the demo scripts (seqtools.pl et al.).
 - Removed "Modifications" notes from Blast-related modules. Added
   pointer to distribution site instead, which consolidates this info.
 - Modules can be used by copying directly from the lib/ directory into
   your perl/lib directory without loss of functionality but at 
   the expense of increased startup time. It is still recommended 
   that you use the standard Makefile.PL procedure, however, since this
   will properly autosplit the modules as well as run other checks.

Have at it.

Steve 
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Steve A. Chervitz                          Department of Genetics
sac@genome.stanford.edu                    Stanford University
http://www-genome.stanford.edu/~sac/       Stanford, CA 94305-5120
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