Bioperl: Bioperl central distribution 0.04.3

Steve Chervitz (Steve A. Chervitz)
Sat, 6 Feb 1999 11:53:44 -0800 (PST)


A maintenance release of the central distribution is now available
(version 0.04.3). It includes a variety of touch-ups. The new Changes
are included at the end of this message.

Bioperl release website:

Download directly: (811K) (962K)


Steve A. Chervitz (on behalf of the Bioperl developers)
Bioperl Coordinator

Changes in release 0.04.3:

  - and now detect when
    script is run as a CGI and suppress output that is only
    appropriate when running interactively.
  - Bio::Root::Err::_set_context() adds name of script ($0).
  - Added comments in and
    regarding the use of the static objects via the qw(:obj) tag.
  - Fixed the ambiguous reverse calls in and to 
    CORE::reverse, avoiding Perl warnings.
  - Bug fixes in Bio::Tools::Blast modules (version 0.074) and 
    example scripts (see Bio::Tools::Blast::CHANGES).
    [ ]
  - examples/seq/ no longer always warns about using 
    -prot or -nucl command-line arguments; only when using the 
    -debug argument.
  - Methods added to Bio::Root::Utilities: create_filehandle(), 
    get_newline_char(), and taste_file() to generalize filehandle 
    creation and autodetect newline characters in files/streams
    (see bug report #19).
  - Bio::Root::IOManager::read() now handles timeouts and uses
  - uses Utilities::get_newline_char()
    instead of hardwiring in "\n".
  - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW

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