FreeBSD Bugzilla – Bug 78963
[maintainer update] update biology/blast
Last modified: 2005-03-18 13:01:30 UTC
I've added PORTREVISION to the port and set it to the release
date as in the lang/gcc* ports. Since the distinfo file is not
used, this would help users know when they have to update their
Although newer release might be made, the idea is to bump
PORTREVISION for important feature releases on when significant
bugs are fixed.
Other minor (cosmetic) changes also applied.
From the release notes:
The [16-Mar-2005] release of WU BLAST 2.0 has been posted. This
is principally a new feature release. Parameter descriptions have
been updated on-line at http://blast.wustl.edu/blast/parameters.html
The new features include:
o Multiple output formats are now supported by the search
programs and are selectable through the new "mformat" parameter.
Tabular output (mformat=2 or mformat=3) is the notable addition.
o An alternative, single-line format for NOTE, WARNING, ERROR
and FATAL messages can be selected with the new "msgstyle" parameter
(msgstyle=1). The single-line format also includes the
identifier of the current query sequence.
o BLASTX and TBLASTX searches can be restricted to a single
reading frame of the query sequence, with the new "qframe" parameter.
o An alternative report format from the xdformat and xdget
programs can be selected with the new -m parameter. When dumping or retrieving
sequences and -m1 is specified, just the sequence identifiers and their
associated sequence lengths are reported.
In the area of bug fixes, perhaps the most important change is:
o Consistency is uniformly enforced between the score thresholds
S, S2 and gapS2. The software now reduces S2 and gapS2 if necessary to
maintain the relationship S >= gapS2 >= S2. A WARNING is emitted if the
original, higher value for S2 or gapS2 was explicitly set on the command line or
indirectly set via the E2 or gapE2 command line parameters.