A patch for EMBOSS 6.1.0 is on the FTP server. This fixes problems with
extractfeat, using format names with dashes (fastq-sanger) in USAs,
scaling issues in plot outputs, and some minor bugs.
The files are on our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/fixes
with a patch file and instructions in the patches subdirectory.
Fix 3. EMBOSS-6.1.0/ajax/ajfeat.c
EMBOSS-6.1.0/ajax/ajfeat.h
EMBOSS-6.1.0/ajax/ajgraph.c
EMBOSS-6.1.0/ajax/ajmath.c
EMBOSS-6.1.0/ajax/ajseq.c
EMBOSS-6.1.0/ajax/ajseqread.c
EMBOSS-6.1.0/ajax/ajseqwrite.c
EMBOSS-6.1.0/nucleus/embmisc.c
EMBOSS-6.1.0/nucleus/embmisc.h
EMBOSS-6.1.0/nucleus/embpat.c
EMBOSS-6.1.0/emboss/coderet.c
EMBOSS-6.1.0/emboss/extractfeat.c
EMBOSS-6.1.0/emboss/notseq.c
EMBOSS-6.1.0/emboss/prettyplot.c
EMBOSS-6.1.0/emboss/seqmatchall.c
EMBOSS-6.1.0/emboss/showfeat.c
EMBOSS-6.1.0/emboss/showpep.c
EMBOSS-6.1.0/emboss/showseq.c
EMBOSS-6.1.0/emboss/twofeat.c
EMBOSS-6.1.0/jemboss/utils/install-jemboss-server.sh
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/server/AppendToLogFileThread.java
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
02-Dec-2009: Fixes problems with extractfeat. The fix includes cleaner
definitions of functions used to match feature tags and
feature types which result in minor updates to 6 other
applications.
Extractfeat in previous versions used its own text parser
to extract feature data from only a limited set of
formats. In release 6.1.0 it was replaced by the standard
EMBOSS feature table. With no options set, extractfeat
rejected all features (type '*' was needed to extract
features). Extractfeat default settings now extract all
features from an entry.
Features on the reverse strand were incorrectly processed
(an effect caused by some of the old extractfeat code
remaining). Reverse strand features are now correctly
parsed, including both "join(complement())" and
"complement(join())" syntax in EMBL/GenBank/DDBJ feature
tables.
Fixes an issue in GenBank parsing where the ORIGIN line is
absent.
Fixes scaling errors in prettyplot, especially in mEMBOSS
when plotting to a window on screen (the default
output). The plplot library does not report the true
width and height for several devices. The assumptions in
prettyplot depend on reasonable size estimates. Release
6.2.0 will have further corrections to plplot device
scaling.
Fixes the counting of non-coding features in coderet.
Fixes a seqmatchall error for short sequences with perfect matches
When reverse-complementing sequences, also reverses
the quality scores.
Allows '-' in format names in the USA syntax, to allow
fastq-sanger fastq-illumina and fastq-solexa format names
to be used.
When reading protein sequences, a sequence with only a
stop is now recognized as empty (zero length) after
processing ambiguity codes and stops.
Fixes a problem writing features in PIR format when the
feature table is empty, for example a report file with no hits.
Fixes a dependency on 'ant' to install a Jemboss server.
Fixes a problem in logging Jemboss info/error messages.
regards,
Peter Rice
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